Starting phenix.real_space_refine on Sun Feb 25 05:27:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/02_2024/6c3o_7338_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/02_2024/6c3o_7338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/02_2024/6c3o_7338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/02_2024/6c3o_7338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/02_2024/6c3o_7338_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c3o_7338/02_2024/6c3o_7338_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 3 8.98 5 P 32 5.49 5 Mg 8 5.21 5 S 272 5.16 5 C 31812 2.51 5 N 8272 2.21 5 O 8656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 16": "NH1" <-> "NH2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 527": "NH1" <-> "NH2" Residue "E ARG 702": "NH1" <-> "NH2" Residue "E ARG 841": "NH1" <-> "NH2" Residue "E ARG 1123": "NH1" <-> "NH2" Residue "E ARG 1221": "NH1" <-> "NH2" Residue "E ARG 1313": "NH1" <-> "NH2" Residue "E ARG 1418": "NH1" <-> "NH2" Residue "E ARG 1436": "NH1" <-> "NH2" Residue "E ARG 1486": "NH1" <-> "NH2" Residue "E ARG 1493": "NH1" <-> "NH2" Residue "E ARG 1497": "NH1" <-> "NH2" Residue "H ARG 16": "NH1" <-> "NH2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H ARG 527": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H ARG 841": "NH1" <-> "NH2" Residue "H ARG 1123": "NH1" <-> "NH2" Residue "H ARG 1221": "NH1" <-> "NH2" Residue "H ARG 1313": "NH1" <-> "NH2" Residue "H ARG 1418": "NH1" <-> "NH2" Residue "H ARG 1436": "NH1" <-> "NH2" Residue "H ARG 1486": "NH1" <-> "NH2" Residue "H ARG 1493": "NH1" <-> "NH2" Residue "H ARG 1497": "NH1" <-> "NH2" Residue "G ARG 16": "NH1" <-> "NH2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 527": "NH1" <-> "NH2" Residue "G ARG 702": "NH1" <-> "NH2" Residue "G ARG 841": "NH1" <-> "NH2" Residue "G ARG 1123": "NH1" <-> "NH2" Residue "G ARG 1221": "NH1" <-> "NH2" Residue "G ARG 1313": "NH1" <-> "NH2" Residue "G ARG 1418": "NH1" <-> "NH2" Residue "G ARG 1436": "NH1" <-> "NH2" Residue "G ARG 1486": "NH1" <-> "NH2" Residue "G ARG 1493": "NH1" <-> "NH2" Residue "G ARG 1497": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 527": "NH1" <-> "NH2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "F ARG 841": "NH1" <-> "NH2" Residue "F ARG 1123": "NH1" <-> "NH2" Residue "F ARG 1221": "NH1" <-> "NH2" Residue "F ARG 1313": "NH1" <-> "NH2" Residue "F ARG 1418": "NH1" <-> "NH2" Residue "F ARG 1436": "NH1" <-> "NH2" Residue "F ARG 1486": "NH1" <-> "NH2" Residue "F ARG 1493": "NH1" <-> "NH2" Residue "F ARG 1497": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49055 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 2501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2501 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 314} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "H" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "G" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "F" Number of atoms: 9671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1290, 9671 Classifications: {'peptide': 1290} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 39, 'TRANS': 1250} Chain breaks: 9 Unresolved non-hydrogen bonds: 494 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 5, 'GLU:plan': 22, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 327 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' K': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 25.18, per 1000 atoms: 0.51 Number of scatterers: 49055 At special positions: 0 Unit cell: (180.7, 180.7, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 3 19.00 S 272 16.00 P 32 15.00 Mg 8 11.99 O 8656 8.00 N 8272 7.00 C 31812 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.04 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.23 Conformation dependent library (CDL) restraints added in 9.5 seconds 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12216 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 36 sheets defined 58.2% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.75 Creating SS restraints... Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.074A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 68 through 96 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.073A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 266 through 269 removed outlier: 4.075A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 171 Processing helix chain 'D' and resid 266 through 269 removed outlier: 4.074A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 25 through 43 removed outlier: 3.682A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Proline residue: E 35 - end of helix Processing helix chain 'E' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 96 removed outlier: 3.690A pdb=" N ASP E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 127 Processing helix chain 'E' and resid 137 through 159 removed outlier: 3.924A pdb=" N ASP E 159 " --> pdb=" O VAL E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 191 Processing helix chain 'E' and resid 263 through 276 Processing helix chain 'E' and resid 288 through 314 removed outlier: 6.800A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU E 299 " --> pdb=" O PHE E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 327 Processing helix chain 'E' and resid 355 through 401 removed outlier: 3.525A pdb=" N ALA E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 Processing helix chain 'E' and resid 414 through 454 removed outlier: 4.273A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Proline residue: E 436 - end of helix Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 462 through 504 removed outlier: 3.735A pdb=" N ALA E 471 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 472 - end of helix removed outlier: 3.891A pdb=" N ARG E 486 " --> pdb=" O GLN E 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR E 491 " --> pdb=" O THR E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 511 Processing helix chain 'E' and resid 515 through 562 removed outlier: 3.508A pdb=" N THR E 525 " --> pdb=" O ARG E 521 " (cutoff:3.500A) Proline residue: E 551 - end of helix removed outlier: 4.042A pdb=" N HIS E 562 " --> pdb=" O THR E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 615 Proline residue: E 589 - end of helix removed outlier: 3.710A pdb=" N LEU E 592 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG E 598 " --> pdb=" O SER E 594 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER E 615 " --> pdb=" O SER E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 727 Processing helix chain 'E' and resid 783 through 788 Processing helix chain 'E' and resid 795 through 805 Processing helix chain 'E' and resid 808 through 812 Processing helix chain 'E' and resid 817 through 819 No H-bonds generated for 'chain 'E' and resid 817 through 819' Processing helix chain 'E' and resid 831 through 843 removed outlier: 3.604A pdb=" N ALA E 842 " --> pdb=" O SER E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 861 through 877 Processing helix chain 'E' and resid 890 through 892 No H-bonds generated for 'chain 'E' and resid 890 through 892' Processing helix chain 'E' and resid 920 through 929 removed outlier: 5.011A pdb=" N THR E 929 " --> pdb=" O GLU E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 995 through 1006 Processing helix chain 'E' and resid 1010 through 1035 Processing helix chain 'E' and resid 1062 through 1106 removed outlier: 3.731A pdb=" N LEU E1106 " --> pdb=" O ASN E1102 " (cutoff:3.500A) Processing helix chain 'E' and resid 1109 through 1114 Processing helix chain 'E' and resid 1117 through 1125 removed outlier: 3.945A pdb=" N ARG E1123 " --> pdb=" O SER E1119 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE E1124 " --> pdb=" O ILE E1120 " (cutoff:3.500A) Processing helix chain 'E' and resid 1127 through 1159 Proline residue: E1136 - end of helix Processing helix chain 'E' and resid 1161 through 1207 removed outlier: 3.723A pdb=" N LEU E1164 " --> pdb=" O PRO E1161 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU E1168 " --> pdb=" O VAL E1165 " (cutoff:3.500A) Proline residue: E1169 - end of helix removed outlier: 4.020A pdb=" N ARG E1186 " --> pdb=" O VAL E1183 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E1197 " --> pdb=" O THR E1194 " (cutoff:3.500A) Proline residue: E1198 - end of helix Processing helix chain 'E' and resid 1210 through 1216 Processing helix chain 'E' and resid 1219 through 1272 Processing helix chain 'E' and resid 1278 through 1318 removed outlier: 4.855A pdb=" N ASN E1295 " --> pdb=" O SER E1291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP E1296 " --> pdb=" O ASN E1292 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1392 removed outlier: 4.270A pdb=" N PHE E1391 " --> pdb=" O PHE E1387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE E1392 " --> pdb=" O SER E1388 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1419 Processing helix chain 'E' and resid 1435 through 1439 Processing helix chain 'E' and resid 1447 through 1455 Processing helix chain 'E' and resid 1460 through 1464 Processing helix chain 'E' and resid 1476 through 1478 No H-bonds generated for 'chain 'E' and resid 1476 through 1478' Processing helix chain 'E' and resid 1483 through 1495 Processing helix chain 'E' and resid 1513 through 1526 Processing helix chain 'E' and resid 1542 through 1544 No H-bonds generated for 'chain 'E' and resid 1542 through 1544' Processing helix chain 'E' and resid 1562 through 1568 Processing helix chain 'E' and resid 1572 through 1580 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 25 through 43 removed outlier: 3.681A pdb=" N VAL H 33 " --> pdb=" O ASP H 29 " (cutoff:3.500A) Proline residue: H 35 - end of helix Processing helix chain 'H' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 96 removed outlier: 3.690A pdb=" N ASP H 96 " --> pdb=" O GLY H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 106 No H-bonds generated for 'chain 'H' and resid 104 through 106' Processing helix chain 'H' and resid 108 through 127 Processing helix chain 'H' and resid 137 through 159 removed outlier: 3.924A pdb=" N ASP H 159 " --> pdb=" O VAL H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 191 Processing helix chain 'H' and resid 263 through 276 Processing helix chain 'H' and resid 288 through 314 removed outlier: 6.799A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 327 Processing helix chain 'H' and resid 355 through 401 removed outlier: 3.526A pdb=" N ALA H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 408 Processing helix chain 'H' and resid 414 through 454 removed outlier: 4.273A pdb=" N THR H 425 " --> pdb=" O VAL H 421 " (cutoff:3.500A) Proline residue: H 436 - end of helix Proline residue: H 442 - end of helix Processing helix chain 'H' and resid 462 through 504 removed outlier: 3.735A pdb=" N ALA H 471 " --> pdb=" O ILE H 468 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.892A pdb=" N ARG H 486 " --> pdb=" O GLN H 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR H 491 " --> pdb=" O THR H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 507 through 511 Processing helix chain 'H' and resid 515 through 562 removed outlier: 3.509A pdb=" N THR H 525 " --> pdb=" O ARG H 521 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 4.041A pdb=" N HIS H 562 " --> pdb=" O THR H 558 " (cutoff:3.500A) Processing helix chain 'H' and resid 575 through 615 Proline residue: H 589 - end of helix removed outlier: 3.710A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG H 598 " --> pdb=" O SER H 594 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER H 615 " --> pdb=" O SER H 611 " (cutoff:3.500A) Processing helix chain 'H' and resid 721 through 727 Processing helix chain 'H' and resid 783 through 788 Processing helix chain 'H' and resid 795 through 805 Processing helix chain 'H' and resid 808 through 812 Processing helix chain 'H' and resid 817 through 819 No H-bonds generated for 'chain 'H' and resid 817 through 819' Processing helix chain 'H' and resid 831 through 843 removed outlier: 3.605A pdb=" N ALA H 842 " --> pdb=" O SER H 838 " (cutoff:3.500A) Processing helix chain 'H' and resid 861 through 877 Processing helix chain 'H' and resid 890 through 892 No H-bonds generated for 'chain 'H' and resid 890 through 892' Processing helix chain 'H' and resid 920 through 929 removed outlier: 5.012A pdb=" N THR H 929 " --> pdb=" O GLU H 925 " (cutoff:3.500A) Processing helix chain 'H' and resid 995 through 1006 Processing helix chain 'H' and resid 1010 through 1035 Processing helix chain 'H' and resid 1062 through 1106 removed outlier: 3.732A pdb=" N LEU H1106 " --> pdb=" O ASN H1102 " (cutoff:3.500A) Processing helix chain 'H' and resid 1109 through 1114 Processing helix chain 'H' and resid 1117 through 1125 removed outlier: 3.946A pdb=" N ARG H1123 " --> pdb=" O SER H1119 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE H1124 " --> pdb=" O ILE H1120 " (cutoff:3.500A) Processing helix chain 'H' and resid 1127 through 1159 Proline residue: H1136 - end of helix Processing helix chain 'H' and resid 1161 through 1207 removed outlier: 3.722A pdb=" N LEU H1164 " --> pdb=" O PRO H1161 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LEU H1168 " --> pdb=" O VAL H1165 " (cutoff:3.500A) Proline residue: H1169 - end of helix removed outlier: 4.019A pdb=" N ARG H1186 " --> pdb=" O VAL H1183 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU H1197 " --> pdb=" O THR H1194 " (cutoff:3.500A) Proline residue: H1198 - end of helix Processing helix chain 'H' and resid 1210 through 1216 Processing helix chain 'H' and resid 1219 through 1272 Processing helix chain 'H' and resid 1278 through 1318 removed outlier: 4.855A pdb=" N ASN H1295 " --> pdb=" O SER H1291 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP H1296 " --> pdb=" O ASN H1292 " (cutoff:3.500A) Processing helix chain 'H' and resid 1384 through 1392 removed outlier: 4.269A pdb=" N PHE H1391 " --> pdb=" O PHE H1387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE H1392 " --> pdb=" O SER H1388 " (cutoff:3.500A) Processing helix chain 'H' and resid 1414 through 1419 Processing helix chain 'H' and resid 1435 through 1439 Processing helix chain 'H' and resid 1447 through 1455 Processing helix chain 'H' and resid 1460 through 1464 Processing helix chain 'H' and resid 1476 through 1478 No H-bonds generated for 'chain 'H' and resid 1476 through 1478' Processing helix chain 'H' and resid 1483 through 1495 Processing helix chain 'H' and resid 1513 through 1526 Processing helix chain 'H' and resid 1542 through 1544 No H-bonds generated for 'chain 'H' and resid 1542 through 1544' Processing helix chain 'H' and resid 1562 through 1568 Processing helix chain 'H' and resid 1572 through 1580 Processing helix chain 'G' and resid 21 through 23 No H-bonds generated for 'chain 'G' and resid 21 through 23' Processing helix chain 'G' and resid 25 through 43 removed outlier: 3.682A pdb=" N VAL G 33 " --> pdb=" O ASP G 29 " (cutoff:3.500A) Proline residue: G 35 - end of helix Processing helix chain 'G' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY G 50 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 96 removed outlier: 3.691A pdb=" N ASP G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 108 through 127 Processing helix chain 'G' and resid 137 through 159 removed outlier: 3.923A pdb=" N ASP G 159 " --> pdb=" O VAL G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 191 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 288 through 314 removed outlier: 6.799A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU G 299 " --> pdb=" O PHE G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 355 through 401 removed outlier: 3.524A pdb=" N ALA G 375 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 408 Processing helix chain 'G' and resid 414 through 454 removed outlier: 4.272A pdb=" N THR G 425 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Proline residue: G 436 - end of helix Proline residue: G 442 - end of helix Processing helix chain 'G' and resid 462 through 504 removed outlier: 3.736A pdb=" N ALA G 471 " --> pdb=" O ILE G 468 " (cutoff:3.500A) Proline residue: G 472 - end of helix removed outlier: 3.890A pdb=" N ARG G 486 " --> pdb=" O GLN G 483 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR G 491 " --> pdb=" O THR G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 511 Processing helix chain 'G' and resid 515 through 562 removed outlier: 3.507A pdb=" N THR G 525 " --> pdb=" O ARG G 521 " (cutoff:3.500A) Proline residue: G 551 - end of helix removed outlier: 4.041A pdb=" N HIS G 562 " --> pdb=" O THR G 558 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 615 Proline residue: G 589 - end of helix removed outlier: 3.710A pdb=" N LEU G 592 " --> pdb=" O THR G 588 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER G 595 " --> pdb=" O PHE G 591 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG G 598 " --> pdb=" O SER G 594 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER G 615 " --> pdb=" O SER G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 727 Processing helix chain 'G' and resid 783 through 788 Processing helix chain 'G' and resid 795 through 805 Processing helix chain 'G' and resid 808 through 812 Processing helix chain 'G' and resid 817 through 819 No H-bonds generated for 'chain 'G' and resid 817 through 819' Processing helix chain 'G' and resid 831 through 843 removed outlier: 3.605A pdb=" N ALA G 842 " --> pdb=" O SER G 838 " (cutoff:3.500A) Processing helix chain 'G' and resid 861 through 877 Processing helix chain 'G' and resid 890 through 892 No H-bonds generated for 'chain 'G' and resid 890 through 892' Processing helix chain 'G' and resid 920 through 929 removed outlier: 5.012A pdb=" N THR G 929 " --> pdb=" O GLU G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 995 through 1006 Processing helix chain 'G' and resid 1010 through 1035 Processing helix chain 'G' and resid 1062 through 1106 removed outlier: 3.733A pdb=" N LEU G1106 " --> pdb=" O ASN G1102 " (cutoff:3.500A) Processing helix chain 'G' and resid 1109 through 1114 Processing helix chain 'G' and resid 1117 through 1125 removed outlier: 3.945A pdb=" N ARG G1123 " --> pdb=" O SER G1119 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE G1124 " --> pdb=" O ILE G1120 " (cutoff:3.500A) Processing helix chain 'G' and resid 1127 through 1159 Proline residue: G1136 - end of helix Processing helix chain 'G' and resid 1161 through 1207 removed outlier: 3.723A pdb=" N LEU G1164 " --> pdb=" O PRO G1161 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU G1168 " --> pdb=" O VAL G1165 " (cutoff:3.500A) Proline residue: G1169 - end of helix removed outlier: 4.022A pdb=" N ARG G1186 " --> pdb=" O VAL G1183 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU G1197 " --> pdb=" O THR G1194 " (cutoff:3.500A) Proline residue: G1198 - end of helix Processing helix chain 'G' and resid 1210 through 1216 Processing helix chain 'G' and resid 1219 through 1272 Processing helix chain 'G' and resid 1278 through 1318 removed outlier: 4.854A pdb=" N ASN G1295 " --> pdb=" O SER G1291 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP G1296 " --> pdb=" O ASN G1292 " (cutoff:3.500A) Processing helix chain 'G' and resid 1384 through 1392 removed outlier: 4.270A pdb=" N PHE G1391 " --> pdb=" O PHE G1387 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE G1392 " --> pdb=" O SER G1388 " (cutoff:3.500A) Processing helix chain 'G' and resid 1414 through 1419 Processing helix chain 'G' and resid 1435 through 1439 Processing helix chain 'G' and resid 1447 through 1455 Processing helix chain 'G' and resid 1460 through 1464 Processing helix chain 'G' and resid 1476 through 1478 No H-bonds generated for 'chain 'G' and resid 1476 through 1478' Processing helix chain 'G' and resid 1483 through 1495 Processing helix chain 'G' and resid 1513 through 1526 Processing helix chain 'G' and resid 1542 through 1544 No H-bonds generated for 'chain 'G' and resid 1542 through 1544' Processing helix chain 'G' and resid 1562 through 1568 Processing helix chain 'G' and resid 1572 through 1580 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 25 through 43 removed outlier: 3.682A pdb=" N VAL F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) Proline residue: F 35 - end of helix Processing helix chain 'F' and resid 45 through 51 removed outlier: 4.891A pdb=" N GLY F 50 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 96 removed outlier: 3.689A pdb=" N ASP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 108 through 127 Processing helix chain 'F' and resid 137 through 159 removed outlier: 3.923A pdb=" N ASP F 159 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 191 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 288 through 314 removed outlier: 6.800A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 327 Processing helix chain 'F' and resid 355 through 401 removed outlier: 3.525A pdb=" N ALA F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 414 through 454 removed outlier: 4.273A pdb=" N THR F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) Proline residue: F 436 - end of helix Proline residue: F 442 - end of helix Processing helix chain 'F' and resid 462 through 504 removed outlier: 3.736A pdb=" N ALA F 471 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.891A pdb=" N ARG F 486 " --> pdb=" O GLN F 483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 491 " --> pdb=" O THR F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 511 Processing helix chain 'F' and resid 515 through 562 removed outlier: 3.507A pdb=" N THR F 525 " --> pdb=" O ARG F 521 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 4.042A pdb=" N HIS F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 615 Proline residue: F 589 - end of helix removed outlier: 3.710A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG F 598 " --> pdb=" O SER F 594 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER F 615 " --> pdb=" O SER F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 727 Processing helix chain 'F' and resid 783 through 788 Processing helix chain 'F' and resid 795 through 805 Processing helix chain 'F' and resid 808 through 812 Processing helix chain 'F' and resid 817 through 819 No H-bonds generated for 'chain 'F' and resid 817 through 819' Processing helix chain 'F' and resid 831 through 843 removed outlier: 3.604A pdb=" N ALA F 842 " --> pdb=" O SER F 838 " (cutoff:3.500A) Processing helix chain 'F' and resid 861 through 877 Processing helix chain 'F' and resid 890 through 892 No H-bonds generated for 'chain 'F' and resid 890 through 892' Processing helix chain 'F' and resid 920 through 929 removed outlier: 5.012A pdb=" N THR F 929 " --> pdb=" O GLU F 925 " (cutoff:3.500A) Processing helix chain 'F' and resid 995 through 1006 Processing helix chain 'F' and resid 1010 through 1035 Processing helix chain 'F' and resid 1062 through 1106 removed outlier: 3.731A pdb=" N LEU F1106 " --> pdb=" O ASN F1102 " (cutoff:3.500A) Processing helix chain 'F' and resid 1109 through 1114 Processing helix chain 'F' and resid 1117 through 1125 removed outlier: 3.944A pdb=" N ARG F1123 " --> pdb=" O SER F1119 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE F1124 " --> pdb=" O ILE F1120 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1159 Proline residue: F1136 - end of helix Processing helix chain 'F' and resid 1161 through 1207 removed outlier: 3.722A pdb=" N LEU F1164 " --> pdb=" O PRO F1161 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU F1168 " --> pdb=" O VAL F1165 " (cutoff:3.500A) Proline residue: F1169 - end of helix removed outlier: 4.020A pdb=" N ARG F1186 " --> pdb=" O VAL F1183 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU F1197 " --> pdb=" O THR F1194 " (cutoff:3.500A) Proline residue: F1198 - end of helix Processing helix chain 'F' and resid 1210 through 1216 Processing helix chain 'F' and resid 1219 through 1272 Processing helix chain 'F' and resid 1278 through 1318 removed outlier: 4.855A pdb=" N ASN F1295 " --> pdb=" O SER F1291 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP F1296 " --> pdb=" O ASN F1292 " (cutoff:3.500A) Processing helix chain 'F' and resid 1384 through 1392 removed outlier: 4.269A pdb=" N PHE F1391 " --> pdb=" O PHE F1387 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE F1392 " --> pdb=" O SER F1388 " (cutoff:3.500A) Processing helix chain 'F' and resid 1414 through 1419 Processing helix chain 'F' and resid 1435 through 1439 Processing helix chain 'F' and resid 1447 through 1455 Processing helix chain 'F' and resid 1460 through 1464 Processing helix chain 'F' and resid 1476 through 1478 No H-bonds generated for 'chain 'F' and resid 1476 through 1478' Processing helix chain 'F' and resid 1483 through 1495 Processing helix chain 'F' and resid 1513 through 1526 Processing helix chain 'F' and resid 1542 through 1544 No H-bonds generated for 'chain 'F' and resid 1542 through 1544' Processing helix chain 'F' and resid 1562 through 1568 Processing helix chain 'F' and resid 1572 through 1580 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 188 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.092A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 322 Processing sheet with id= F, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'C' and resid 188 through 192 Processing sheet with id= H, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.091A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= J, first strand: chain 'C' and resid 319 through 322 Processing sheet with id= K, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'B' and resid 188 through 192 Processing sheet with id= M, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.092A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'B' and resid 319 through 322 Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'D' and resid 188 through 192 Processing sheet with id= R, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.091A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'D' and resid 319 through 322 Processing sheet with id= U, first strand: chain 'E' and resid 736 through 738 removed outlier: 3.993A pdb=" N ALA E 736 " --> pdb=" O MET E 682 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET E 682 " --> pdb=" O ALA E 736 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE E 699 " --> pdb=" O GLY E 683 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 906 through 910 removed outlier: 7.091A pdb=" N ALA E 901 " --> pdb=" O GLN E 908 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU E 910 " --> pdb=" O ILE E 899 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 899 " --> pdb=" O GLU E 910 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL E 883 " --> pdb=" O THR E 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE E 711 " --> pdb=" O VAL E 883 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU E 885 " --> pdb=" O ILE E 711 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N GLY E 713 " --> pdb=" O LEU E 885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL E 886 " --> pdb=" O LEU E 852 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 1366 through 1368 Processing sheet with id= X, first strand: chain 'E' and resid 1548 through 1550 removed outlier: 6.480A pdb=" N GLY E1375 " --> pdb=" O ILE E1549 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E1534 " --> pdb=" O ILE E1374 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'H' and resid 736 through 738 removed outlier: 3.992A pdb=" N ALA H 736 " --> pdb=" O MET H 682 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET H 682 " --> pdb=" O ALA H 736 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE H 699 " --> pdb=" O GLY H 683 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'H' and resid 906 through 910 removed outlier: 7.091A pdb=" N ALA H 901 " --> pdb=" O GLN H 908 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU H 910 " --> pdb=" O ILE H 899 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE H 899 " --> pdb=" O GLU H 910 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL H 883 " --> pdb=" O THR H 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE H 711 " --> pdb=" O VAL H 883 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU H 885 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLY H 713 " --> pdb=" O LEU H 885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL H 886 " --> pdb=" O LEU H 852 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 1366 through 1368 Processing sheet with id= AB, first strand: chain 'H' and resid 1548 through 1550 removed outlier: 6.479A pdb=" N GLY H1375 " --> pdb=" O ILE H1549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR H1534 " --> pdb=" O ILE H1374 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 736 through 738 removed outlier: 3.993A pdb=" N ALA G 736 " --> pdb=" O MET G 682 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET G 682 " --> pdb=" O ALA G 736 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE G 699 " --> pdb=" O GLY G 683 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 906 through 910 removed outlier: 7.092A pdb=" N ALA G 901 " --> pdb=" O GLN G 908 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU G 910 " --> pdb=" O ILE G 899 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE G 899 " --> pdb=" O GLU G 910 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL G 883 " --> pdb=" O THR G 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE G 711 " --> pdb=" O VAL G 883 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU G 885 " --> pdb=" O ILE G 711 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N GLY G 713 " --> pdb=" O LEU G 885 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 886 " --> pdb=" O LEU G 852 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 1366 through 1368 Processing sheet with id= AF, first strand: chain 'G' and resid 1548 through 1550 removed outlier: 6.479A pdb=" N GLY G1375 " --> pdb=" O ILE G1549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR G1534 " --> pdb=" O ILE G1374 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 736 through 738 removed outlier: 3.993A pdb=" N ALA F 736 " --> pdb=" O MET F 682 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET F 682 " --> pdb=" O ALA F 736 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE F 699 " --> pdb=" O GLY F 683 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 906 through 910 removed outlier: 7.092A pdb=" N ALA F 901 " --> pdb=" O GLN F 908 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU F 910 " --> pdb=" O ILE F 899 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 899 " --> pdb=" O GLU F 910 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL F 883 " --> pdb=" O THR F 709 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE F 711 " --> pdb=" O VAL F 883 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU F 885 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N GLY F 713 " --> pdb=" O LEU F 885 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 886 " --> pdb=" O LEU F 852 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 1366 through 1368 Processing sheet with id= AJ, first strand: chain 'F' and resid 1548 through 1550 removed outlier: 6.480A pdb=" N GLY F1375 " --> pdb=" O ILE F1549 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR F1534 " --> pdb=" O ILE F1374 " (cutoff:3.500A) 2984 hydrogen bonds defined for protein. 7968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.01 Time building geometry restraints manager: 23.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15468 1.34 - 1.46: 9400 1.46 - 1.57: 24712 1.57 - 1.69: 52 1.69 - 1.81: 424 Bond restraints: 50056 Sorted by residual: bond pdb=" C4 ATP F2004 " pdb=" C5 ATP F2004 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.05e+01 bond pdb=" C4 ATP E2004 " pdb=" C5 ATP E2004 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.03e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.96e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.88e+01 ... (remaining 50051 not shown) Histogram of bond angle deviations from ideal: 98.52 - 106.03: 1017 106.03 - 113.55: 30013 113.55 - 121.06: 24559 121.06 - 128.57: 12255 128.57 - 136.08: 436 Bond angle restraints: 68280 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 118.98 20.89 1.00e+00 1.00e+00 4.36e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 116.17 20.66 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 119.46 20.41 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.48 20.39 1.00e+00 1.00e+00 4.16e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 119.73 20.14 1.00e+00 1.00e+00 4.06e+02 ... (remaining 68275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 28875 24.82 - 49.63: 679 49.63 - 74.45: 63 74.45 - 99.26: 23 99.26 - 124.08: 4 Dihedral angle restraints: 29644 sinusoidal: 10848 harmonic: 18796 Sorted by residual: dihedral pdb=" O1B ADP E2001 " pdb=" O3A ADP E2001 " pdb=" PB ADP E2001 " pdb=" PA ADP E2001 " ideal model delta sinusoidal sigma weight residual -60.00 64.08 -124.08 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O1B ADP G2001 " pdb=" O3A ADP G2001 " pdb=" PB ADP G2001 " pdb=" PA ADP G2001 " ideal model delta sinusoidal sigma weight residual -60.00 64.06 -124.06 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" O1B ADP H2001 " pdb=" O3A ADP H2001 " pdb=" PB ADP H2001 " pdb=" PA ADP H2001 " ideal model delta sinusoidal sigma weight residual -60.00 64.03 -124.03 1 2.00e+01 2.50e-03 3.74e+01 ... (remaining 29641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 5432 0.040 - 0.081: 2204 0.081 - 0.121: 607 0.121 - 0.162: 102 0.162 - 0.202: 11 Chirality restraints: 8356 Sorted by residual: chirality pdb=" CB THR E1081 " pdb=" CA THR E1081 " pdb=" OG1 THR E1081 " pdb=" CG2 THR E1081 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR F1081 " pdb=" CA THR F1081 " pdb=" OG1 THR F1081 " pdb=" CG2 THR F1081 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR H1081 " pdb=" CA THR H1081 " pdb=" OG1 THR H1081 " pdb=" CG2 THR H1081 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 8353 not shown) Planarity restraints: 8388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 577 " -0.026 2.00e-02 2.50e+03 1.90e-02 6.30e+00 pdb=" CG PHE H 577 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE H 577 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 577 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE H 577 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 577 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE H 577 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 577 " 0.026 2.00e-02 2.50e+03 1.89e-02 6.22e+00 pdb=" CG PHE F 577 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE F 577 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 577 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 577 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE F 577 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 577 " 0.026 2.00e-02 2.50e+03 1.88e-02 6.19e+00 pdb=" CG PHE G 577 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 577 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 577 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 577 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 577 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 577 " 0.009 2.00e-02 2.50e+03 ... (remaining 8385 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.36: 199 2.36 - 3.05: 35669 3.05 - 3.75: 90499 3.75 - 4.44: 136701 4.44 - 5.14: 218563 Nonbonded interactions: 481631 Sorted by model distance: nonbonded pdb=" ND1 HIS H 888 " pdb=" OD1 ASP H1512 " model vdw 1.661 2.520 nonbonded pdb=" ND1 HIS F 888 " pdb=" OD1 ASP F1512 " model vdw 1.661 2.520 nonbonded pdb=" ND1 HIS G 888 " pdb=" OD1 ASP G1512 " model vdw 1.662 2.520 nonbonded pdb=" ND1 HIS E 888 " pdb=" OD1 ASP E1512 " model vdw 1.662 2.520 nonbonded pdb=" O1B ADP G2001 " pdb="MG MG G2003 " model vdw 1.893 2.170 ... (remaining 481626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 359 or resid 501)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.690 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 134.480 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5448 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 50056 Z= 0.403 Angle : 0.920 20.887 68280 Z= 0.590 Chirality : 0.046 0.202 8356 Planarity : 0.004 0.056 8388 Dihedral : 10.781 124.080 17404 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.32 % Allowed : 4.18 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.09), residues: 6384 helix: -1.31 (0.07), residues: 3864 sheet: -2.49 (0.20), residues: 592 loop : -3.11 (0.12), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP F 143 HIS 0.012 0.002 HIS G1272 PHE 0.041 0.003 PHE H 577 TYR 0.020 0.002 TYR G 539 ARG 0.009 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1649 time to evaluate : 5.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7359 (m110) cc_final: 0.7133 (m-40) REVERT: A 48 ASN cc_start: 0.7724 (m-40) cc_final: 0.6966 (m110) REVERT: A 57 GLN cc_start: 0.6508 (pt0) cc_final: 0.5667 (tp40) REVERT: A 195 ARG cc_start: 0.6772 (mmm-85) cc_final: 0.5568 (mmm160) REVERT: A 209 MET cc_start: 0.7404 (tpp) cc_final: 0.5309 (tpp) REVERT: A 217 MET cc_start: 0.8076 (mtm) cc_final: 0.7525 (mtp) REVERT: A 248 SER cc_start: 0.8210 (m) cc_final: 0.7737 (p) REVERT: C 37 SER cc_start: 0.6794 (t) cc_final: 0.6592 (t) REVERT: C 41 ASN cc_start: 0.6950 (m110) cc_final: 0.6594 (m-40) REVERT: C 48 ASN cc_start: 0.7574 (m-40) cc_final: 0.7076 (m110) REVERT: C 57 GLN cc_start: 0.7062 (pt0) cc_final: 0.6446 (tm-30) REVERT: C 155 VAL cc_start: 0.5239 (t) cc_final: 0.4999 (t) REVERT: C 195 ARG cc_start: 0.5851 (mmm-85) cc_final: 0.5137 (mmm160) REVERT: C 217 MET cc_start: 0.7763 (mtm) cc_final: 0.7546 (mtp) REVERT: C 248 SER cc_start: 0.8298 (m) cc_final: 0.8024 (p) REVERT: C 280 ASP cc_start: 0.8174 (t70) cc_final: 0.7824 (t0) REVERT: C 308 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6405 (mt-10) REVERT: B 41 ASN cc_start: 0.7191 (m110) cc_final: 0.6914 (m-40) REVERT: B 57 GLN cc_start: 0.6617 (pt0) cc_final: 0.5845 (tp40) REVERT: B 195 ARG cc_start: 0.6582 (mmm-85) cc_final: 0.5826 (mmm160) REVERT: B 209 MET cc_start: 0.7650 (tpp) cc_final: 0.7006 (tpp) REVERT: B 223 THR cc_start: 0.8275 (t) cc_final: 0.7879 (p) REVERT: B 258 TYR cc_start: 0.7736 (p90) cc_final: 0.7266 (p90) REVERT: B 280 ASP cc_start: 0.8137 (t70) cc_final: 0.7632 (t0) REVERT: B 301 ARG cc_start: 0.7686 (mpp-170) cc_final: 0.6728 (mpp-170) REVERT: D 48 ASN cc_start: 0.7511 (m-40) cc_final: 0.6835 (m110) REVERT: D 57 GLN cc_start: 0.6715 (pt0) cc_final: 0.5883 (tp40) REVERT: D 195 ARG cc_start: 0.6455 (mmm-85) cc_final: 0.5498 (mmm160) REVERT: D 209 MET cc_start: 0.7337 (tpp) cc_final: 0.6646 (tpp) REVERT: D 217 MET cc_start: 0.7919 (mtm) cc_final: 0.7366 (mtp) REVERT: D 248 SER cc_start: 0.8158 (m) cc_final: 0.7872 (p) REVERT: D 292 GLU cc_start: 0.6612 (tt0) cc_final: 0.6284 (tt0) REVERT: D 321 GLU cc_start: 0.6130 (tm-30) cc_final: 0.5535 (tm-30) REVERT: E 42 ILE cc_start: 0.7240 (tt) cc_final: 0.7009 (tp) REVERT: E 112 MET cc_start: 0.7888 (mmp) cc_final: 0.7649 (mmm) REVERT: E 298 ARG cc_start: 0.5272 (mtt-85) cc_final: 0.5070 (tpt-90) REVERT: E 312 LEU cc_start: 0.6178 (tp) cc_final: 0.5827 (mp) REVERT: E 394 LYS cc_start: 0.6265 (tttt) cc_final: 0.6063 (ttmm) REVERT: E 426 ASN cc_start: 0.6816 (m-40) cc_final: 0.6574 (m-40) REVERT: E 429 MET cc_start: 0.4242 (ttp) cc_final: 0.3785 (ttp) REVERT: E 451 LEU cc_start: 0.6070 (tm) cc_final: 0.5342 (mm) REVERT: E 485 GLN cc_start: 0.7236 (tp40) cc_final: 0.6351 (tm-30) REVERT: E 502 MET cc_start: 0.5948 (ttt) cc_final: 0.5469 (ttm) REVERT: E 601 VAL cc_start: 0.5576 (t) cc_final: 0.5307 (m) REVERT: E 682 MET cc_start: 0.7224 (ptp) cc_final: 0.6539 (mmt) REVERT: E 732 LYS cc_start: 0.7455 (pttm) cc_final: 0.7173 (pttp) REVERT: E 800 MET cc_start: 0.6384 (ttp) cc_final: 0.6060 (ttp) REVERT: E 846 HIS cc_start: 0.6632 (t-90) cc_final: 0.6420 (m90) REVERT: E 1024 MET cc_start: 0.6331 (ttt) cc_final: 0.5877 (tpt) REVERT: E 1065 MET cc_start: 0.5830 (tpt) cc_final: 0.5370 (ttt) REVERT: E 1145 SER cc_start: 0.6793 (m) cc_final: 0.6422 (p) REVERT: E 1206 THR cc_start: 0.6208 (m) cc_final: 0.5945 (m) REVERT: E 1208 GLU cc_start: 0.6588 (tp30) cc_final: 0.6307 (tp30) REVERT: E 1222 PHE cc_start: 0.5088 (m-10) cc_final: 0.4697 (m-10) REVERT: E 1252 GLU cc_start: 0.5972 (tp30) cc_final: 0.5184 (tp30) REVERT: E 1359 PRO cc_start: 0.8262 (Cg_endo) cc_final: 0.7945 (Cg_exo) REVERT: E 1362 LYS cc_start: 0.6617 (ptpt) cc_final: 0.6259 (pttm) REVERT: E 1365 ASN cc_start: 0.7204 (p0) cc_final: 0.6947 (p0) REVERT: E 1402 ILE cc_start: 0.6618 (tt) cc_final: 0.6265 (mt) REVERT: E 1451 TRP cc_start: 0.5867 (m100) cc_final: 0.5175 (m-10) REVERT: E 1504 MET cc_start: 0.5103 (mtt) cc_final: 0.4815 (mtm) REVERT: E 1513 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6057 (mtt) REVERT: E 1538 ARG cc_start: 0.6908 (mmt180) cc_final: 0.6480 (mtt180) REVERT: E 1569 LYS cc_start: 0.8520 (tmtp) cc_final: 0.8123 (ttpp) REVERT: H 108 MET cc_start: 0.6975 (tpp) cc_final: 0.6513 (tmm) REVERT: H 188 ASN cc_start: 0.6251 (t160) cc_final: 0.5980 (t0) REVERT: H 361 LEU cc_start: 0.6631 (tp) cc_final: 0.6387 (mt) REVERT: H 441 MET cc_start: 0.4235 (ttt) cc_final: 0.3678 (tmm) REVERT: H 496 LEU cc_start: 0.6724 (tm) cc_final: 0.6422 (mp) REVERT: H 497 LYS cc_start: 0.6242 (ttpp) cc_final: 0.6013 (ttpt) REVERT: H 502 MET cc_start: 0.5276 (ttt) cc_final: 0.4924 (ttm) REVERT: H 550 ILE cc_start: 0.5341 (pp) cc_final: 0.5074 (pp) REVERT: H 612 GLU cc_start: 0.5522 (tt0) cc_final: 0.5117 (mm-30) REVERT: H 800 MET cc_start: 0.6476 (ttp) cc_final: 0.5798 (ttp) REVERT: H 845 GLN cc_start: 0.7824 (tp40) cc_final: 0.7577 (tm-30) REVERT: H 874 GLU cc_start: 0.5783 (tm-30) cc_final: 0.5329 (tt0) REVERT: H 1024 MET cc_start: 0.5338 (ttt) cc_final: 0.4683 (mmp) REVERT: H 1251 MET cc_start: 0.5486 (mmm) cc_final: 0.4523 (mmm) REVERT: H 1270 SER cc_start: 0.5852 (t) cc_final: 0.5348 (m) REVERT: H 1363 HIS cc_start: 0.7186 (m90) cc_final: 0.6540 (m90) REVERT: H 1416 THR cc_start: 0.5982 (p) cc_final: 0.5772 (p) REVERT: H 1455 GLU cc_start: 0.6452 (tp30) cc_final: 0.6109 (tt0) REVERT: H 1460 LYS cc_start: 0.4381 (tttt) cc_final: 0.3830 (tttt) REVERT: H 1464 LYS cc_start: 0.5117 (mmmm) cc_final: 0.4896 (mtmm) REVERT: H 1480 ASN cc_start: 0.4571 (t0) cc_final: 0.3796 (t0) REVERT: G 112 MET cc_start: 0.7890 (mmp) cc_final: 0.7478 (mmm) REVERT: G 152 ILE cc_start: 0.6413 (mm) cc_final: 0.6179 (mt) REVERT: G 291 LEU cc_start: 0.7123 (tt) cc_final: 0.6658 (tp) REVERT: G 298 ARG cc_start: 0.6357 (mtt-85) cc_final: 0.5913 (tpt-90) REVERT: G 429 MET cc_start: 0.3545 (ttp) cc_final: 0.2928 (ttp) REVERT: G 502 MET cc_start: 0.6347 (ttt) cc_final: 0.6136 (ttm) REVERT: G 845 GLN cc_start: 0.7934 (tp40) cc_final: 0.7370 (tm-30) REVERT: G 846 HIS cc_start: 0.6142 (t-90) cc_final: 0.5823 (m-70) REVERT: G 1024 MET cc_start: 0.6337 (ttt) cc_final: 0.5831 (tpt) REVERT: G 1145 SER cc_start: 0.6881 (m) cc_final: 0.6545 (p) REVERT: G 1270 SER cc_start: 0.5766 (t) cc_final: 0.5335 (m) REVERT: G 1363 HIS cc_start: 0.7867 (m90) cc_final: 0.7207 (m90) REVERT: G 1460 LYS cc_start: 0.6267 (tttt) cc_final: 0.5828 (tmtt) REVERT: G 1513 MET cc_start: 0.4604 (OUTLIER) cc_final: 0.3625 (mtt) REVERT: G 1538 ARG cc_start: 0.5678 (mmt180) cc_final: 0.5209 (mtp-110) REVERT: F 112 MET cc_start: 0.7949 (mmp) cc_final: 0.7676 (mmm) REVERT: F 181 MET cc_start: 0.6612 (mmt) cc_final: 0.6190 (mmt) REVERT: F 295 PHE cc_start: 0.6005 (t80) cc_final: 0.5531 (t80) REVERT: F 298 ARG cc_start: 0.6481 (mtt-85) cc_final: 0.6078 (mtp85) REVERT: F 361 LEU cc_start: 0.6530 (tp) cc_final: 0.6291 (mt) REVERT: F 394 LYS cc_start: 0.5789 (tttt) cc_final: 0.5505 (tttp) REVERT: F 441 MET cc_start: 0.4563 (ttt) cc_final: 0.4150 (ttp) REVERT: F 451 LEU cc_start: 0.6089 (tm) cc_final: 0.5875 (mp) REVERT: F 496 LEU cc_start: 0.6814 (tm) cc_final: 0.6205 (mp) REVERT: F 502 MET cc_start: 0.4990 (ttt) cc_final: 0.4561 (ttm) REVERT: F 503 LEU cc_start: 0.5847 (mt) cc_final: 0.5609 (mt) REVERT: F 536 PHE cc_start: 0.6760 (t80) cc_final: 0.6533 (t80) REVERT: F 793 PHE cc_start: 0.8525 (t80) cc_final: 0.8277 (t80) REVERT: F 900 ILE cc_start: 0.5510 (mt) cc_final: 0.5224 (mp) REVERT: F 1024 MET cc_start: 0.5434 (ttt) cc_final: 0.4841 (mmp) REVERT: F 1026 LEU cc_start: 0.7436 (tm) cc_final: 0.7195 (tm) REVERT: F 1084 THR cc_start: 0.6762 (m) cc_final: 0.6561 (m) REVERT: F 1192 ASP cc_start: 0.6105 (t70) cc_final: 0.5856 (t0) REVERT: F 1208 GLU cc_start: 0.6447 (tp30) cc_final: 0.6182 (tp30) REVERT: F 1365 ASN cc_start: 0.4628 (p0) cc_final: 0.4163 (p0) REVERT: F 1399 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5639 (mm-30) REVERT: F 1435 ILE cc_start: 0.6301 (mm) cc_final: 0.5811 (mt) REVERT: F 1541 THR cc_start: 0.7566 (m) cc_final: 0.7340 (p) REVERT: F 1560 ASP cc_start: 0.7402 (t0) cc_final: 0.7104 (p0) outliers start: 16 outliers final: 7 residues processed: 1660 average time/residue: 0.5917 time to fit residues: 1647.7017 Evaluate side-chains 1145 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1136 time to evaluate : 5.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1511 ILE Chi-restraints excluded: chain E residue 1513 MET Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1271 LEU Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1513 MET Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1271 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 4.9990 chunk 488 optimal weight: 0.0970 chunk 270 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 260 optimal weight: 0.9980 chunk 504 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 306 optimal weight: 0.1980 chunk 375 optimal weight: 1.9990 chunk 584 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 193 HIS A 277 HIS A 335 ASN C 46 HIS C 186 HIS C 277 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN B 186 HIS B 193 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN D 41 ASN D 186 HIS D 193 HIS ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 HIS ** D 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN E 36 HIS E 126 ASN E 188 ASN E 374 GLN E 416 GLN E 419 ASN E 427 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN E 714 GLN E 821 GLN E 845 GLN E1019 GLN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1223 GLN E1233 ASN E1272 HIS E1295 ASN E1483 GLN ** H 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 ASN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 ASN H 416 GLN H 419 ASN H 437 ASN H 707 GLN H 714 GLN H 821 GLN H1122 ASN H1233 ASN H1272 HIS H1292 ASN ** H1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1347 GLN G 36 HIS G 126 ASN G 188 ASN G 374 GLN G 416 GLN G 427 GLN G 714 GLN G 821 GLN G 845 GLN G1019 GLN G1272 HIS F 36 HIS ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN F 419 ASN F 426 ASN F 437 ASN F 498 GLN ** F 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 821 GLN ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 ASN F1272 HIS F1295 ASN F1347 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 50056 Z= 0.218 Angle : 0.683 10.969 68280 Z= 0.344 Chirality : 0.044 0.199 8356 Planarity : 0.005 0.062 8388 Dihedral : 8.261 116.369 7168 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.28 % Allowed : 12.81 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.10), residues: 6384 helix: 0.25 (0.08), residues: 3904 sheet: -1.72 (0.21), residues: 544 loop : -2.54 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 514 HIS 0.010 0.001 HIS F1272 PHE 0.030 0.002 PHE F 577 TYR 0.025 0.002 TYR F 798 ARG 0.010 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1370 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1206 time to evaluate : 5.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7318 (m110) cc_final: 0.7044 (m-40) REVERT: A 57 GLN cc_start: 0.6581 (pt0) cc_final: 0.5674 (tp40) REVERT: A 195 ARG cc_start: 0.6812 (mmm-85) cc_final: 0.5592 (mmm160) REVERT: A 209 MET cc_start: 0.7625 (tpp) cc_final: 0.6971 (tpp) REVERT: A 217 MET cc_start: 0.7948 (mtm) cc_final: 0.7486 (mtp) REVERT: A 248 SER cc_start: 0.8302 (m) cc_final: 0.7829 (p) REVERT: C 37 SER cc_start: 0.7067 (t) cc_final: 0.6847 (m) REVERT: C 41 ASN cc_start: 0.7103 (m110) cc_final: 0.6721 (m-40) REVERT: C 48 ASN cc_start: 0.7342 (m-40) cc_final: 0.6845 (m110) REVERT: C 57 GLN cc_start: 0.7182 (pt0) cc_final: 0.6294 (tp40) REVERT: C 195 ARG cc_start: 0.6162 (mmm-85) cc_final: 0.5323 (mmm160) REVERT: C 217 MET cc_start: 0.7793 (mtm) cc_final: 0.7452 (mtp) REVERT: C 248 SER cc_start: 0.8199 (m) cc_final: 0.7847 (p) REVERT: C 280 ASP cc_start: 0.8074 (t70) cc_final: 0.7705 (t0) REVERT: B 41 ASN cc_start: 0.7165 (m110) cc_final: 0.6915 (m-40) REVERT: B 57 GLN cc_start: 0.6772 (pt0) cc_final: 0.6181 (tp40) REVERT: B 195 ARG cc_start: 0.6599 (mmm-85) cc_final: 0.5832 (mmm160) REVERT: B 209 MET cc_start: 0.7630 (tpp) cc_final: 0.7260 (tpp) REVERT: B 248 SER cc_start: 0.8613 (m) cc_final: 0.8180 (p) REVERT: B 280 ASP cc_start: 0.8074 (t70) cc_final: 0.7522 (t0) REVERT: B 325 ARG cc_start: 0.6220 (mtm-85) cc_final: 0.5965 (mtm-85) REVERT: D 48 ASN cc_start: 0.7360 (m-40) cc_final: 0.6712 (m110) REVERT: D 57 GLN cc_start: 0.6792 (pt0) cc_final: 0.5949 (tp40) REVERT: D 68 TRP cc_start: 0.7462 (m-10) cc_final: 0.7142 (m-10) REVERT: D 183 PHE cc_start: 0.8027 (m-80) cc_final: 0.7812 (m-80) REVERT: D 195 ARG cc_start: 0.6502 (mmm-85) cc_final: 0.5458 (mmm160) REVERT: D 209 MET cc_start: 0.7341 (tpp) cc_final: 0.6909 (tpp) REVERT: D 217 MET cc_start: 0.7894 (mtm) cc_final: 0.7280 (mtp) REVERT: D 248 SER cc_start: 0.8181 (m) cc_final: 0.7855 (p) REVERT: D 305 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6966 (mp) REVERT: D 321 GLU cc_start: 0.6152 (tm-30) cc_final: 0.5481 (tm-30) REVERT: E 29 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: E 42 ILE cc_start: 0.7378 (tt) cc_final: 0.7113 (tp) REVERT: E 78 THR cc_start: 0.6856 (m) cc_final: 0.6551 (m) REVERT: E 112 MET cc_start: 0.7793 (mmp) cc_final: 0.7438 (mmm) REVERT: E 298 ARG cc_start: 0.5294 (mtt-85) cc_final: 0.5039 (tpt-90) REVERT: E 312 LEU cc_start: 0.6282 (tp) cc_final: 0.5892 (mp) REVERT: E 451 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5601 (mt) REVERT: E 502 MET cc_start: 0.5662 (ttt) cc_final: 0.5455 (ttm) REVERT: E 732 LYS cc_start: 0.7585 (pttm) cc_final: 0.7131 (pttp) REVERT: E 1024 MET cc_start: 0.6310 (ttt) cc_final: 0.5756 (tpt) REVERT: E 1035 LYS cc_start: 0.6869 (tttt) cc_final: 0.6152 (tptp) REVERT: E 1065 MET cc_start: 0.5791 (tpt) cc_final: 0.5409 (ttt) REVERT: E 1070 LEU cc_start: 0.5809 (mp) cc_final: 0.5577 (mp) REVERT: E 1110 ARG cc_start: 0.7227 (mmm160) cc_final: 0.6702 (mmm160) REVERT: E 1145 SER cc_start: 0.7196 (m) cc_final: 0.6697 (p) REVERT: E 1229 TYR cc_start: 0.5931 (m-10) cc_final: 0.5719 (m-80) REVERT: E 1244 ASN cc_start: 0.7056 (m110) cc_final: 0.6805 (m-40) REVERT: E 1275 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5765 (pp) REVERT: E 1289 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.4373 (ttm) REVERT: E 1352 ARG cc_start: 0.4694 (ptt180) cc_final: 0.3960 (ptt-90) REVERT: E 1359 PRO cc_start: 0.8162 (Cg_endo) cc_final: 0.7960 (Cg_exo) REVERT: E 1362 LYS cc_start: 0.6485 (ptpt) cc_final: 0.6181 (pttm) REVERT: E 1365 ASN cc_start: 0.7187 (p0) cc_final: 0.6937 (p0) REVERT: E 1416 THR cc_start: 0.6503 (p) cc_final: 0.6240 (t) REVERT: E 1464 LYS cc_start: 0.6885 (tppt) cc_final: 0.5859 (mttt) REVERT: E 1569 LYS cc_start: 0.8486 (tmtp) cc_final: 0.7948 (ttpp) REVERT: H 108 MET cc_start: 0.7095 (tpp) cc_final: 0.6647 (tmm) REVERT: H 174 LEU cc_start: 0.7043 (tt) cc_final: 0.6830 (tt) REVERT: H 361 LEU cc_start: 0.6589 (tp) cc_final: 0.6309 (mt) REVERT: H 441 MET cc_start: 0.4147 (ttt) cc_final: 0.3809 (tmm) REVERT: H 540 THR cc_start: 0.5164 (t) cc_final: 0.4865 (t) REVERT: H 730 MET cc_start: 0.6931 (mtm) cc_final: 0.6486 (mtm) REVERT: H 816 HIS cc_start: 0.7307 (m90) cc_final: 0.7002 (m-70) REVERT: H 844 TYR cc_start: 0.7376 (t80) cc_final: 0.7030 (t80) REVERT: H 902 MET cc_start: 0.5032 (mtm) cc_final: 0.4488 (mtm) REVERT: H 1003 TYR cc_start: 0.6474 (t80) cc_final: 0.5676 (t80) REVERT: H 1024 MET cc_start: 0.5171 (ttt) cc_final: 0.4846 (mmp) REVERT: H 1195 THR cc_start: 0.5490 (t) cc_final: 0.5259 (t) REVERT: H 1208 GLU cc_start: 0.5867 (tp30) cc_final: 0.5639 (tp30) REVERT: H 1244 ASN cc_start: 0.7477 (m110) cc_final: 0.7217 (m-40) REVERT: H 1270 SER cc_start: 0.5833 (t) cc_final: 0.5400 (m) REVERT: H 1285 THR cc_start: 0.5536 (m) cc_final: 0.5334 (m) REVERT: H 1363 HIS cc_start: 0.7518 (m90) cc_final: 0.6817 (m90) REVERT: H 1460 LYS cc_start: 0.4973 (tttt) cc_final: 0.4705 (tmtt) REVERT: H 1470 LEU cc_start: 0.6846 (pp) cc_final: 0.6424 (pp) REVERT: H 1524 MET cc_start: 0.6450 (mmm) cc_final: 0.6111 (mmt) REVERT: G 29 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: G 42 ILE cc_start: 0.7224 (tt) cc_final: 0.7006 (tp) REVERT: G 112 MET cc_start: 0.8022 (mmp) cc_final: 0.7514 (mmm) REVERT: G 298 ARG cc_start: 0.6272 (mtt-85) cc_final: 0.5962 (tpt-90) REVERT: G 314 PHE cc_start: 0.6150 (t80) cc_final: 0.5916 (t80) REVERT: G 370 ARG cc_start: 0.5352 (mmm160) cc_final: 0.5096 (mmm160) REVERT: G 441 MET cc_start: 0.5564 (ttp) cc_final: 0.5148 (ttp) REVERT: G 546 MET cc_start: 0.6389 (tpp) cc_final: 0.6047 (ttm) REVERT: G 583 PHE cc_start: 0.5045 (m-10) cc_final: 0.4830 (m-80) REVERT: G 612 GLU cc_start: 0.7049 (tt0) cc_final: 0.6590 (mt-10) REVERT: G 618 GLU cc_start: 0.6468 (pt0) cc_final: 0.6250 (mt-10) REVERT: G 800 MET cc_start: 0.6355 (ttp) cc_final: 0.5351 (ptm) REVERT: G 803 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6458 (pp20) REVERT: G 846 HIS cc_start: 0.6126 (t-90) cc_final: 0.5781 (m-70) REVERT: G 1024 MET cc_start: 0.6181 (ttt) cc_final: 0.5758 (tpt) REVERT: G 1125 SER cc_start: 0.6785 (t) cc_final: 0.6493 (m) REVERT: G 1133 GLN cc_start: 0.6025 (tt0) cc_final: 0.5644 (tp40) REVERT: G 1145 SER cc_start: 0.7085 (m) cc_final: 0.6633 (p) REVERT: G 1208 GLU cc_start: 0.6274 (tp30) cc_final: 0.6059 (tp30) REVERT: G 1244 ASN cc_start: 0.7513 (m110) cc_final: 0.7214 (m-40) REVERT: G 1252 GLU cc_start: 0.5464 (tp30) cc_final: 0.4936 (tp30) REVERT: G 1275 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5243 (pp) REVERT: G 1295 ASN cc_start: 0.6835 (m110) cc_final: 0.6291 (m110) REVERT: G 1352 ARG cc_start: 0.2993 (ptp-170) cc_final: 0.2778 (ptp-170) REVERT: G 1357 LEU cc_start: 0.7049 (mm) cc_final: 0.6727 (mt) REVERT: G 1363 HIS cc_start: 0.7824 (m90) cc_final: 0.7161 (m90) REVERT: G 1368 ILE cc_start: 0.4893 (OUTLIER) cc_final: 0.4269 (mp) REVERT: G 1460 LYS cc_start: 0.5757 (tttt) cc_final: 0.5556 (tmtt) REVERT: G 1504 MET cc_start: 0.4894 (mtt) cc_final: 0.4481 (mtt) REVERT: G 1513 MET cc_start: 0.4100 (OUTLIER) cc_final: 0.3722 (mmp) REVERT: F 172 THR cc_start: 0.7238 (m) cc_final: 0.6983 (m) REVERT: F 178 LEU cc_start: 0.7182 (tp) cc_final: 0.6911 (tp) REVERT: F 181 MET cc_start: 0.6591 (mmt) cc_final: 0.6196 (mmt) REVERT: F 295 PHE cc_start: 0.6133 (t80) cc_final: 0.5902 (t80) REVERT: F 298 ARG cc_start: 0.6329 (mtt-85) cc_final: 0.5928 (mtp85) REVERT: F 361 LEU cc_start: 0.6493 (tp) cc_final: 0.6285 (mt) REVERT: F 394 LYS cc_start: 0.5758 (tttt) cc_final: 0.5522 (tttp) REVERT: F 496 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6345 (mt) REVERT: F 793 PHE cc_start: 0.8662 (t80) cc_final: 0.8405 (t80) REVERT: F 897 ASP cc_start: 0.5617 (t0) cc_final: 0.4968 (m-30) REVERT: F 1024 MET cc_start: 0.5412 (ttt) cc_final: 0.4916 (mmp) REVERT: F 1160 THR cc_start: 0.6352 (OUTLIER) cc_final: 0.6108 (t) REVERT: F 1244 ASN cc_start: 0.7638 (m110) cc_final: 0.7368 (m-40) REVERT: F 1275 LEU cc_start: 0.5381 (OUTLIER) cc_final: 0.5006 (pp) REVERT: F 1365 ASN cc_start: 0.4907 (p0) cc_final: 0.4698 (p0) REVERT: F 1399 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5798 (mm-30) REVERT: F 1435 ILE cc_start: 0.6301 (mm) cc_final: 0.5902 (mt) REVERT: F 1470 LEU cc_start: 0.6448 (pp) cc_final: 0.6214 (pp) REVERT: F 1541 THR cc_start: 0.7335 (m) cc_final: 0.7023 (p) outliers start: 164 outliers final: 88 residues processed: 1294 average time/residue: 0.5750 time to fit residues: 1263.3404 Evaluate side-chains 1182 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1082 time to evaluate : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 562 HIS Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 1119 SER Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1147 LEU Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1289 MET Chi-restraints excluded: chain E residue 1314 ILE Chi-restraints excluded: chain E residue 1364 VAL Chi-restraints excluded: chain E residue 1404 ILE Chi-restraints excluded: chain E residue 1415 HIS Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1447 ASP Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 326 HIS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 601 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 852 LEU Chi-restraints excluded: chain H residue 876 LEU Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1188 LEU Chi-restraints excluded: chain H residue 1206 THR Chi-restraints excluded: chain H residue 1271 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1346 ILE Chi-restraints excluded: chain H residue 1376 ILE Chi-restraints excluded: chain H residue 1447 ASP Chi-restraints excluded: chain H residue 1521 LYS Chi-restraints excluded: chain H residue 1551 LEU Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 488 THR Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 837 ILE Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1314 ILE Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1513 MET Chi-restraints excluded: chain G residue 1519 LEU Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain G residue 1547 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 601 VAL Chi-restraints excluded: chain F residue 721 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 1081 THR Chi-restraints excluded: chain F residue 1091 LYS Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1160 THR Chi-restraints excluded: chain F residue 1271 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1551 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 486 optimal weight: 6.9990 chunk 398 optimal weight: 1.9990 chunk 161 optimal weight: 0.0270 chunk 585 optimal weight: 7.9990 chunk 632 optimal weight: 7.9990 chunk 521 optimal weight: 0.9990 chunk 580 optimal weight: 3.9990 chunk 199 optimal weight: 0.6980 chunk 470 optimal weight: 3.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS B 46 HIS D 46 HIS E 103 HIS E 707 GLN E 845 GLN E1097 HIS ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS E1347 GLN ** H 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1234 ASN H1347 GLN H1401 HIS H1483 GLN G 103 HIS G 419 ASN G 835 GLN G 895 HIS G1019 GLN G1272 HIS F 188 ASN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN F 474 GLN F1019 GLN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 ASN F1234 ASN F1347 GLN F1401 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 50056 Z= 0.252 Angle : 0.666 14.138 68280 Z= 0.333 Chirality : 0.044 0.331 8356 Planarity : 0.005 0.063 8388 Dihedral : 8.300 111.765 7163 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.68 % Allowed : 14.07 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 6384 helix: 0.68 (0.08), residues: 3920 sheet: -1.18 (0.21), residues: 524 loop : -2.34 (0.12), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H1032 HIS 0.013 0.001 HIS G 103 PHE 0.029 0.002 PHE H 577 TYR 0.025 0.002 TYR G 123 ARG 0.013 0.001 ARG G1538 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1201 time to evaluate : 6.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7315 (m110) cc_final: 0.7036 (m-40) REVERT: A 48 ASN cc_start: 0.7164 (m-40) cc_final: 0.6911 (m110) REVERT: A 57 GLN cc_start: 0.6537 (pt0) cc_final: 0.5722 (tp40) REVERT: A 195 ARG cc_start: 0.6970 (mmm-85) cc_final: 0.5785 (mmm160) REVERT: A 209 MET cc_start: 0.7716 (tpp) cc_final: 0.6964 (tpp) REVERT: A 217 MET cc_start: 0.8079 (mtm) cc_final: 0.7614 (mtp) REVERT: A 248 SER cc_start: 0.8518 (m) cc_final: 0.8058 (p) REVERT: A 280 ASP cc_start: 0.8134 (t70) cc_final: 0.7590 (t0) REVERT: C 38 LYS cc_start: 0.7164 (mmmt) cc_final: 0.6862 (mmmt) REVERT: C 41 ASN cc_start: 0.6875 (m110) cc_final: 0.6571 (m-40) REVERT: C 48 ASN cc_start: 0.7219 (m-40) cc_final: 0.6687 (m110) REVERT: C 57 GLN cc_start: 0.7171 (pt0) cc_final: 0.6317 (tp40) REVERT: C 195 ARG cc_start: 0.6495 (mmm-85) cc_final: 0.5502 (mmm160) REVERT: C 217 MET cc_start: 0.7935 (mtm) cc_final: 0.7459 (mtp) REVERT: C 248 SER cc_start: 0.8325 (m) cc_final: 0.7914 (p) REVERT: C 280 ASP cc_start: 0.8014 (t70) cc_final: 0.7601 (t0) REVERT: B 57 GLN cc_start: 0.6674 (pt0) cc_final: 0.6136 (tp40) REVERT: B 195 ARG cc_start: 0.6661 (mmm-85) cc_final: 0.5764 (mmm160) REVERT: B 223 THR cc_start: 0.8255 (t) cc_final: 0.7673 (p) REVERT: B 240 MET cc_start: 0.7292 (ttp) cc_final: 0.7084 (ttp) REVERT: B 248 SER cc_start: 0.8706 (m) cc_final: 0.8249 (p) REVERT: B 280 ASP cc_start: 0.8042 (t70) cc_final: 0.7772 (t0) REVERT: D 38 LYS cc_start: 0.6898 (mmmt) cc_final: 0.6698 (mmmt) REVERT: D 57 GLN cc_start: 0.6728 (pt0) cc_final: 0.5915 (tp40) REVERT: D 68 TRP cc_start: 0.7446 (m-10) cc_final: 0.7192 (m-10) REVERT: D 195 ARG cc_start: 0.6444 (mmm-85) cc_final: 0.5365 (mmm160) REVERT: D 209 MET cc_start: 0.7530 (tpp) cc_final: 0.7115 (tpp) REVERT: D 217 MET cc_start: 0.7935 (mtm) cc_final: 0.7269 (mtp) REVERT: D 223 THR cc_start: 0.8511 (t) cc_final: 0.8010 (p) REVERT: D 229 GLU cc_start: 0.7101 (pt0) cc_final: 0.6713 (pt0) REVERT: D 248 SER cc_start: 0.8345 (m) cc_final: 0.8027 (p) REVERT: D 280 ASP cc_start: 0.8222 (t70) cc_final: 0.7847 (t0) REVERT: D 321 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5520 (tm-30) REVERT: E 42 ILE cc_start: 0.7413 (tt) cc_final: 0.7170 (tp) REVERT: E 112 MET cc_start: 0.7800 (mmp) cc_final: 0.7350 (mmm) REVERT: E 295 PHE cc_start: 0.6580 (t80) cc_final: 0.6236 (t80) REVERT: E 298 ARG cc_start: 0.5261 (mtt-85) cc_final: 0.5000 (mtt-85) REVERT: E 306 ARG cc_start: 0.4351 (tpp-160) cc_final: 0.4150 (tpt170) REVERT: E 312 LEU cc_start: 0.6244 (tp) cc_final: 0.5788 (mp) REVERT: E 381 ILE cc_start: 0.5676 (tt) cc_final: 0.5359 (tt) REVERT: E 396 TYR cc_start: 0.6649 (t80) cc_final: 0.6412 (t80) REVERT: E 412 MET cc_start: 0.7426 (mtm) cc_final: 0.6489 (mpp) REVERT: E 686 PHE cc_start: 0.6754 (m-80) cc_final: 0.6526 (m-80) REVERT: E 732 LYS cc_start: 0.7547 (pttm) cc_final: 0.7205 (pttp) REVERT: E 800 MET cc_start: 0.6645 (ttp) cc_final: 0.6171 (ptp) REVERT: E 845 GLN cc_start: 0.7184 (tp40) cc_final: 0.6973 (tm-30) REVERT: E 1024 MET cc_start: 0.6335 (ttt) cc_final: 0.5863 (tpt) REVERT: E 1065 MET cc_start: 0.5872 (tpt) cc_final: 0.5279 (ttt) REVERT: E 1110 ARG cc_start: 0.7223 (mmm160) cc_final: 0.6637 (mmm160) REVERT: E 1145 SER cc_start: 0.7179 (m) cc_final: 0.6570 (p) REVERT: E 1167 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6416 (tp) REVERT: E 1226 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.5108 (tp) REVERT: E 1244 ASN cc_start: 0.7222 (m110) cc_final: 0.6837 (m-40) REVERT: E 1275 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5277 (pp) REVERT: E 1289 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.4598 (ttm) REVERT: E 1297 MET cc_start: 0.7272 (ttm) cc_final: 0.7058 (ttm) REVERT: E 1352 ARG cc_start: 0.4693 (ptt180) cc_final: 0.3938 (ptt-90) REVERT: E 1359 PRO cc_start: 0.8051 (Cg_endo) cc_final: 0.7698 (Cg_exo) REVERT: E 1362 LYS cc_start: 0.6670 (ptpt) cc_final: 0.6317 (pttm) REVERT: E 1402 ILE cc_start: 0.6984 (OUTLIER) cc_final: 0.6529 (mt) REVERT: E 1464 LYS cc_start: 0.6814 (tppt) cc_final: 0.5679 (mttt) REVERT: E 1538 ARG cc_start: 0.7091 (mmm160) cc_final: 0.6369 (mtt-85) REVERT: E 1569 LYS cc_start: 0.8564 (tmtp) cc_final: 0.7983 (ttpp) REVERT: H 108 MET cc_start: 0.6943 (tpp) cc_final: 0.6541 (tmm) REVERT: H 361 LEU cc_start: 0.6666 (tp) cc_final: 0.6288 (mt) REVERT: H 441 MET cc_start: 0.4357 (ttt) cc_final: 0.3904 (tmm) REVERT: H 540 THR cc_start: 0.5483 (t) cc_final: 0.5216 (t) REVERT: H 844 TYR cc_start: 0.7466 (t80) cc_final: 0.7080 (t80) REVERT: H 1003 TYR cc_start: 0.6374 (t80) cc_final: 0.5653 (t80) REVERT: H 1011 LEU cc_start: 0.3537 (mt) cc_final: 0.3302 (mt) REVERT: H 1024 MET cc_start: 0.5435 (ttt) cc_final: 0.5132 (mmp) REVERT: H 1132 ASP cc_start: 0.7501 (p0) cc_final: 0.7210 (p0) REVERT: H 1167 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6231 (tp) REVERT: H 1195 THR cc_start: 0.5651 (t) cc_final: 0.5386 (t) REVERT: H 1208 GLU cc_start: 0.6637 (tp30) cc_final: 0.6325 (tp30) REVERT: H 1244 ASN cc_start: 0.7613 (m110) cc_final: 0.7270 (m-40) REVERT: H 1363 HIS cc_start: 0.7794 (m90) cc_final: 0.7114 (m90) REVERT: H 1460 LYS cc_start: 0.5479 (tttt) cc_final: 0.4794 (tmtt) REVERT: H 1464 LYS cc_start: 0.6477 (tppt) cc_final: 0.6006 (tppt) REVERT: H 1470 LEU cc_start: 0.7002 (pp) cc_final: 0.6608 (pp) REVERT: H 1524 MET cc_start: 0.6945 (mmm) cc_final: 0.6651 (mmm) REVERT: G 298 ARG cc_start: 0.6168 (mtt-85) cc_final: 0.5829 (tpt-90) REVERT: G 314 PHE cc_start: 0.5953 (t80) cc_final: 0.5658 (t80) REVERT: G 325 ASP cc_start: 0.5353 (m-30) cc_final: 0.5113 (m-30) REVERT: G 370 ARG cc_start: 0.5493 (mmm160) cc_final: 0.5255 (mmm160) REVERT: G 441 MET cc_start: 0.5197 (ttp) cc_final: 0.4987 (ttp) REVERT: G 550 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5674 (tp) REVERT: G 612 GLU cc_start: 0.7023 (tt0) cc_final: 0.6498 (mt-10) REVERT: G 846 HIS cc_start: 0.6100 (t-90) cc_final: 0.5692 (m-70) REVERT: G 1019 GLN cc_start: 0.6677 (mm-40) cc_final: 0.6473 (mt0) REVERT: G 1020 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6844 (mm) REVERT: G 1024 MET cc_start: 0.6048 (ttt) cc_final: 0.5698 (tpt) REVERT: G 1035 LYS cc_start: 0.6774 (ttpt) cc_final: 0.6243 (tptp) REVERT: G 1124 PHE cc_start: 0.6539 (m-80) cc_final: 0.6187 (m-80) REVERT: G 1125 SER cc_start: 0.6772 (t) cc_final: 0.6459 (m) REVERT: G 1131 ILE cc_start: 0.5292 (mt) cc_final: 0.5041 (mt) REVERT: G 1145 SER cc_start: 0.7240 (m) cc_final: 0.6763 (p) REVERT: G 1208 GLU cc_start: 0.6746 (tp30) cc_final: 0.6399 (tp30) REVERT: G 1244 ASN cc_start: 0.7745 (m110) cc_final: 0.7422 (m-40) REVERT: G 1272 HIS cc_start: 0.6305 (OUTLIER) cc_final: 0.6089 (m-70) REVERT: G 1275 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5140 (pp) REVERT: G 1284 LEU cc_start: 0.5544 (OUTLIER) cc_final: 0.5179 (pp) REVERT: G 1357 LEU cc_start: 0.7283 (mm) cc_final: 0.7060 (mt) REVERT: G 1363 HIS cc_start: 0.8035 (m90) cc_final: 0.7426 (m90) REVERT: G 1402 ILE cc_start: 0.6336 (tt) cc_final: 0.5741 (mt) REVERT: G 1460 LYS cc_start: 0.6046 (tttt) cc_final: 0.5777 (tmtt) REVERT: G 1475 THR cc_start: 0.6521 (m) cc_final: 0.5888 (p) REVERT: G 1479 GLU cc_start: 0.4909 (tt0) cc_final: 0.4154 (tt0) REVERT: G 1541 THR cc_start: 0.6756 (m) cc_final: 0.5982 (m) REVERT: F 178 LEU cc_start: 0.7225 (tp) cc_final: 0.6823 (tp) REVERT: F 181 MET cc_start: 0.6739 (mmt) cc_final: 0.6323 (mmt) REVERT: F 298 ARG cc_start: 0.6541 (mtt-85) cc_final: 0.6149 (mtp85) REVERT: F 361 LEU cc_start: 0.6623 (tp) cc_final: 0.6413 (mt) REVERT: F 496 LEU cc_start: 0.6059 (tm) cc_final: 0.5732 (mp) REVERT: F 604 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6309 (mt) REVERT: F 682 MET cc_start: 0.6748 (ptp) cc_final: 0.6532 (ptp) REVERT: F 793 PHE cc_start: 0.8676 (t80) cc_final: 0.8426 (t80) REVERT: F 897 ASP cc_start: 0.5216 (t0) cc_final: 0.4932 (m-30) REVERT: F 1024 MET cc_start: 0.5582 (ttt) cc_final: 0.5030 (mmp) REVERT: F 1082 SER cc_start: 0.6461 (m) cc_final: 0.6164 (t) REVERT: F 1111 PHE cc_start: 0.6895 (t80) cc_final: 0.6612 (t80) REVERT: F 1125 SER cc_start: 0.7108 (t) cc_final: 0.6812 (m) REVERT: F 1160 THR cc_start: 0.6513 (OUTLIER) cc_final: 0.6292 (t) REVERT: F 1167 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6315 (tp) REVERT: F 1244 ASN cc_start: 0.7824 (m110) cc_final: 0.7495 (m-40) REVERT: F 1252 GLU cc_start: 0.5843 (tp30) cc_final: 0.5054 (tp30) REVERT: F 1275 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5329 (pp) REVERT: F 1284 LEU cc_start: 0.5295 (OUTLIER) cc_final: 0.5075 (pp) REVERT: F 1399 GLU cc_start: 0.6258 (mm-30) cc_final: 0.5944 (mm-30) REVERT: F 1480 ASN cc_start: 0.5925 (t0) cc_final: 0.5665 (t0) outliers start: 234 outliers final: 119 residues processed: 1329 average time/residue: 0.5469 time to fit residues: 1237.7622 Evaluate side-chains 1218 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1083 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 890 LEU Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 1037 THR Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1226 LEU Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1241 THR Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1289 MET Chi-restraints excluded: chain E residue 1314 ILE Chi-restraints excluded: chain E residue 1364 VAL Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1415 HIS Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1447 ASP Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 601 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 895 HIS Chi-restraints excluded: chain H residue 1038 ASP Chi-restraints excluded: chain H residue 1075 ILE Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1167 LEU Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1271 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1395 VAL Chi-restraints excluded: chain H residue 1416 THR Chi-restraints excluded: chain H residue 1447 ASP Chi-restraints excluded: chain H residue 1503 ILE Chi-restraints excluded: chain H residue 1519 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 550 ILE Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 715 VAL Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1031 TYR Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1230 THR Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1272 HIS Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1314 ILE Chi-restraints excluded: chain G residue 1395 VAL Chi-restraints excluded: chain G residue 1419 SER Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1519 LEU Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1547 LEU Chi-restraints excluded: chain G residue 1551 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 721 SER Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1026 LEU Chi-restraints excluded: chain F residue 1069 VAL Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1160 THR Chi-restraints excluded: chain F residue 1167 LEU Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1271 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1318 LEU Chi-restraints excluded: chain F residue 1395 VAL Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1503 ILE Chi-restraints excluded: chain F residue 1551 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 5.9990 chunk 440 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 279 optimal weight: 3.9990 chunk 393 optimal weight: 0.0000 chunk 587 optimal weight: 20.0000 chunk 622 optimal weight: 2.9990 chunk 307 optimal weight: 0.5980 chunk 557 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN E 437 ASN E 891 GLN ** E1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS H 36 HIS ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN ** H 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 426 ASN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 HIS ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 GLN ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 821 GLN G1097 HIS G1272 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1097 HIS ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5722 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 50056 Z= 0.331 Angle : 0.739 16.104 68280 Z= 0.367 Chirality : 0.047 0.503 8356 Planarity : 0.005 0.070 8388 Dihedral : 8.314 109.354 7160 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.78 % Allowed : 15.57 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6384 helix: 0.75 (0.08), residues: 3904 sheet: -1.11 (0.21), residues: 580 loop : -2.07 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H1032 HIS 0.058 0.002 HIS G1272 PHE 0.036 0.002 PHE E 577 TYR 0.020 0.002 TYR G 123 ARG 0.010 0.001 ARG G1538 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1236 time to evaluate : 6.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7068 (m-40) cc_final: 0.6798 (m110) REVERT: A 57 GLN cc_start: 0.6564 (pt0) cc_final: 0.5772 (tp40) REVERT: A 195 ARG cc_start: 0.7019 (mmm-85) cc_final: 0.5799 (mmm160) REVERT: A 204 ASP cc_start: 0.6434 (t0) cc_final: 0.6171 (t0) REVERT: A 209 MET cc_start: 0.7701 (tpp) cc_final: 0.7114 (tpp) REVERT: A 217 MET cc_start: 0.8350 (mtm) cc_final: 0.7940 (mtp) REVERT: A 224 THR cc_start: 0.7436 (m) cc_final: 0.7163 (t) REVERT: A 248 SER cc_start: 0.8611 (m) cc_final: 0.8178 (p) REVERT: A 255 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6252 (pp) REVERT: A 280 ASP cc_start: 0.8081 (t70) cc_final: 0.7517 (t0) REVERT: A 286 ILE cc_start: 0.7173 (mt) cc_final: 0.6964 (mp) REVERT: C 57 GLN cc_start: 0.7215 (pt0) cc_final: 0.6404 (tp40) REVERT: C 195 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.5662 (mmm160) REVERT: C 217 MET cc_start: 0.7975 (mtm) cc_final: 0.7443 (mtp) REVERT: C 248 SER cc_start: 0.8323 (m) cc_final: 0.7844 (p) REVERT: C 280 ASP cc_start: 0.8279 (t70) cc_final: 0.7815 (t0) REVERT: C 308 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 57 GLN cc_start: 0.6679 (pt0) cc_final: 0.5923 (tp40) REVERT: B 99 ASP cc_start: 0.7704 (t70) cc_final: 0.7397 (m-30) REVERT: B 195 ARG cc_start: 0.6714 (mmm-85) cc_final: 0.5573 (mmm160) REVERT: B 248 SER cc_start: 0.8642 (m) cc_final: 0.8183 (p) REVERT: B 325 ARG cc_start: 0.6692 (mtm-85) cc_final: 0.5818 (ttp-110) REVERT: D 57 GLN cc_start: 0.6564 (pt0) cc_final: 0.5803 (tp40) REVERT: D 66 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6759 (tt) REVERT: D 68 TRP cc_start: 0.7455 (m-10) cc_final: 0.7221 (m-10) REVERT: D 88 MET cc_start: 0.7258 (tpp) cc_final: 0.6947 (tpt) REVERT: D 195 ARG cc_start: 0.6664 (mmm-85) cc_final: 0.5351 (mmm160) REVERT: D 209 MET cc_start: 0.7636 (tpp) cc_final: 0.7259 (tpp) REVERT: D 217 MET cc_start: 0.8034 (mtm) cc_final: 0.7555 (mtp) REVERT: D 248 SER cc_start: 0.8406 (m) cc_final: 0.7973 (p) REVERT: D 280 ASP cc_start: 0.8200 (t70) cc_final: 0.7724 (t0) REVERT: D 286 ILE cc_start: 0.7170 (mt) cc_final: 0.6956 (mp) REVERT: D 321 GLU cc_start: 0.6394 (tm-30) cc_final: 0.6058 (tm-30) REVERT: E 42 ILE cc_start: 0.7483 (tt) cc_final: 0.7235 (tp) REVERT: E 74 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5586 (ttp-170) REVERT: E 308 LEU cc_start: 0.3371 (OUTLIER) cc_final: 0.3021 (tt) REVERT: E 312 LEU cc_start: 0.6347 (tp) cc_final: 0.5794 (mp) REVERT: E 361 LEU cc_start: 0.6625 (tp) cc_final: 0.6391 (mt) REVERT: E 381 ILE cc_start: 0.5566 (tt) cc_final: 0.5254 (tt) REVERT: E 412 MET cc_start: 0.7379 (mtm) cc_final: 0.7055 (mtt) REVERT: E 451 LEU cc_start: 0.6148 (tm) cc_final: 0.5816 (mt) REVERT: E 682 MET cc_start: 0.7303 (mtt) cc_final: 0.6076 (mmt) REVERT: E 732 LYS cc_start: 0.7587 (pttm) cc_final: 0.7161 (pttp) REVERT: E 827 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6108 (pt) REVERT: E 845 GLN cc_start: 0.7347 (tp40) cc_final: 0.6968 (tm-30) REVERT: E 861 ILE cc_start: 0.6502 (mm) cc_final: 0.5766 (mm) REVERT: E 865 ASP cc_start: 0.7036 (m-30) cc_final: 0.6357 (m-30) REVERT: E 1024 MET cc_start: 0.6497 (ttt) cc_final: 0.6051 (tpt) REVERT: E 1065 MET cc_start: 0.6294 (tpt) cc_final: 0.5256 (ttt) REVERT: E 1098 ARG cc_start: 0.6142 (tpp80) cc_final: 0.5797 (ttm-80) REVERT: E 1110 ARG cc_start: 0.7050 (mmm160) cc_final: 0.6619 (mmp-170) REVERT: E 1145 SER cc_start: 0.7229 (m) cc_final: 0.6617 (p) REVERT: E 1167 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6289 (tp) REVERT: E 1275 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5837 (pp) REVERT: E 1284 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.5005 (pp) REVERT: E 1289 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4527 (ttm) REVERT: E 1293 TYR cc_start: 0.5883 (m-80) cc_final: 0.5444 (m-80) REVERT: E 1297 MET cc_start: 0.7409 (ttm) cc_final: 0.6821 (ttm) REVERT: E 1352 ARG cc_start: 0.4846 (ptt180) cc_final: 0.4054 (ptt-90) REVERT: E 1359 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7972 (Cg_exo) REVERT: E 1362 LYS cc_start: 0.6552 (ptpt) cc_final: 0.6108 (pttm) REVERT: E 1569 LYS cc_start: 0.8678 (tmtp) cc_final: 0.8205 (ttpp) REVERT: H 108 MET cc_start: 0.6954 (tpp) cc_final: 0.6668 (tmm) REVERT: H 152 ILE cc_start: 0.6648 (mm) cc_final: 0.6298 (mt) REVERT: H 183 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7129 (tm) REVERT: H 314 PHE cc_start: 0.6176 (t80) cc_final: 0.5744 (t80) REVERT: H 361 LEU cc_start: 0.6657 (tp) cc_final: 0.6337 (mt) REVERT: H 370 ARG cc_start: 0.5250 (mtp180) cc_final: 0.4933 (mtp85) REVERT: H 429 MET cc_start: 0.3822 (OUTLIER) cc_final: 0.3440 (ttp) REVERT: H 441 MET cc_start: 0.5172 (ttt) cc_final: 0.4703 (tmm) REVERT: H 501 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5974 (pt0) REVERT: H 502 MET cc_start: 0.5341 (ttt) cc_final: 0.5031 (ttm) REVERT: H 534 ARG cc_start: 0.4991 (ttp-170) cc_final: 0.4740 (tmm160) REVERT: H 546 MET cc_start: 0.5732 (tmm) cc_final: 0.5350 (mtp) REVERT: H 582 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5635 (tt) REVERT: H 1020 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6729 (mm) REVERT: H 1024 MET cc_start: 0.5601 (ttt) cc_final: 0.5316 (mmp) REVERT: H 1035 LYS cc_start: 0.6935 (mtpm) cc_final: 0.6668 (tptp) REVERT: H 1038 ASP cc_start: 0.5294 (OUTLIER) cc_final: 0.4927 (p0) REVERT: H 1065 MET cc_start: 0.5244 (ttm) cc_final: 0.4958 (ttp) REVERT: H 1122 ASN cc_start: 0.5497 (m-40) cc_final: 0.5235 (m110) REVERT: H 1125 SER cc_start: 0.6985 (t) cc_final: 0.6668 (m) REVERT: H 1133 GLN cc_start: 0.5887 (mt0) cc_final: 0.5528 (mt0) REVERT: H 1195 THR cc_start: 0.5702 (t) cc_final: 0.5472 (t) REVERT: H 1244 ASN cc_start: 0.7760 (m110) cc_final: 0.7323 (m-40) REVERT: H 1363 HIS cc_start: 0.8217 (m90) cc_final: 0.7663 (m90) REVERT: H 1464 LYS cc_start: 0.6366 (tppt) cc_final: 0.5502 (mtmt) REVERT: H 1470 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7052 (pp) REVERT: H 1485 GLN cc_start: 0.5959 (OUTLIER) cc_final: 0.5125 (mp10) REVERT: H 1524 MET cc_start: 0.6877 (mmm) cc_final: 0.6645 (mmm) REVERT: G 298 ARG cc_start: 0.6095 (mtt-85) cc_final: 0.5713 (tpt-90) REVERT: G 308 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3768 (tt) REVERT: G 312 LEU cc_start: 0.6451 (tp) cc_final: 0.5918 (mp) REVERT: G 314 PHE cc_start: 0.5549 (t80) cc_final: 0.5286 (t80) REVERT: G 361 LEU cc_start: 0.6557 (tp) cc_final: 0.6260 (mt) REVERT: G 381 ILE cc_start: 0.5844 (tt) cc_final: 0.5617 (tt) REVERT: G 550 ILE cc_start: 0.6327 (tp) cc_final: 0.5936 (tp) REVERT: G 800 MET cc_start: 0.6879 (ttp) cc_final: 0.5763 (ptp) REVERT: G 803 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6599 (pp20) REVERT: G 845 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7454 (tm-30) REVERT: G 846 HIS cc_start: 0.6354 (t-90) cc_final: 0.5934 (m-70) REVERT: G 869 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6681 (tt0) REVERT: G 1020 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7025 (mm) REVERT: G 1024 MET cc_start: 0.6544 (ttt) cc_final: 0.6220 (tpt) REVERT: G 1082 SER cc_start: 0.7487 (m) cc_final: 0.6968 (t) REVERT: G 1125 SER cc_start: 0.6788 (t) cc_final: 0.6569 (m) REVERT: G 1145 SER cc_start: 0.7251 (m) cc_final: 0.6825 (p) REVERT: G 1164 LEU cc_start: 0.6802 (mp) cc_final: 0.6586 (mp) REVERT: G 1208 GLU cc_start: 0.7339 (tp30) cc_final: 0.7102 (tp30) REVERT: G 1219 GLU cc_start: 0.6366 (pt0) cc_final: 0.5959 (pm20) REVERT: G 1275 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5496 (pp) REVERT: G 1284 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4933 (pp) REVERT: G 1352 ARG cc_start: 0.4147 (ptp-170) cc_final: 0.3792 (ptp-170) REVERT: G 1357 LEU cc_start: 0.7477 (mm) cc_final: 0.7135 (mt) REVERT: G 1363 HIS cc_start: 0.8245 (m90) cc_final: 0.7728 (m90) REVERT: G 1460 LYS cc_start: 0.6094 (tttt) cc_final: 0.5702 (tmtt) REVERT: G 1475 THR cc_start: 0.6650 (m) cc_final: 0.6242 (p) REVERT: G 1479 GLU cc_start: 0.5196 (tt0) cc_final: 0.4672 (tt0) REVERT: G 1524 MET cc_start: 0.7344 (mmm) cc_final: 0.6909 (mmt) REVERT: G 1541 THR cc_start: 0.7382 (m) cc_final: 0.6467 (m) REVERT: F 175 LEU cc_start: 0.7390 (mm) cc_final: 0.7136 (mm) REVERT: F 178 LEU cc_start: 0.7271 (tp) cc_final: 0.6744 (tp) REVERT: F 181 MET cc_start: 0.6803 (mmt) cc_final: 0.6445 (mmt) REVERT: F 298 ARG cc_start: 0.6504 (mtt-85) cc_final: 0.6144 (mtp85) REVERT: F 496 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6211 (mp) REVERT: F 501 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5815 (pt0) REVERT: F 518 PHE cc_start: 0.5642 (m-80) cc_final: 0.5396 (m-80) REVERT: F 788 ILE cc_start: 0.7104 (mt) cc_final: 0.6830 (mt) REVERT: F 1020 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6898 (mm) REVERT: F 1024 MET cc_start: 0.5614 (ttt) cc_final: 0.5129 (mmp) REVERT: F 1082 SER cc_start: 0.7094 (m) cc_final: 0.6687 (t) REVERT: F 1111 PHE cc_start: 0.6921 (t80) cc_final: 0.6676 (t80) REVERT: F 1125 SER cc_start: 0.7223 (t) cc_final: 0.6893 (m) REVERT: F 1132 ASP cc_start: 0.7702 (p0) cc_final: 0.7434 (p0) REVERT: F 1244 ASN cc_start: 0.7846 (m110) cc_final: 0.7430 (m-40) REVERT: F 1275 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.6003 (pp) REVERT: F 1284 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.5045 (pp) REVERT: F 1313 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.6094 (ttm110) REVERT: F 1399 GLU cc_start: 0.6436 (mm-30) cc_final: 0.6225 (mm-30) outliers start: 289 outliers final: 175 residues processed: 1406 average time/residue: 0.5960 time to fit residues: 1436.5535 Evaluate side-chains 1320 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1118 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 87 CYS Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 314 PHE Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 450 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1083 VAL Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1241 THR Chi-restraints excluded: chain E residue 1257 CYS Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1284 LEU Chi-restraints excluded: chain E residue 1289 MET Chi-restraints excluded: chain E residue 1364 VAL Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1415 HIS Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 305 PHE Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 429 MET Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 501 GLU Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 582 LEU Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 715 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 876 LEU Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 895 HIS Chi-restraints excluded: chain H residue 1020 LEU Chi-restraints excluded: chain H residue 1038 ASP Chi-restraints excluded: chain H residue 1080 VAL Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1270 SER Chi-restraints excluded: chain H residue 1271 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1374 ILE Chi-restraints excluded: chain H residue 1395 VAL Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1470 LEU Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain H residue 1503 ILE Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 488 THR Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 607 VAL Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 682 MET Chi-restraints excluded: chain G residue 715 VAL Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1026 LEU Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1230 THR Chi-restraints excluded: chain G residue 1257 CYS Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1318 LEU Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1395 VAL Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1419 SER Chi-restraints excluded: chain G residue 1447 ASP Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1525 THR Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain G residue 1547 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 169 PHE Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 607 VAL Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 802 ILE Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1069 VAL Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1162 VAL Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1298 VAL Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1313 ARG Chi-restraints excluded: chain F residue 1318 LEU Chi-restraints excluded: chain F residue 1374 ILE Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1503 ILE Chi-restraints excluded: chain F residue 1551 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 463 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 531 optimal weight: 4.9990 chunk 430 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 558 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 437 ASN ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS E1295 ASN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 833 GLN H1019 GLN H1233 ASN H1295 ASN H1401 HIS G 103 HIS ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1019 GLN G1233 ASN ** G1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1122 ASN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 50056 Z= 0.272 Angle : 0.676 11.055 68280 Z= 0.336 Chirality : 0.044 0.291 8356 Planarity : 0.005 0.064 8388 Dihedral : 8.194 110.067 7158 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.92 % Allowed : 17.69 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.10), residues: 6384 helix: 0.95 (0.08), residues: 3888 sheet: -0.96 (0.21), residues: 552 loop : -2.01 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F1032 HIS 0.010 0.001 HIS G1272 PHE 0.029 0.002 PHE G 577 TYR 0.024 0.002 TYR G 123 ARG 0.017 0.001 ARG H 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1180 time to evaluate : 6.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7084 (m-40) cc_final: 0.6829 (m110) REVERT: A 57 GLN cc_start: 0.6488 (pt0) cc_final: 0.5792 (tp40) REVERT: A 195 ARG cc_start: 0.7016 (mmm-85) cc_final: 0.5795 (mmm160) REVERT: A 204 ASP cc_start: 0.6491 (t0) cc_final: 0.6160 (t0) REVERT: A 209 MET cc_start: 0.7759 (tpp) cc_final: 0.7228 (tpp) REVERT: A 217 MET cc_start: 0.8364 (mtm) cc_final: 0.8037 (mtp) REVERT: A 224 THR cc_start: 0.7547 (m) cc_final: 0.7276 (t) REVERT: A 248 SER cc_start: 0.8622 (m) cc_final: 0.8173 (p) REVERT: A 280 ASP cc_start: 0.8082 (t70) cc_final: 0.7493 (t0) REVERT: C 38 LYS cc_start: 0.6823 (mmmt) cc_final: 0.6513 (mmmt) REVERT: C 57 GLN cc_start: 0.7146 (pt0) cc_final: 0.6361 (tp40) REVERT: C 170 LYS cc_start: 0.5713 (ttmm) cc_final: 0.5430 (ttmm) REVERT: C 195 ARG cc_start: 0.6926 (mmm-85) cc_final: 0.5703 (mmm160) REVERT: C 217 MET cc_start: 0.8218 (mtm) cc_final: 0.7628 (mtp) REVERT: C 248 SER cc_start: 0.8308 (m) cc_final: 0.7807 (p) REVERT: C 275 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6726 (pp) REVERT: C 280 ASP cc_start: 0.8210 (t70) cc_final: 0.7720 (t0) REVERT: B 48 ASN cc_start: 0.6765 (m-40) cc_final: 0.6482 (m110) REVERT: B 57 GLN cc_start: 0.6564 (pt0) cc_final: 0.5893 (tp40) REVERT: B 195 ARG cc_start: 0.6704 (mmm-85) cc_final: 0.5557 (mmm160) REVERT: B 223 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7964 (m) REVERT: B 248 SER cc_start: 0.8604 (m) cc_final: 0.8155 (p) REVERT: B 255 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6246 (pp) REVERT: B 275 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7285 (pp) REVERT: B 325 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.5727 (ttp-110) REVERT: D 57 GLN cc_start: 0.6509 (pt0) cc_final: 0.5847 (tp40) REVERT: D 99 ASP cc_start: 0.7639 (t70) cc_final: 0.7184 (m-30) REVERT: D 195 ARG cc_start: 0.6740 (mmm-85) cc_final: 0.5335 (mmm160) REVERT: D 209 MET cc_start: 0.7637 (tpp) cc_final: 0.7338 (tpp) REVERT: D 217 MET cc_start: 0.8322 (mtm) cc_final: 0.7979 (mtp) REVERT: D 224 THR cc_start: 0.7183 (m) cc_final: 0.6957 (t) REVERT: D 229 GLU cc_start: 0.6882 (pt0) cc_final: 0.6552 (tt0) REVERT: D 248 SER cc_start: 0.8396 (m) cc_final: 0.7962 (p) REVERT: D 275 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6743 (pp) REVERT: D 280 ASP cc_start: 0.8176 (t70) cc_final: 0.7697 (t0) REVERT: D 321 GLU cc_start: 0.6282 (tm-30) cc_final: 0.5979 (tm-30) REVERT: E 42 ILE cc_start: 0.7467 (tt) cc_final: 0.7218 (tp) REVERT: E 74 ARG cc_start: 0.5769 (OUTLIER) cc_final: 0.5452 (ttp-170) REVERT: E 308 LEU cc_start: 0.3353 (OUTLIER) cc_final: 0.2917 (tt) REVERT: E 312 LEU cc_start: 0.6443 (tp) cc_final: 0.5920 (mp) REVERT: E 323 ILE cc_start: 0.5621 (OUTLIER) cc_final: 0.5390 (mt) REVERT: E 361 LEU cc_start: 0.6721 (tp) cc_final: 0.6478 (mt) REVERT: E 378 TYR cc_start: 0.6076 (t80) cc_final: 0.5508 (t80) REVERT: E 381 ILE cc_start: 0.5619 (tt) cc_final: 0.5332 (tt) REVERT: E 411 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: E 441 MET cc_start: 0.5553 (ttm) cc_final: 0.5304 (ttp) REVERT: E 461 LEU cc_start: 0.3521 (OUTLIER) cc_final: 0.3283 (pp) REVERT: E 606 SER cc_start: 0.4920 (OUTLIER) cc_final: 0.4704 (m) REVERT: E 682 MET cc_start: 0.7155 (mtt) cc_final: 0.6132 (mmt) REVERT: E 732 LYS cc_start: 0.7481 (pttm) cc_final: 0.7073 (pttp) REVERT: E 827 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6096 (pt) REVERT: E 845 GLN cc_start: 0.7380 (tp40) cc_final: 0.7024 (tm-30) REVERT: E 865 ASP cc_start: 0.7100 (m-30) cc_final: 0.6448 (m-30) REVERT: E 1020 LEU cc_start: 0.7112 (mm) cc_final: 0.6897 (mm) REVERT: E 1024 MET cc_start: 0.6656 (ttt) cc_final: 0.6281 (tpt) REVERT: E 1065 MET cc_start: 0.6297 (tpt) cc_final: 0.5277 (ttt) REVERT: E 1098 ARG cc_start: 0.6222 (tpp80) cc_final: 0.5861 (ttm-80) REVERT: E 1145 SER cc_start: 0.7162 (m) cc_final: 0.6704 (p) REVERT: E 1167 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6338 (tp) REVERT: E 1244 ASN cc_start: 0.7382 (m-40) cc_final: 0.7133 (m-40) REVERT: E 1273 ARG cc_start: 0.5370 (OUTLIER) cc_final: 0.5058 (ttt90) REVERT: E 1275 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5727 (pp) REVERT: E 1284 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.5132 (pp) REVERT: E 1293 TYR cc_start: 0.6084 (m-80) cc_final: 0.5574 (m-80) REVERT: E 1352 ARG cc_start: 0.5099 (ptt180) cc_final: 0.4320 (ptt-90) REVERT: E 1359 PRO cc_start: 0.8188 (Cg_endo) cc_final: 0.7958 (Cg_exo) REVERT: E 1362 LYS cc_start: 0.6606 (ptpt) cc_final: 0.6111 (pttm) REVERT: E 1543 LEU cc_start: 0.5830 (mt) cc_final: 0.5515 (pp) REVERT: E 1569 LYS cc_start: 0.8662 (tmtp) cc_final: 0.8193 (ttpp) REVERT: H 108 MET cc_start: 0.6938 (tpp) cc_final: 0.6724 (tmm) REVERT: H 114 PHE cc_start: 0.8261 (t80) cc_final: 0.7891 (t80) REVERT: H 152 ILE cc_start: 0.6903 (mm) cc_final: 0.6702 (mt) REVERT: H 178 LEU cc_start: 0.7095 (tp) cc_final: 0.6791 (tp) REVERT: H 298 ARG cc_start: 0.6678 (mtp-110) cc_final: 0.6069 (ttp80) REVERT: H 314 PHE cc_start: 0.5817 (t80) cc_final: 0.5307 (t80) REVERT: H 361 LEU cc_start: 0.6675 (tp) cc_final: 0.6412 (mt) REVERT: H 369 GLN cc_start: 0.5363 (OUTLIER) cc_final: 0.4572 (tp-100) REVERT: H 441 MET cc_start: 0.4993 (ttt) cc_final: 0.4670 (tmm) REVERT: H 534 ARG cc_start: 0.5035 (ttp-170) cc_final: 0.4778 (tmm160) REVERT: H 546 MET cc_start: 0.5618 (tmm) cc_final: 0.5305 (mtp) REVERT: H 1020 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6896 (mm) REVERT: H 1035 LYS cc_start: 0.6789 (mtpm) cc_final: 0.6511 (tptp) REVERT: H 1125 SER cc_start: 0.7356 (t) cc_final: 0.7063 (m) REVERT: H 1226 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.4971 (tp) REVERT: H 1244 ASN cc_start: 0.7814 (m110) cc_final: 0.7336 (m-40) REVERT: H 1252 GLU cc_start: 0.6409 (tp30) cc_final: 0.5927 (tp30) REVERT: H 1363 HIS cc_start: 0.8136 (m90) cc_final: 0.7566 (m90) REVERT: H 1464 LYS cc_start: 0.6314 (tppt) cc_final: 0.5458 (mtmt) REVERT: H 1470 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7220 (pp) REVERT: H 1485 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5058 (mp10) REVERT: G 175 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7126 (mm) REVERT: G 295 PHE cc_start: 0.5937 (t80) cc_final: 0.5719 (t80) REVERT: G 298 ARG cc_start: 0.6112 (mtt-85) cc_final: 0.5728 (tpt-90) REVERT: G 308 LEU cc_start: 0.4177 (OUTLIER) cc_final: 0.3763 (tt) REVERT: G 312 LEU cc_start: 0.6224 (tp) cc_final: 0.5818 (mp) REVERT: G 314 PHE cc_start: 0.5616 (t80) cc_final: 0.5393 (t80) REVERT: G 361 LEU cc_start: 0.6626 (tp) cc_final: 0.6290 (mt) REVERT: G 381 ILE cc_start: 0.5734 (tt) cc_final: 0.5510 (tt) REVERT: G 394 LYS cc_start: 0.6497 (tppp) cc_final: 0.6184 (tttp) REVERT: G 519 ARG cc_start: 0.6089 (tmm-80) cc_final: 0.5881 (tmm-80) REVERT: G 612 GLU cc_start: 0.6972 (tt0) cc_final: 0.6097 (mt-10) REVERT: G 803 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6750 (pp20) REVERT: G 827 ILE cc_start: 0.6232 (tt) cc_final: 0.5856 (pt) REVERT: G 845 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7611 (tm-30) REVERT: G 869 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6627 (tt0) REVERT: G 1020 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7078 (mm) REVERT: G 1024 MET cc_start: 0.6627 (ttt) cc_final: 0.6264 (tpt) REVERT: G 1038 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5687 (p0) REVERT: G 1082 SER cc_start: 0.7544 (m) cc_final: 0.7009 (t) REVERT: G 1125 SER cc_start: 0.6996 (t) cc_final: 0.6716 (m) REVERT: G 1145 SER cc_start: 0.7120 (m) cc_final: 0.6769 (p) REVERT: G 1275 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5660 (pp) REVERT: G 1284 LEU cc_start: 0.5334 (OUTLIER) cc_final: 0.5128 (pp) REVERT: G 1357 LEU cc_start: 0.7575 (mm) cc_final: 0.7346 (mt) REVERT: G 1363 HIS cc_start: 0.8480 (m90) cc_final: 0.8036 (m90) REVERT: G 1524 MET cc_start: 0.7309 (mmm) cc_final: 0.6684 (mmm) REVERT: G 1538 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5873 (ptt90) REVERT: G 1540 HIS cc_start: 0.7375 (t-90) cc_final: 0.7057 (t-90) REVERT: G 1541 THR cc_start: 0.6734 (m) cc_final: 0.6515 (m) REVERT: G 1551 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.5376 (mt) REVERT: F 175 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7043 (mm) REVERT: F 178 LEU cc_start: 0.7482 (tp) cc_final: 0.6868 (tp) REVERT: F 181 MET cc_start: 0.6789 (mmt) cc_final: 0.6395 (mmt) REVERT: F 298 ARG cc_start: 0.6503 (mtt-85) cc_final: 0.6126 (mtp85) REVERT: F 370 ARG cc_start: 0.5486 (mmm160) cc_final: 0.4934 (mmm160) REVERT: F 885 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6170 (pt) REVERT: F 1020 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6892 (mm) REVERT: F 1065 MET cc_start: 0.6465 (tpt) cc_final: 0.5209 (ttt) REVERT: F 1082 SER cc_start: 0.7413 (m) cc_final: 0.6931 (t) REVERT: F 1125 SER cc_start: 0.7237 (t) cc_final: 0.6880 (p) REVERT: F 1132 ASP cc_start: 0.7499 (p0) cc_final: 0.7267 (p0) REVERT: F 1244 ASN cc_start: 0.7692 (m110) cc_final: 0.7426 (m110) REVERT: F 1275 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6031 (pp) REVERT: F 1284 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.5069 (pp) REVERT: F 1313 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.6054 (ttm110) outliers start: 296 outliers final: 182 residues processed: 1351 average time/residue: 0.5500 time to fit residues: 1265.1387 Evaluate side-chains 1318 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1101 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 775 LYS Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1087 TRP Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1241 THR Chi-restraints excluded: chain E residue 1273 ARG Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1284 LEU Chi-restraints excluded: chain E residue 1364 VAL Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1415 HIS Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1447 ASP Chi-restraints excluded: chain E residue 1466 LEU Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 369 GLN Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 682 MET Chi-restraints excluded: chain H residue 715 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 782 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 864 SER Chi-restraints excluded: chain H residue 886 VAL Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 895 HIS Chi-restraints excluded: chain H residue 1020 LEU Chi-restraints excluded: chain H residue 1080 VAL Chi-restraints excluded: chain H residue 1082 SER Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1165 VAL Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1226 LEU Chi-restraints excluded: chain H residue 1271 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1314 ILE Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1346 ILE Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1470 LEU Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain H residue 1488 LEU Chi-restraints excluded: chain H residue 1503 ILE Chi-restraints excluded: chain H residue 1521 LYS Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 579 SER Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 724 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 886 VAL Chi-restraints excluded: chain G residue 895 HIS Chi-restraints excluded: chain G residue 902 MET Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1038 ASP Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1178 GLN Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1230 THR Chi-restraints excluded: chain G residue 1257 CYS Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1294 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1318 LEU Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1409 ILE Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain G residue 1538 ARG Chi-restraints excluded: chain G residue 1542 ILE Chi-restraints excluded: chain G residue 1547 LEU Chi-restraints excluded: chain G residue 1551 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 802 ILE Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1020 LEU Chi-restraints excluded: chain F residue 1037 THR Chi-restraints excluded: chain F residue 1069 VAL Chi-restraints excluded: chain F residue 1083 VAL Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1313 ARG Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1501 ILE Chi-restraints excluded: chain F residue 1503 ILE Chi-restraints excluded: chain F residue 1551 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 209 optimal weight: 4.9990 chunk 560 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 365 optimal weight: 0.0050 chunk 153 optimal weight: 4.9990 chunk 623 optimal weight: 0.6980 chunk 517 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 327 optimal weight: 7.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN E 891 GLN E1019 GLN ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS H 103 HIS H 289 GLN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 GLN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 821 GLN ** H1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 427 GLN ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1019 GLN G1244 ASN G1272 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 289 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1122 ASN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1233 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 50056 Z= 0.292 Angle : 0.689 13.919 68280 Z= 0.343 Chirality : 0.044 0.277 8356 Planarity : 0.005 0.064 8388 Dihedral : 8.150 110.172 7158 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 6.22 % Allowed : 18.33 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 6384 helix: 0.95 (0.08), residues: 3908 sheet: -1.00 (0.21), residues: 560 loop : -1.93 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F1032 HIS 0.014 0.001 HIS H 103 PHE 0.028 0.002 PHE G 577 TYR 0.024 0.002 TYR E 123 ARG 0.018 0.001 ARG F 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1165 time to evaluate : 5.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.6934 (m-40) cc_final: 0.6672 (m110) REVERT: A 57 GLN cc_start: 0.6485 (pt0) cc_final: 0.5800 (tp40) REVERT: A 195 ARG cc_start: 0.7037 (mmm-85) cc_final: 0.5798 (mmm160) REVERT: A 204 ASP cc_start: 0.6522 (t0) cc_final: 0.6225 (t0) REVERT: A 209 MET cc_start: 0.7868 (tpp) cc_final: 0.7355 (tpp) REVERT: A 217 MET cc_start: 0.8419 (mtm) cc_final: 0.8122 (mtp) REVERT: A 224 THR cc_start: 0.7293 (m) cc_final: 0.7043 (t) REVERT: A 248 SER cc_start: 0.8634 (m) cc_final: 0.8147 (p) REVERT: A 255 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6095 (pp) REVERT: A 275 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6835 (pp) REVERT: A 280 ASP cc_start: 0.8177 (t70) cc_final: 0.7606 (t0) REVERT: C 57 GLN cc_start: 0.7100 (pt0) cc_final: 0.6346 (tp40) REVERT: C 170 LYS cc_start: 0.5708 (ttmm) cc_final: 0.5446 (ttmm) REVERT: C 195 ARG cc_start: 0.6991 (mmm-85) cc_final: 0.5754 (mmm160) REVERT: C 209 MET cc_start: 0.6488 (ttm) cc_final: 0.6281 (ttm) REVERT: C 217 MET cc_start: 0.8180 (mtm) cc_final: 0.7733 (mtp) REVERT: C 248 SER cc_start: 0.8328 (m) cc_final: 0.7792 (p) REVERT: C 275 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6779 (pp) REVERT: C 280 ASP cc_start: 0.8157 (t70) cc_final: 0.7641 (t0) REVERT: B 48 ASN cc_start: 0.6796 (m-40) cc_final: 0.6501 (m110) REVERT: B 57 GLN cc_start: 0.6565 (pt0) cc_final: 0.5893 (tp40) REVERT: B 195 ARG cc_start: 0.6729 (mmm-85) cc_final: 0.5599 (mmm160) REVERT: B 248 SER cc_start: 0.8604 (m) cc_final: 0.8137 (p) REVERT: B 255 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6296 (pp) REVERT: B 275 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7202 (pp) REVERT: B 325 ARG cc_start: 0.6653 (mtm-85) cc_final: 0.5925 (ttp-110) REVERT: D 57 GLN cc_start: 0.6758 (pt0) cc_final: 0.5860 (tp40) REVERT: D 80 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6189 (mm) REVERT: D 99 ASP cc_start: 0.7552 (t70) cc_final: 0.7155 (m-30) REVERT: D 108 GLU cc_start: 0.7524 (mp0) cc_final: 0.7301 (mp0) REVERT: D 195 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.5440 (mmm160) REVERT: D 209 MET cc_start: 0.7646 (tpp) cc_final: 0.7372 (tpp) REVERT: D 211 ILE cc_start: 0.7321 (mm) cc_final: 0.7062 (mm) REVERT: D 217 MET cc_start: 0.8328 (mtm) cc_final: 0.7932 (mtp) REVERT: D 229 GLU cc_start: 0.6992 (pt0) cc_final: 0.6658 (tt0) REVERT: D 248 SER cc_start: 0.8437 (m) cc_final: 0.7960 (p) REVERT: D 275 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6722 (pp) REVERT: D 280 ASP cc_start: 0.8167 (t70) cc_final: 0.7666 (t0) REVERT: D 305 LEU cc_start: 0.7145 (pt) cc_final: 0.6923 (mp) REVERT: D 321 GLU cc_start: 0.6284 (tm-30) cc_final: 0.5993 (tm-30) REVERT: E 42 ILE cc_start: 0.7484 (tt) cc_final: 0.7254 (tp) REVERT: E 108 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7203 (ttp) REVERT: E 361 LEU cc_start: 0.6718 (tp) cc_final: 0.6415 (mt) REVERT: E 378 TYR cc_start: 0.6147 (t80) cc_final: 0.5642 (t80) REVERT: E 411 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: E 461 LEU cc_start: 0.4061 (OUTLIER) cc_final: 0.3847 (pp) REVERT: E 485 GLN cc_start: 0.7555 (tp40) cc_final: 0.6931 (tm-30) REVERT: E 606 SER cc_start: 0.5361 (OUTLIER) cc_final: 0.5114 (m) REVERT: E 682 MET cc_start: 0.7204 (mtt) cc_final: 0.6138 (mmt) REVERT: E 703 ILE cc_start: 0.6011 (OUTLIER) cc_final: 0.5753 (mt) REVERT: E 732 LYS cc_start: 0.7462 (pttm) cc_final: 0.7062 (pttp) REVERT: E 800 MET cc_start: 0.5983 (ttp) cc_final: 0.5729 (ptp) REVERT: E 827 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6276 (pt) REVERT: E 845 GLN cc_start: 0.7441 (tp40) cc_final: 0.6855 (tm-30) REVERT: E 865 ASP cc_start: 0.6986 (m-30) cc_final: 0.6358 (m-30) REVERT: E 1024 MET cc_start: 0.6687 (ttt) cc_final: 0.6279 (tpt) REVERT: E 1065 MET cc_start: 0.6216 (tpt) cc_final: 0.5192 (ttt) REVERT: E 1098 ARG cc_start: 0.6299 (tpp80) cc_final: 0.5948 (ttm-80) REVERT: E 1145 SER cc_start: 0.7186 (m) cc_final: 0.6717 (p) REVERT: E 1208 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7692 (tp30) REVERT: E 1244 ASN cc_start: 0.7392 (m-40) cc_final: 0.7102 (m-40) REVERT: E 1273 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.5128 (ttt90) REVERT: E 1275 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5777 (pp) REVERT: E 1284 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4970 (pp) REVERT: E 1293 TYR cc_start: 0.6109 (m-80) cc_final: 0.5561 (m-80) REVERT: E 1352 ARG cc_start: 0.5186 (ptt180) cc_final: 0.4331 (ptt-90) REVERT: E 1511 ILE cc_start: 0.6610 (mm) cc_final: 0.6352 (mt) REVERT: E 1513 MET cc_start: 0.5990 (mmt) cc_final: 0.5789 (mtt) REVERT: E 1538 ARG cc_start: 0.7411 (mmm160) cc_final: 0.6129 (mtt180) REVERT: E 1569 LYS cc_start: 0.8663 (tmtp) cc_final: 0.8140 (ttpt) REVERT: H 108 MET cc_start: 0.6935 (tpp) cc_final: 0.6716 (tmm) REVERT: H 152 ILE cc_start: 0.6958 (mm) cc_final: 0.6736 (mt) REVERT: H 175 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6863 (mm) REVERT: H 178 LEU cc_start: 0.7155 (tp) cc_final: 0.6816 (tp) REVERT: H 298 ARG cc_start: 0.6598 (mtp-110) cc_final: 0.6209 (ttm110) REVERT: H 314 PHE cc_start: 0.5881 (t80) cc_final: 0.5594 (t80) REVERT: H 361 LEU cc_start: 0.6681 (tp) cc_final: 0.6362 (mt) REVERT: H 378 TYR cc_start: 0.5965 (t80) cc_final: 0.5543 (t80) REVERT: H 441 MET cc_start: 0.5009 (ttt) cc_final: 0.4640 (tmm) REVERT: H 534 ARG cc_start: 0.5112 (ttp-170) cc_final: 0.4761 (tmm160) REVERT: H 885 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5564 (pt) REVERT: H 1020 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6912 (mm) REVERT: H 1125 SER cc_start: 0.7277 (t) cc_final: 0.6965 (m) REVERT: H 1133 GLN cc_start: 0.5520 (mt0) cc_final: 0.5158 (mm-40) REVERT: H 1226 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5172 (tp) REVERT: H 1244 ASN cc_start: 0.7756 (m110) cc_final: 0.7453 (t0) REVERT: H 1273 ARG cc_start: 0.5961 (ttm170) cc_final: 0.5636 (ttm170) REVERT: H 1363 HIS cc_start: 0.8293 (m90) cc_final: 0.7988 (m-70) REVERT: H 1470 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7284 (pp) REVERT: H 1485 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5065 (mp10) REVERT: G 175 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7127 (mm) REVERT: G 298 ARG cc_start: 0.6129 (mtt-85) cc_final: 0.5726 (tpt-90) REVERT: G 357 VAL cc_start: 0.7074 (t) cc_final: 0.6774 (m) REVERT: G 361 LEU cc_start: 0.6618 (tp) cc_final: 0.6333 (mt) REVERT: G 370 ARG cc_start: 0.5235 (mtp180) cc_final: 0.4945 (mtp85) REVERT: G 381 ILE cc_start: 0.5747 (tt) cc_final: 0.5503 (tt) REVERT: G 394 LYS cc_start: 0.6496 (tppp) cc_final: 0.6189 (tttp) REVERT: G 612 GLU cc_start: 0.7072 (tt0) cc_final: 0.6202 (mt-10) REVERT: G 800 MET cc_start: 0.6749 (ttp) cc_final: 0.5742 (ptp) REVERT: G 803 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6676 (pp20) REVERT: G 820 THR cc_start: 0.8325 (t) cc_final: 0.8067 (p) REVERT: G 827 ILE cc_start: 0.6461 (tt) cc_final: 0.5970 (pt) REVERT: G 845 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7661 (tm-30) REVERT: G 865 ASP cc_start: 0.6709 (m-30) cc_final: 0.6268 (m-30) REVERT: G 1011 LEU cc_start: 0.5550 (mt) cc_final: 0.5246 (mt) REVERT: G 1020 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6936 (mm) REVERT: G 1024 MET cc_start: 0.6651 (ttt) cc_final: 0.6258 (tpt) REVERT: G 1038 ASP cc_start: 0.5918 (OUTLIER) cc_final: 0.5565 (p0) REVERT: G 1082 SER cc_start: 0.7731 (m) cc_final: 0.7175 (t) REVERT: G 1125 SER cc_start: 0.7354 (t) cc_final: 0.7059 (m) REVERT: G 1145 SER cc_start: 0.7176 (m) cc_final: 0.6794 (p) REVERT: G 1226 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5634 (tp) REVERT: G 1275 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5620 (pp) REVERT: G 1284 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4931 (pp) REVERT: G 1363 HIS cc_start: 0.8384 (m90) cc_final: 0.7974 (m90) REVERT: G 1402 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6772 (tt) REVERT: G 1524 MET cc_start: 0.7229 (mmm) cc_final: 0.6849 (mmm) REVERT: G 1540 HIS cc_start: 0.7737 (t-90) cc_final: 0.7186 (t-90) REVERT: F 175 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7130 (mm) REVERT: F 178 LEU cc_start: 0.7498 (tp) cc_final: 0.6838 (tp) REVERT: F 181 MET cc_start: 0.6812 (mmt) cc_final: 0.6407 (mmt) REVERT: F 298 ARG cc_start: 0.6379 (mtt-85) cc_final: 0.6000 (tpt-90) REVERT: F 730 MET cc_start: 0.6944 (mtp) cc_final: 0.6615 (mtt) REVERT: F 885 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6272 (pt) REVERT: F 1038 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5664 (p0) REVERT: F 1065 MET cc_start: 0.6574 (tpt) cc_final: 0.5265 (ttt) REVERT: F 1082 SER cc_start: 0.7502 (m) cc_final: 0.7011 (t) REVERT: F 1110 ARG cc_start: 0.7463 (mmm160) cc_final: 0.6852 (mmp-170) REVERT: F 1111 PHE cc_start: 0.7030 (t80) cc_final: 0.6754 (t80) REVERT: F 1124 PHE cc_start: 0.8002 (m-80) cc_final: 0.7628 (m-80) REVERT: F 1125 SER cc_start: 0.7138 (t) cc_final: 0.6870 (p) REVERT: F 1132 ASP cc_start: 0.7408 (p0) cc_final: 0.7197 (p0) REVERT: F 1244 ASN cc_start: 0.7703 (m110) cc_final: 0.7410 (m110) REVERT: F 1275 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5779 (pp) REVERT: F 1284 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4935 (pp) REVERT: F 1313 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.6056 (ttm110) REVERT: F 1357 LEU cc_start: 0.6965 (mm) cc_final: 0.6632 (mt) REVERT: F 1362 LYS cc_start: 0.6407 (ptpt) cc_final: 0.6197 (pttm) REVERT: F 1399 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6176 (mm-30) outliers start: 311 outliers final: 219 residues processed: 1340 average time/residue: 0.5834 time to fit residues: 1329.5034 Evaluate side-chains 1353 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1098 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 703 ILE Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 775 LYS Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 802 ILE Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 874 GLU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 890 LEU Chi-restraints excluded: chain E residue 892 TYR Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1087 TRP Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1183 VAL Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1241 THR Chi-restraints excluded: chain E residue 1273 ARG Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1284 LEU Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1415 HIS Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1447 ASP Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain E residue 1539 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 289 GLN Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 682 MET Chi-restraints excluded: chain H residue 715 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 782 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 885 LEU Chi-restraints excluded: chain H residue 886 VAL Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 1020 LEU Chi-restraints excluded: chain H residue 1025 VAL Chi-restraints excluded: chain H residue 1080 VAL Chi-restraints excluded: chain H residue 1082 SER Chi-restraints excluded: chain H residue 1087 TRP Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1165 VAL Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1226 LEU Chi-restraints excluded: chain H residue 1271 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1294 LEU Chi-restraints excluded: chain H residue 1297 MET Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1314 ILE Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1374 ILE Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1409 ILE Chi-restraints excluded: chain H residue 1470 LEU Chi-restraints excluded: chain H residue 1475 THR Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain H residue 1488 LEU Chi-restraints excluded: chain H residue 1503 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 579 SER Chi-restraints excluded: chain G residue 582 LEU Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 724 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 874 GLU Chi-restraints excluded: chain G residue 886 VAL Chi-restraints excluded: chain G residue 897 ASP Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1038 ASP Chi-restraints excluded: chain G residue 1087 TRP Chi-restraints excluded: chain G residue 1120 ILE Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1178 GLN Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1226 LEU Chi-restraints excluded: chain G residue 1230 THR Chi-restraints excluded: chain G residue 1257 CYS Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1294 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1376 ILE Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1409 ILE Chi-restraints excluded: chain G residue 1419 SER Chi-restraints excluded: chain G residue 1447 ASP Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1488 LEU Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain G residue 1542 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 607 VAL Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 800 MET Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1038 ASP Chi-restraints excluded: chain F residue 1069 VAL Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1165 VAL Chi-restraints excluded: chain F residue 1167 LEU Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1313 ARG Chi-restraints excluded: chain F residue 1374 ILE Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1501 ILE Chi-restraints excluded: chain F residue 1503 ILE Chi-restraints excluded: chain F residue 1551 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 600 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 355 optimal weight: 3.9990 chunk 455 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 524 optimal weight: 2.9990 chunk 347 optimal weight: 2.9990 chunk 620 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 378 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS ** E 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS E1347 GLN H 103 HIS ** H 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 HIS H1019 GLN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 833 GLN G1019 GLN G1272 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 289 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 821 GLN ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 50056 Z= 0.350 Angle : 0.726 12.519 68280 Z= 0.363 Chirality : 0.046 0.254 8356 Planarity : 0.005 0.088 8388 Dihedral : 8.246 111.063 7158 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 6.83 % Allowed : 18.55 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.10), residues: 6384 helix: 0.81 (0.08), residues: 3916 sheet: -1.13 (0.22), residues: 516 loop : -1.99 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 288 HIS 0.012 0.001 HIS H 103 PHE 0.057 0.002 PHE E 433 TYR 0.023 0.002 TYR G 123 ARG 0.019 0.001 ARG F 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1152 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.6901 (m-40) cc_final: 0.6684 (m110) REVERT: A 57 GLN cc_start: 0.6477 (pt0) cc_final: 0.5853 (tp40) REVERT: A 99 ASP cc_start: 0.6677 (m-30) cc_final: 0.5825 (m-30) REVERT: A 195 ARG cc_start: 0.7075 (mmm-85) cc_final: 0.5819 (mmm160) REVERT: A 204 ASP cc_start: 0.6438 (t0) cc_final: 0.6170 (t0) REVERT: A 209 MET cc_start: 0.7874 (tpp) cc_final: 0.7434 (tpp) REVERT: A 217 MET cc_start: 0.8423 (mtm) cc_final: 0.8057 (mtp) REVERT: A 224 THR cc_start: 0.7474 (m) cc_final: 0.7263 (t) REVERT: A 248 SER cc_start: 0.8612 (m) cc_final: 0.8123 (p) REVERT: A 255 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6216 (pp) REVERT: A 275 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6840 (pp) REVERT: A 325 ARG cc_start: 0.5517 (ttm-80) cc_final: 0.5034 (ttm-80) REVERT: C 57 GLN cc_start: 0.6873 (pt0) cc_final: 0.6254 (tp40) REVERT: C 80 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6115 (mm) REVERT: C 170 LYS cc_start: 0.5537 (ttmm) cc_final: 0.5328 (ttmm) REVERT: C 195 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.5695 (mmm160) REVERT: C 209 MET cc_start: 0.6505 (ttm) cc_final: 0.6281 (ttm) REVERT: C 217 MET cc_start: 0.8325 (mtm) cc_final: 0.7937 (mtp) REVERT: C 248 SER cc_start: 0.8461 (m) cc_final: 0.7975 (p) REVERT: C 275 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6878 (pp) REVERT: C 280 ASP cc_start: 0.8164 (t70) cc_final: 0.7605 (t0) REVERT: C 308 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7524 (mt-10) REVERT: C 321 GLU cc_start: 0.5639 (tm-30) cc_final: 0.5083 (tm-30) REVERT: B 48 ASN cc_start: 0.6803 (m-40) cc_final: 0.6514 (m110) REVERT: B 57 GLN cc_start: 0.6482 (pt0) cc_final: 0.5889 (tp40) REVERT: B 80 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6274 (mm) REVERT: B 195 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.5709 (mmm160) REVERT: B 248 SER cc_start: 0.8621 (m) cc_final: 0.8149 (p) REVERT: B 255 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6302 (pp) REVERT: B 275 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7133 (pp) REVERT: B 325 ARG cc_start: 0.6768 (mtm-85) cc_final: 0.5967 (ttp-110) REVERT: D 57 GLN cc_start: 0.6751 (pt0) cc_final: 0.5850 (tp40) REVERT: D 80 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.6216 (mm) REVERT: D 99 ASP cc_start: 0.7751 (t70) cc_final: 0.7334 (m-30) REVERT: D 195 ARG cc_start: 0.6867 (mmm-85) cc_final: 0.5451 (mmm160) REVERT: D 209 MET cc_start: 0.7738 (tpp) cc_final: 0.7530 (tpp) REVERT: D 217 MET cc_start: 0.8436 (mtm) cc_final: 0.7991 (mtp) REVERT: D 248 SER cc_start: 0.8418 (m) cc_final: 0.7896 (p) REVERT: D 275 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6769 (pp) REVERT: D 280 ASP cc_start: 0.8154 (t70) cc_final: 0.7645 (t0) REVERT: D 321 GLU cc_start: 0.6247 (tm-30) cc_final: 0.5969 (tm-30) REVERT: E 42 ILE cc_start: 0.7502 (tt) cc_final: 0.7251 (tp) REVERT: E 108 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7219 (ttp) REVERT: E 312 LEU cc_start: 0.6394 (tp) cc_final: 0.5963 (mp) REVERT: E 361 LEU cc_start: 0.6628 (tp) cc_final: 0.6379 (mt) REVERT: E 378 TYR cc_start: 0.6034 (t80) cc_final: 0.5499 (t80) REVERT: E 411 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: E 429 MET cc_start: 0.4840 (ttp) cc_final: 0.4588 (ttp) REVERT: E 431 PHE cc_start: 0.6709 (t80) cc_final: 0.6495 (t80) REVERT: E 432 PHE cc_start: 0.6914 (m-80) cc_final: 0.6324 (m-10) REVERT: E 485 GLN cc_start: 0.7645 (tp40) cc_final: 0.7018 (tm-30) REVERT: E 682 MET cc_start: 0.7176 (mtt) cc_final: 0.6136 (mmt) REVERT: E 732 LYS cc_start: 0.7341 (pttm) cc_final: 0.7015 (pttt) REVERT: E 827 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6327 (pt) REVERT: E 861 ILE cc_start: 0.5919 (mm) cc_final: 0.5111 (mp) REVERT: E 865 ASP cc_start: 0.6750 (m-30) cc_final: 0.5996 (m-30) REVERT: E 868 MET cc_start: 0.6401 (tpp) cc_final: 0.6096 (ttt) REVERT: E 1024 MET cc_start: 0.6671 (ttt) cc_final: 0.6201 (tpt) REVERT: E 1065 MET cc_start: 0.6213 (tpt) cc_final: 0.5169 (ttt) REVERT: E 1098 ARG cc_start: 0.6342 (tpp80) cc_final: 0.5982 (ttm-80) REVERT: E 1110 ARG cc_start: 0.7259 (mmm160) cc_final: 0.6940 (mmp-170) REVERT: E 1145 SER cc_start: 0.7251 (m) cc_final: 0.6812 (p) REVERT: E 1208 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: E 1244 ASN cc_start: 0.7455 (m-40) cc_final: 0.7225 (m-40) REVERT: E 1273 ARG cc_start: 0.5865 (OUTLIER) cc_final: 0.5484 (ttt90) REVERT: E 1275 LEU cc_start: 0.6213 (OUTLIER) cc_final: 0.5729 (pp) REVERT: E 1284 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4837 (pp) REVERT: E 1352 ARG cc_start: 0.5099 (ptt180) cc_final: 0.4372 (ptt-90) REVERT: E 1427 ASP cc_start: 0.8061 (m-30) cc_final: 0.7767 (m-30) REVERT: E 1569 LYS cc_start: 0.8730 (tmtp) cc_final: 0.8271 (ttpt) REVERT: H 108 MET cc_start: 0.7070 (tpp) cc_final: 0.6848 (tmm) REVERT: H 114 PHE cc_start: 0.8132 (t80) cc_final: 0.7841 (t80) REVERT: H 152 ILE cc_start: 0.7288 (mm) cc_final: 0.7081 (mt) REVERT: H 175 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7057 (mm) REVERT: H 178 LEU cc_start: 0.7124 (tp) cc_final: 0.6738 (tp) REVERT: H 298 ARG cc_start: 0.6603 (mtp-110) cc_final: 0.6002 (ttp-110) REVERT: H 361 LEU cc_start: 0.6555 (tp) cc_final: 0.6161 (mt) REVERT: H 378 TYR cc_start: 0.6033 (t80) cc_final: 0.5650 (t80) REVERT: H 441 MET cc_start: 0.5043 (ttt) cc_final: 0.4667 (tmm) REVERT: H 827 ILE cc_start: 0.6823 (tt) cc_final: 0.6263 (pt) REVERT: H 885 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6035 (pt) REVERT: H 1020 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6836 (mm) REVERT: H 1125 SER cc_start: 0.7323 (t) cc_final: 0.6974 (m) REVERT: H 1226 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5140 (tp) REVERT: H 1244 ASN cc_start: 0.7752 (m110) cc_final: 0.7492 (t0) REVERT: H 1273 ARG cc_start: 0.5935 (ttm170) cc_final: 0.5594 (ttm170) REVERT: H 1362 LYS cc_start: 0.6382 (ptpt) cc_final: 0.6181 (pttm) REVERT: H 1363 HIS cc_start: 0.8359 (m90) cc_final: 0.8141 (m-70) REVERT: H 1402 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6654 (mt) REVERT: H 1470 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7512 (pp) REVERT: H 1485 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5338 (mp10) REVERT: H 1569 LYS cc_start: 0.8468 (tppt) cc_final: 0.8268 (ttpt) REVERT: G 298 ARG cc_start: 0.6117 (mtt-85) cc_final: 0.5717 (tpt-90) REVERT: G 369 GLN cc_start: 0.5151 (OUTLIER) cc_final: 0.4249 (tp-100) REVERT: G 370 ARG cc_start: 0.5267 (mtp180) cc_final: 0.4941 (mtp180) REVERT: G 394 LYS cc_start: 0.5936 (tppp) cc_final: 0.5646 (tttp) REVERT: G 400 MET cc_start: 0.7704 (mmm) cc_final: 0.7125 (mmm) REVERT: G 612 GLU cc_start: 0.7102 (tt0) cc_final: 0.6229 (mt-10) REVERT: G 803 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6787 (pp20) REVERT: G 827 ILE cc_start: 0.6636 (tt) cc_final: 0.6189 (pt) REVERT: G 845 GLN cc_start: 0.7812 (tp-100) cc_final: 0.7604 (tm-30) REVERT: G 865 ASP cc_start: 0.6736 (m-30) cc_final: 0.6289 (m-30) REVERT: G 1012 LEU cc_start: 0.6676 (mm) cc_final: 0.6382 (mm) REVERT: G 1020 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6896 (mm) REVERT: G 1024 MET cc_start: 0.6692 (ttt) cc_final: 0.6206 (tpt) REVERT: G 1038 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.5524 (p0) REVERT: G 1082 SER cc_start: 0.8102 (m) cc_final: 0.7477 (t) REVERT: G 1125 SER cc_start: 0.7541 (t) cc_final: 0.7187 (m) REVERT: G 1145 SER cc_start: 0.7270 (m) cc_final: 0.6845 (p) REVERT: G 1226 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5667 (tp) REVERT: G 1244 ASN cc_start: 0.7404 (m-40) cc_final: 0.7002 (m-40) REVERT: G 1252 GLU cc_start: 0.6452 (tp30) cc_final: 0.5414 (tp30) REVERT: G 1275 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5642 (pp) REVERT: G 1284 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4944 (pp) REVERT: G 1362 LYS cc_start: 0.6332 (ptpt) cc_final: 0.6056 (ptpp) REVERT: G 1402 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6906 (tt) REVERT: G 1479 GLU cc_start: 0.5480 (tt0) cc_final: 0.5200 (tt0) REVERT: G 1524 MET cc_start: 0.7107 (mmm) cc_final: 0.6617 (mmm) REVERT: G 1540 HIS cc_start: 0.7722 (t-90) cc_final: 0.7421 (t-90) REVERT: F 112 MET cc_start: 0.7949 (mmp) cc_final: 0.7632 (mmm) REVERT: F 175 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7108 (mm) REVERT: F 181 MET cc_start: 0.6836 (mmt) cc_final: 0.6448 (mmt) REVERT: F 298 ARG cc_start: 0.6331 (mtt-85) cc_final: 0.5933 (tpt-90) REVERT: F 369 GLN cc_start: 0.5192 (OUTLIER) cc_final: 0.4626 (tp-100) REVERT: F 502 MET cc_start: 0.5019 (ttm) cc_final: 0.4815 (ttm) REVERT: F 585 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6469 (tt) REVERT: F 730 MET cc_start: 0.6767 (mtp) cc_final: 0.6532 (mtt) REVERT: F 827 ILE cc_start: 0.6706 (tt) cc_final: 0.6263 (pt) REVERT: F 845 GLN cc_start: 0.7142 (tm-30) cc_final: 0.6768 (tm-30) REVERT: F 846 HIS cc_start: 0.6913 (t-90) cc_final: 0.5938 (m170) REVERT: F 885 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6073 (pt) REVERT: F 1065 MET cc_start: 0.6535 (tpt) cc_final: 0.5251 (ttt) REVERT: F 1110 ARG cc_start: 0.7403 (mmm160) cc_final: 0.6735 (mmp-170) REVERT: F 1124 PHE cc_start: 0.7945 (m-80) cc_final: 0.7640 (m-80) REVERT: F 1125 SER cc_start: 0.7102 (t) cc_final: 0.6835 (p) REVERT: F 1244 ASN cc_start: 0.7657 (m110) cc_final: 0.7322 (m110) REVERT: F 1275 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5790 (pp) REVERT: F 1284 LEU cc_start: 0.4978 (OUTLIER) cc_final: 0.4757 (pp) REVERT: F 1313 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.6052 (ttm110) REVERT: F 1399 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6436 (mm-30) REVERT: F 1440 ASP cc_start: 0.5115 (m-30) cc_final: 0.4869 (p0) REVERT: F 1569 LYS cc_start: 0.8106 (tmtp) cc_final: 0.7789 (tppt) outliers start: 342 outliers final: 237 residues processed: 1359 average time/residue: 0.5705 time to fit residues: 1322.7538 Evaluate side-chains 1373 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1099 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TRP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 562 HIS Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 775 LYS Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 813 ILE Chi-restraints excluded: chain E residue 827 ILE Chi-restraints excluded: chain E residue 874 GLU Chi-restraints excluded: chain E residue 885 LEU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1037 THR Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1087 TRP Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1183 VAL Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1273 ARG Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1284 LEU Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1347 GLN Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1415 HIS Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1447 ASP Chi-restraints excluded: chain E residue 1462 VAL Chi-restraints excluded: chain E residue 1466 LEU Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 488 THR Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 682 MET Chi-restraints excluded: chain H residue 715 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 782 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 857 SER Chi-restraints excluded: chain H residue 864 SER Chi-restraints excluded: chain H residue 883 VAL Chi-restraints excluded: chain H residue 885 LEU Chi-restraints excluded: chain H residue 886 VAL Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 1020 LEU Chi-restraints excluded: chain H residue 1025 VAL Chi-restraints excluded: chain H residue 1080 VAL Chi-restraints excluded: chain H residue 1082 SER Chi-restraints excluded: chain H residue 1087 TRP Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1165 VAL Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1226 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1294 LEU Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1314 ILE Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1374 ILE Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1409 ILE Chi-restraints excluded: chain H residue 1470 LEU Chi-restraints excluded: chain H residue 1475 THR Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain H residue 1488 LEU Chi-restraints excluded: chain H residue 1503 ILE Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 579 SER Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 682 MET Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 886 VAL Chi-restraints excluded: chain G residue 897 ASP Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1038 ASP Chi-restraints excluded: chain G residue 1065 MET Chi-restraints excluded: chain G residue 1087 TRP Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1199 LEU Chi-restraints excluded: chain G residue 1226 LEU Chi-restraints excluded: chain G residue 1230 THR Chi-restraints excluded: chain G residue 1257 CYS Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1294 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1376 ILE Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1409 ILE Chi-restraints excluded: chain G residue 1419 SER Chi-restraints excluded: chain G residue 1447 ASP Chi-restraints excluded: chain G residue 1488 LEU Chi-restraints excluded: chain G residue 1501 ILE Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1525 THR Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 501 GLU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 607 VAL Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1069 VAL Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1162 VAL Chi-restraints excluded: chain F residue 1165 VAL Chi-restraints excluded: chain F residue 1167 LEU Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1313 ARG Chi-restraints excluded: chain F residue 1374 ILE Chi-restraints excluded: chain F residue 1409 ILE Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1501 ILE Chi-restraints excluded: chain F residue 1503 ILE Chi-restraints excluded: chain F residue 1551 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 384 optimal weight: 0.0870 chunk 247 optimal weight: 3.9990 chunk 370 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 422 optimal weight: 0.8980 chunk 306 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 487 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 HIS E 426 ASN E1122 ASN ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS H 103 HIS H 289 GLN ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1019 GLN H1233 ASN ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1272 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 50056 Z= 0.243 Angle : 0.684 12.466 68280 Z= 0.338 Chirality : 0.044 0.242 8356 Planarity : 0.005 0.064 8388 Dihedral : 8.111 110.335 7156 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 5.88 % Allowed : 20.20 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.10), residues: 6384 helix: 1.02 (0.08), residues: 3900 sheet: -1.16 (0.23), residues: 444 loop : -1.91 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 288 HIS 0.013 0.001 HIS H 103 PHE 0.075 0.002 PHE E 433 TYR 0.022 0.002 TYR G 123 ARG 0.009 0.001 ARG H 598 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1132 time to evaluate : 6.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7013 (m-40) cc_final: 0.6764 (m110) REVERT: A 57 GLN cc_start: 0.6434 (pt0) cc_final: 0.5832 (tp40) REVERT: A 80 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6169 (mm) REVERT: A 99 ASP cc_start: 0.6738 (m-30) cc_final: 0.6181 (m-30) REVERT: A 195 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.5806 (mmm160) REVERT: A 204 ASP cc_start: 0.6457 (t0) cc_final: 0.6157 (t0) REVERT: A 209 MET cc_start: 0.7915 (tpp) cc_final: 0.7525 (tpp) REVERT: A 217 MET cc_start: 0.8429 (mtm) cc_final: 0.8043 (mtp) REVERT: A 224 THR cc_start: 0.7352 (m) cc_final: 0.7145 (t) REVERT: A 248 SER cc_start: 0.8588 (m) cc_final: 0.8120 (p) REVERT: A 255 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.6062 (pp) REVERT: A 275 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6910 (pp) REVERT: A 308 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7584 (mt-10) REVERT: C 57 GLN cc_start: 0.6836 (pt0) cc_final: 0.6284 (tp40) REVERT: C 80 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6138 (mm) REVERT: C 170 LYS cc_start: 0.5616 (ttmm) cc_final: 0.5407 (ttmm) REVERT: C 192 ARG cc_start: 0.5153 (OUTLIER) cc_final: 0.4278 (mtt90) REVERT: C 195 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.5821 (mmm160) REVERT: C 209 MET cc_start: 0.6541 (ttm) cc_final: 0.6289 (ttm) REVERT: C 217 MET cc_start: 0.8270 (mtm) cc_final: 0.7889 (mtp) REVERT: C 248 SER cc_start: 0.8445 (m) cc_final: 0.7993 (p) REVERT: C 275 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6935 (pp) REVERT: C 280 ASP cc_start: 0.8109 (t70) cc_final: 0.7540 (t0) REVERT: C 308 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 321 GLU cc_start: 0.5847 (tm-30) cc_final: 0.5391 (tm-30) REVERT: B 48 ASN cc_start: 0.6741 (m-40) cc_final: 0.6478 (m110) REVERT: B 57 GLN cc_start: 0.6449 (pt0) cc_final: 0.5887 (tp40) REVERT: B 80 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6190 (mm) REVERT: B 195 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.5692 (mmm160) REVERT: B 248 SER cc_start: 0.8600 (m) cc_final: 0.8132 (p) REVERT: B 255 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6185 (pp) REVERT: B 275 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7055 (pp) REVERT: B 325 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6095 (ttp-110) REVERT: D 57 GLN cc_start: 0.6724 (pt0) cc_final: 0.5849 (tp40) REVERT: D 66 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.6519 (mt) REVERT: D 80 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6232 (mm) REVERT: D 88 MET cc_start: 0.7413 (tpp) cc_final: 0.7190 (tpt) REVERT: D 99 ASP cc_start: 0.7636 (t70) cc_final: 0.7292 (m-30) REVERT: D 195 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.5641 (mmm160) REVERT: D 248 SER cc_start: 0.8402 (m) cc_final: 0.7948 (p) REVERT: D 275 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6920 (pp) REVERT: D 280 ASP cc_start: 0.8123 (t70) cc_final: 0.7621 (t0) REVERT: D 321 GLU cc_start: 0.6240 (tm-30) cc_final: 0.5966 (tm-30) REVERT: E 32 ASN cc_start: 0.7840 (t0) cc_final: 0.7179 (m-40) REVERT: E 42 ILE cc_start: 0.7467 (tt) cc_final: 0.7221 (tp) REVERT: E 108 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7193 (ttp) REVERT: E 312 LEU cc_start: 0.6397 (tp) cc_final: 0.5924 (mp) REVERT: E 361 LEU cc_start: 0.6613 (tp) cc_final: 0.6326 (mt) REVERT: E 378 TYR cc_start: 0.6017 (t80) cc_final: 0.5471 (t80) REVERT: E 411 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6490 (pm20) REVERT: E 432 PHE cc_start: 0.6897 (m-80) cc_final: 0.6672 (m-10) REVERT: E 682 MET cc_start: 0.7161 (mtt) cc_final: 0.6090 (mmt) REVERT: E 732 LYS cc_start: 0.7336 (pttm) cc_final: 0.7018 (pttt) REVERT: E 827 ILE cc_start: 0.6785 (tt) cc_final: 0.6348 (pt) REVERT: E 861 ILE cc_start: 0.5542 (mm) cc_final: 0.4739 (mp) REVERT: E 865 ASP cc_start: 0.6738 (m-30) cc_final: 0.5980 (m-30) REVERT: E 1024 MET cc_start: 0.6695 (ttt) cc_final: 0.6267 (tpt) REVERT: E 1065 MET cc_start: 0.6341 (tpt) cc_final: 0.5318 (ttt) REVERT: E 1098 ARG cc_start: 0.6353 (tpp80) cc_final: 0.6018 (ttm-80) REVERT: E 1110 ARG cc_start: 0.7213 (mmm160) cc_final: 0.6776 (mmp-170) REVERT: E 1145 SER cc_start: 0.7018 (m) cc_final: 0.6624 (p) REVERT: E 1208 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7683 (tp30) REVERT: E 1244 ASN cc_start: 0.7421 (m-40) cc_final: 0.7104 (m-40) REVERT: E 1273 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5591 (ttt90) REVERT: E 1275 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5683 (pp) REVERT: E 1284 LEU cc_start: 0.5208 (OUTLIER) cc_final: 0.4998 (pp) REVERT: E 1352 ARG cc_start: 0.5173 (ptt180) cc_final: 0.4446 (ptt-90) REVERT: E 1427 ASP cc_start: 0.8062 (m-30) cc_final: 0.7781 (m-30) REVERT: E 1569 LYS cc_start: 0.8739 (tmtp) cc_final: 0.8269 (ttpt) REVERT: H 114 PHE cc_start: 0.8146 (t80) cc_final: 0.7889 (t80) REVERT: H 152 ILE cc_start: 0.7283 (mm) cc_final: 0.7075 (mt) REVERT: H 175 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6883 (mm) REVERT: H 298 ARG cc_start: 0.6717 (mtp-110) cc_final: 0.6041 (ttp80) REVERT: H 441 MET cc_start: 0.5091 (ttt) cc_final: 0.4723 (tmm) REVERT: H 827 ILE cc_start: 0.6820 (tt) cc_final: 0.6272 (pt) REVERT: H 846 HIS cc_start: 0.7038 (t-90) cc_final: 0.5948 (m-70) REVERT: H 885 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6255 (pt) REVERT: H 1012 LEU cc_start: 0.6462 (mm) cc_final: 0.6190 (mm) REVERT: H 1125 SER cc_start: 0.7358 (t) cc_final: 0.7094 (m) REVERT: H 1226 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5388 (tp) REVERT: H 1273 ARG cc_start: 0.5939 (ttm170) cc_final: 0.5587 (ttm170) REVERT: H 1275 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5461 (pp) REVERT: H 1297 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6640 (tpp) REVERT: H 1362 LYS cc_start: 0.6532 (ptpt) cc_final: 0.6261 (ptpp) REVERT: H 1485 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5159 (mp10) REVERT: H 1497 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6717 (mtt180) REVERT: H 1569 LYS cc_start: 0.8464 (tppt) cc_final: 0.8244 (ttmt) REVERT: G 298 ARG cc_start: 0.6101 (mtt-85) cc_final: 0.5723 (tpt-90) REVERT: G 369 GLN cc_start: 0.5141 (OUTLIER) cc_final: 0.4510 (tp-100) REVERT: G 394 LYS cc_start: 0.6150 (tppp) cc_final: 0.5863 (tttp) REVERT: G 400 MET cc_start: 0.7650 (mmm) cc_final: 0.7264 (mmm) REVERT: G 411 GLU cc_start: 0.7820 (pm20) cc_final: 0.7498 (pm20) REVERT: G 612 GLU cc_start: 0.7058 (tt0) cc_final: 0.6184 (mt-10) REVERT: G 800 MET cc_start: 0.6786 (ttp) cc_final: 0.5792 (ptp) REVERT: G 803 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6811 (pp20) REVERT: G 820 THR cc_start: 0.8384 (t) cc_final: 0.8063 (p) REVERT: G 827 ILE cc_start: 0.6710 (tt) cc_final: 0.6316 (pt) REVERT: G 865 ASP cc_start: 0.6789 (m-30) cc_final: 0.6295 (m-30) REVERT: G 1012 LEU cc_start: 0.6698 (mm) cc_final: 0.6400 (mm) REVERT: G 1020 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6779 (mm) REVERT: G 1024 MET cc_start: 0.6690 (ttt) cc_final: 0.6312 (tpt) REVERT: G 1038 ASP cc_start: 0.5824 (OUTLIER) cc_final: 0.5526 (p0) REVERT: G 1125 SER cc_start: 0.7566 (t) cc_final: 0.7212 (m) REVERT: G 1145 SER cc_start: 0.7190 (m) cc_final: 0.6753 (p) REVERT: G 1226 LEU cc_start: 0.6184 (OUTLIER) cc_final: 0.5841 (tp) REVERT: G 1244 ASN cc_start: 0.7551 (m-40) cc_final: 0.7202 (m-40) REVERT: G 1275 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5443 (pp) REVERT: G 1282 LEU cc_start: 0.5435 (mt) cc_final: 0.5226 (tp) REVERT: G 1293 TYR cc_start: 0.6107 (m-80) cc_final: 0.5594 (m-80) REVERT: G 1362 LYS cc_start: 0.6346 (ptpt) cc_final: 0.6078 (ptpp) REVERT: G 1459 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.6018 (mt) REVERT: G 1540 HIS cc_start: 0.7694 (t-90) cc_final: 0.7436 (t-90) REVERT: F 112 MET cc_start: 0.8013 (mmp) cc_final: 0.7678 (mmm) REVERT: F 175 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7125 (mm) REVERT: F 181 MET cc_start: 0.6800 (mmt) cc_final: 0.6384 (mmt) REVERT: F 298 ARG cc_start: 0.6354 (mtt-85) cc_final: 0.5975 (tpt-90) REVERT: F 369 GLN cc_start: 0.5157 (OUTLIER) cc_final: 0.4596 (tp-100) REVERT: F 381 ILE cc_start: 0.5682 (tt) cc_final: 0.5474 (tt) REVERT: F 585 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6156 (tt) REVERT: F 703 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5911 (mp) REVERT: F 730 MET cc_start: 0.6599 (mtp) cc_final: 0.6345 (mtt) REVERT: F 827 ILE cc_start: 0.6608 (tt) cc_final: 0.6153 (pt) REVERT: F 845 GLN cc_start: 0.7105 (tm-30) cc_final: 0.6873 (tm-30) REVERT: F 846 HIS cc_start: 0.6913 (t-90) cc_final: 0.5960 (m170) REVERT: F 885 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6088 (pt) REVERT: F 1024 MET cc_start: 0.5671 (mmp) cc_final: 0.5242 (mmp) REVERT: F 1110 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6676 (mmp-170) REVERT: F 1124 PHE cc_start: 0.7910 (m-80) cc_final: 0.7641 (m-80) REVERT: F 1125 SER cc_start: 0.7149 (t) cc_final: 0.6873 (p) REVERT: F 1244 ASN cc_start: 0.7664 (m110) cc_final: 0.7402 (m110) REVERT: F 1252 GLU cc_start: 0.6209 (tp30) cc_final: 0.5388 (tp30) REVERT: F 1275 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5752 (pp) REVERT: F 1284 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4957 (pp) REVERT: F 1313 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.6169 (ttm110) REVERT: F 1399 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6259 (mm-30) REVERT: F 1569 LYS cc_start: 0.8131 (tmtp) cc_final: 0.7794 (tppt) outliers start: 294 outliers final: 207 residues processed: 1305 average time/residue: 0.5868 time to fit residues: 1305.8569 Evaluate side-chains 1338 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1093 time to evaluate : 5.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 68 TRP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 715 VAL Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 813 ILE Chi-restraints excluded: chain E residue 874 GLU Chi-restraints excluded: chain E residue 886 VAL Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1026 LEU Chi-restraints excluded: chain E residue 1037 THR Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1087 TRP Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1183 VAL Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1230 THR Chi-restraints excluded: chain E residue 1273 ARG Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1284 LEU Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1419 SER Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 289 GLN Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 582 LEU Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 682 MET Chi-restraints excluded: chain H residue 715 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 782 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 857 SER Chi-restraints excluded: chain H residue 883 VAL Chi-restraints excluded: chain H residue 885 LEU Chi-restraints excluded: chain H residue 886 VAL Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 1025 VAL Chi-restraints excluded: chain H residue 1080 VAL Chi-restraints excluded: chain H residue 1082 SER Chi-restraints excluded: chain H residue 1087 TRP Chi-restraints excluded: chain H residue 1121 LEU Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1226 LEU Chi-restraints excluded: chain H residue 1275 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1294 LEU Chi-restraints excluded: chain H residue 1297 MET Chi-restraints excluded: chain H residue 1298 VAL Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1306 LEU Chi-restraints excluded: chain H residue 1314 ILE Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1409 ILE Chi-restraints excluded: chain H residue 1475 THR Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain H residue 1488 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 413 THR Chi-restraints excluded: chain G residue 546 MET Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 579 SER Chi-restraints excluded: chain G residue 582 LEU Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 886 VAL Chi-restraints excluded: chain G residue 897 ASP Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1038 ASP Chi-restraints excluded: chain G residue 1087 TRP Chi-restraints excluded: chain G residue 1104 ILE Chi-restraints excluded: chain G residue 1121 LEU Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1226 LEU Chi-restraints excluded: chain G residue 1257 CYS Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1409 ILE Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1501 ILE Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 172 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 607 VAL Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1167 LEU Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1298 VAL Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1313 ARG Chi-restraints excluded: chain F residue 1314 ILE Chi-restraints excluded: chain F residue 1409 ILE Chi-restraints excluded: chain F residue 1415 HIS Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1501 ILE Chi-restraints excluded: chain F residue 1503 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 564 optimal weight: 3.9990 chunk 594 optimal weight: 3.9990 chunk 542 optimal weight: 2.9990 chunk 578 optimal weight: 0.7980 chunk 348 optimal weight: 5.9990 chunk 251 optimal weight: 0.8980 chunk 454 optimal weight: 0.0770 chunk 177 optimal weight: 9.9990 chunk 522 optimal weight: 0.9990 chunk 547 optimal weight: 3.9990 chunk 576 optimal weight: 0.0670 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 HIS E 845 GLN ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS E1347 GLN H 103 HIS H 289 GLN ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1019 GLN ** H1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1272 HIS G1426 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 50056 Z= 0.203 Angle : 0.677 14.854 68280 Z= 0.332 Chirality : 0.043 0.246 8356 Planarity : 0.005 0.063 8388 Dihedral : 7.987 110.013 7156 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.88 % Allowed : 21.32 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 6384 helix: 1.18 (0.08), residues: 3892 sheet: -0.88 (0.22), residues: 500 loop : -1.84 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F1032 HIS 0.013 0.001 HIS H 103 PHE 0.076 0.002 PHE E 433 TYR 0.026 0.001 TYR G 123 ARG 0.009 0.001 ARG F 598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1371 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1127 time to evaluate : 5.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.6937 (mmmt) cc_final: 0.6689 (mmmt) REVERT: A 48 ASN cc_start: 0.6964 (m-40) cc_final: 0.6726 (m110) REVERT: A 57 GLN cc_start: 0.6414 (pt0) cc_final: 0.5832 (tp40) REVERT: A 80 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6118 (mm) REVERT: A 99 ASP cc_start: 0.6825 (m-30) cc_final: 0.6432 (m-30) REVERT: A 108 GLU cc_start: 0.7622 (mp0) cc_final: 0.7240 (mp0) REVERT: A 195 ARG cc_start: 0.7032 (mmm-85) cc_final: 0.5789 (mmm160) REVERT: A 204 ASP cc_start: 0.6488 (t0) cc_final: 0.6178 (t0) REVERT: A 209 MET cc_start: 0.7865 (tpp) cc_final: 0.7583 (tpp) REVERT: A 224 THR cc_start: 0.7312 (m) cc_final: 0.7095 (t) REVERT: A 248 SER cc_start: 0.8595 (m) cc_final: 0.8129 (p) REVERT: A 255 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6200 (pp) REVERT: A 275 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6869 (pp) REVERT: A 280 ASP cc_start: 0.8363 (t0) cc_final: 0.7898 (t0) REVERT: A 308 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 57 GLN cc_start: 0.6885 (pt0) cc_final: 0.6358 (tp40) REVERT: C 80 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6077 (mm) REVERT: C 99 ASP cc_start: 0.6595 (m-30) cc_final: 0.5906 (m-30) REVERT: C 192 ARG cc_start: 0.5004 (OUTLIER) cc_final: 0.4233 (mtt90) REVERT: C 195 ARG cc_start: 0.6953 (mmm-85) cc_final: 0.5796 (mmm160) REVERT: C 209 MET cc_start: 0.6583 (ttm) cc_final: 0.6278 (ttm) REVERT: C 217 MET cc_start: 0.8120 (mtm) cc_final: 0.7726 (mtp) REVERT: C 248 SER cc_start: 0.8283 (m) cc_final: 0.7940 (p) REVERT: C 275 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6894 (pp) REVERT: C 280 ASP cc_start: 0.7986 (t70) cc_final: 0.7434 (t0) REVERT: C 308 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7545 (mt-10) REVERT: C 321 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5863 (tm-30) REVERT: B 48 ASN cc_start: 0.6769 (m-40) cc_final: 0.6496 (m110) REVERT: B 57 GLN cc_start: 0.6504 (pt0) cc_final: 0.5936 (tp40) REVERT: B 80 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6142 (mm) REVERT: B 195 ARG cc_start: 0.6932 (mmm-85) cc_final: 0.5666 (mmm160) REVERT: B 248 SER cc_start: 0.8604 (m) cc_final: 0.8145 (p) REVERT: B 255 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6178 (pp) REVERT: B 275 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7162 (pp) REVERT: B 325 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.6237 (ttp-110) REVERT: D 57 GLN cc_start: 0.6715 (pt0) cc_final: 0.5851 (tp40) REVERT: D 88 MET cc_start: 0.7394 (tpp) cc_final: 0.7173 (tpt) REVERT: D 99 ASP cc_start: 0.7521 (t70) cc_final: 0.7282 (m-30) REVERT: D 195 ARG cc_start: 0.7000 (mmm-85) cc_final: 0.5621 (mmm160) REVERT: D 248 SER cc_start: 0.8281 (m) cc_final: 0.8006 (p) REVERT: D 275 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6867 (pp) REVERT: D 280 ASP cc_start: 0.8107 (t70) cc_final: 0.7599 (t0) REVERT: D 321 GLU cc_start: 0.6320 (tm-30) cc_final: 0.5976 (tm-30) REVERT: E 32 ASN cc_start: 0.7862 (t0) cc_final: 0.7224 (m-40) REVERT: E 108 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7194 (ttp) REVERT: E 312 LEU cc_start: 0.6607 (tp) cc_final: 0.6118 (mp) REVERT: E 361 LEU cc_start: 0.6584 (tp) cc_final: 0.6309 (mt) REVERT: E 378 TYR cc_start: 0.5981 (t80) cc_final: 0.5434 (t80) REVERT: E 411 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6346 (pm20) REVERT: E 424 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6198 (t70) REVERT: E 432 PHE cc_start: 0.6939 (m-80) cc_final: 0.6698 (m-10) REVERT: E 682 MET cc_start: 0.7136 (mtt) cc_final: 0.6088 (mmt) REVERT: E 732 LYS cc_start: 0.7394 (pttm) cc_final: 0.7066 (pttt) REVERT: E 827 ILE cc_start: 0.6821 (tt) cc_final: 0.6391 (pt) REVERT: E 861 ILE cc_start: 0.5553 (mm) cc_final: 0.4773 (mp) REVERT: E 865 ASP cc_start: 0.6737 (m-30) cc_final: 0.5975 (m-30) REVERT: E 1024 MET cc_start: 0.6683 (ttt) cc_final: 0.6352 (tpt) REVERT: E 1065 MET cc_start: 0.6288 (tpt) cc_final: 0.5353 (ttt) REVERT: E 1098 ARG cc_start: 0.6372 (tpp80) cc_final: 0.5991 (ttm-80) REVERT: E 1110 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6846 (mmp-170) REVERT: E 1145 SER cc_start: 0.6888 (m) cc_final: 0.6518 (p) REVERT: E 1208 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7787 (tp30) REVERT: E 1244 ASN cc_start: 0.7467 (m-40) cc_final: 0.7156 (m-40) REVERT: E 1273 ARG cc_start: 0.6068 (OUTLIER) cc_final: 0.5728 (ttt90) REVERT: E 1275 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5532 (pp) REVERT: E 1352 ARG cc_start: 0.5214 (ptt180) cc_final: 0.4478 (ptt-90) REVERT: E 1427 ASP cc_start: 0.8062 (m-30) cc_final: 0.7779 (m-30) REVERT: E 1569 LYS cc_start: 0.8747 (tmtp) cc_final: 0.8319 (ttpt) REVERT: H 114 PHE cc_start: 0.8179 (t80) cc_final: 0.7881 (t80) REVERT: H 152 ILE cc_start: 0.7077 (mm) cc_final: 0.6857 (mt) REVERT: H 175 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6881 (mm) REVERT: H 298 ARG cc_start: 0.6835 (mtp-110) cc_final: 0.6204 (ttp80) REVERT: H 361 LEU cc_start: 0.6657 (tp) cc_final: 0.6381 (mt) REVERT: H 433 PHE cc_start: 0.5633 (m-80) cc_final: 0.5414 (m-80) REVERT: H 441 MET cc_start: 0.5104 (ttt) cc_final: 0.4748 (tmm) REVERT: H 827 ILE cc_start: 0.6876 (tt) cc_final: 0.6378 (pt) REVERT: H 846 HIS cc_start: 0.6985 (t-90) cc_final: 0.5914 (m-70) REVERT: H 885 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6101 (pt) REVERT: H 1012 LEU cc_start: 0.6490 (mm) cc_final: 0.6176 (mm) REVERT: H 1124 PHE cc_start: 0.8149 (m-80) cc_final: 0.7911 (m-80) REVERT: H 1125 SER cc_start: 0.7364 (t) cc_final: 0.7095 (m) REVERT: H 1226 LEU cc_start: 0.5661 (OUTLIER) cc_final: 0.5360 (tp) REVERT: H 1275 LEU cc_start: 0.5544 (OUTLIER) cc_final: 0.5193 (pp) REVERT: H 1293 TYR cc_start: 0.5900 (m-80) cc_final: 0.5382 (m-80) REVERT: H 1297 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6675 (tpp) REVERT: H 1362 LYS cc_start: 0.6503 (ptpt) cc_final: 0.6230 (ptpp) REVERT: H 1485 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.5169 (mp10) REVERT: H 1497 ARG cc_start: 0.6996 (mtt180) cc_final: 0.6761 (mtt180) REVERT: H 1542 ILE cc_start: 0.7292 (tt) cc_final: 0.7068 (tt) REVERT: H 1569 LYS cc_start: 0.8617 (tppt) cc_final: 0.8254 (ttmt) REVERT: G 298 ARG cc_start: 0.6115 (mtt-85) cc_final: 0.5724 (tpt-90) REVERT: G 369 GLN cc_start: 0.5143 (OUTLIER) cc_final: 0.4190 (tp-100) REVERT: G 394 LYS cc_start: 0.6148 (tppp) cc_final: 0.5867 (tttp) REVERT: G 411 GLU cc_start: 0.7812 (pm20) cc_final: 0.7491 (pm20) REVERT: G 577 PHE cc_start: 0.3255 (OUTLIER) cc_final: 0.2961 (m-10) REVERT: G 612 GLU cc_start: 0.7034 (tt0) cc_final: 0.6074 (mt-10) REVERT: G 800 MET cc_start: 0.6788 (ttp) cc_final: 0.5795 (ptp) REVERT: G 803 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6733 (pp20) REVERT: G 820 THR cc_start: 0.8389 (t) cc_final: 0.8054 (p) REVERT: G 827 ILE cc_start: 0.6734 (tt) cc_final: 0.6326 (pt) REVERT: G 865 ASP cc_start: 0.6726 (m-30) cc_final: 0.6189 (m-30) REVERT: G 1011 LEU cc_start: 0.5775 (mt) cc_final: 0.5430 (mt) REVERT: G 1012 LEU cc_start: 0.6795 (mm) cc_final: 0.6457 (mm) REVERT: G 1020 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6536 (mm) REVERT: G 1024 MET cc_start: 0.6799 (ttt) cc_final: 0.6469 (tpt) REVERT: G 1038 ASP cc_start: 0.5806 (OUTLIER) cc_final: 0.5496 (p0) REVERT: G 1098 ARG cc_start: 0.5981 (tpp80) cc_final: 0.5678 (tpp80) REVERT: G 1125 SER cc_start: 0.7643 (t) cc_final: 0.7281 (m) REVERT: G 1145 SER cc_start: 0.7199 (m) cc_final: 0.6769 (p) REVERT: G 1226 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5853 (tp) REVERT: G 1244 ASN cc_start: 0.7529 (m-40) cc_final: 0.7108 (m-40) REVERT: G 1275 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5343 (pp) REVERT: G 1293 TYR cc_start: 0.6124 (m-80) cc_final: 0.5612 (m-80) REVERT: G 1362 LYS cc_start: 0.6362 (ptpt) cc_final: 0.6095 (ptpp) REVERT: G 1459 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5935 (mt) REVERT: G 1470 LEU cc_start: 0.7788 (pp) cc_final: 0.7568 (pp) REVERT: G 1540 HIS cc_start: 0.7855 (t-90) cc_final: 0.7616 (t-90) REVERT: F 175 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6907 (mm) REVERT: F 181 MET cc_start: 0.6788 (mmt) cc_final: 0.6381 (mmt) REVERT: F 298 ARG cc_start: 0.6189 (mtt-85) cc_final: 0.5831 (tpt-90) REVERT: F 369 GLN cc_start: 0.5171 (OUTLIER) cc_final: 0.4227 (tp-100) REVERT: F 502 MET cc_start: 0.5672 (tpp) cc_final: 0.5021 (mtt) REVERT: F 703 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5842 (mp) REVERT: F 730 MET cc_start: 0.6458 (mtp) cc_final: 0.6190 (mtt) REVERT: F 803 GLU cc_start: 0.6949 (pp20) cc_final: 0.6598 (pp20) REVERT: F 827 ILE cc_start: 0.6618 (tt) cc_final: 0.6173 (pt) REVERT: F 845 GLN cc_start: 0.7082 (tm-30) cc_final: 0.6679 (tm-30) REVERT: F 846 HIS cc_start: 0.6776 (t-90) cc_final: 0.5947 (m170) REVERT: F 885 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6127 (pt) REVERT: F 1012 LEU cc_start: 0.6643 (mm) cc_final: 0.6352 (mm) REVERT: F 1024 MET cc_start: 0.5756 (mmp) cc_final: 0.5320 (mmp) REVERT: F 1110 ARG cc_start: 0.7325 (mmm160) cc_final: 0.6657 (mmp-170) REVERT: F 1121 LEU cc_start: 0.6724 (tp) cc_final: 0.6414 (tp) REVERT: F 1124 PHE cc_start: 0.7954 (m-80) cc_final: 0.7717 (m-80) REVERT: F 1125 SER cc_start: 0.7163 (t) cc_final: 0.6885 (p) REVERT: F 1244 ASN cc_start: 0.7660 (m110) cc_final: 0.7400 (m110) REVERT: F 1275 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5814 (pp) REVERT: F 1284 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.5027 (pp) REVERT: F 1399 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6317 (mm-30) REVERT: F 1458 GLN cc_start: 0.6441 (mp10) cc_final: 0.6210 (mp10) outliers start: 244 outliers final: 182 residues processed: 1268 average time/residue: 0.5723 time to fit residues: 1232.9862 Evaluate side-chains 1304 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1087 time to evaluate : 5.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 68 TRP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 433 PHE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 813 ILE Chi-restraints excluded: chain E residue 874 GLU Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1087 TRP Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1183 VAL Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1273 ARG Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 314 PHE Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 582 LEU Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 682 MET Chi-restraints excluded: chain H residue 715 VAL Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 782 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 857 SER Chi-restraints excluded: chain H residue 883 VAL Chi-restraints excluded: chain H residue 885 LEU Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 1025 VAL Chi-restraints excluded: chain H residue 1082 SER Chi-restraints excluded: chain H residue 1087 TRP Chi-restraints excluded: chain H residue 1121 LEU Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1226 LEU Chi-restraints excluded: chain H residue 1275 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1294 LEU Chi-restraints excluded: chain H residue 1297 MET Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1314 ILE Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1409 ILE Chi-restraints excluded: chain H residue 1475 THR Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain H residue 1519 LEU Chi-restraints excluded: chain H residue 1541 THR Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 577 PHE Chi-restraints excluded: chain G residue 579 SER Chi-restraints excluded: chain G residue 582 LEU Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 897 ASP Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1038 ASP Chi-restraints excluded: chain G residue 1087 TRP Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1212 THR Chi-restraints excluded: chain G residue 1226 LEU Chi-restraints excluded: chain G residue 1257 CYS Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1294 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1314 ILE Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1409 ILE Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1501 ILE Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1525 THR Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 607 VAL Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1298 VAL Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1306 LEU Chi-restraints excluded: chain F residue 1314 ILE Chi-restraints excluded: chain F residue 1409 ILE Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 379 optimal weight: 2.9990 chunk 611 optimal weight: 0.9990 chunk 373 optimal weight: 0.7980 chunk 290 optimal weight: 0.6980 chunk 425 optimal weight: 0.6980 chunk 641 optimal weight: 6.9990 chunk 590 optimal weight: 0.9980 chunk 510 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 394 optimal weight: 6.9990 chunk 313 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 HIS D 186 HIS E 103 HIS ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1272 HIS E1295 ASN H 103 HIS ** H 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1272 HIS ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 50056 Z= 0.229 Angle : 0.685 13.130 68280 Z= 0.337 Chirality : 0.044 0.233 8356 Planarity : 0.005 0.063 8388 Dihedral : 7.935 110.622 7156 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.82 % Allowed : 21.96 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 6384 helix: 1.21 (0.08), residues: 3880 sheet: -0.81 (0.22), residues: 500 loop : -1.78 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 430 HIS 0.010 0.001 HIS G 103 PHE 0.078 0.002 PHE E 433 TYR 0.022 0.001 TYR G 123 ARG 0.015 0.001 ARG F 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12768 Ramachandran restraints generated. 6384 Oldfield, 0 Emsley, 6384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1117 time to evaluate : 5.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.6890 (mmmt) cc_final: 0.6648 (mmmt) REVERT: A 48 ASN cc_start: 0.7049 (m-40) cc_final: 0.6814 (m110) REVERT: A 57 GLN cc_start: 0.6635 (pt0) cc_final: 0.5827 (tp40) REVERT: A 80 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6151 (mm) REVERT: A 99 ASP cc_start: 0.6805 (m-30) cc_final: 0.6563 (m-30) REVERT: A 195 ARG cc_start: 0.7030 (mmm-85) cc_final: 0.5789 (mmm160) REVERT: A 209 MET cc_start: 0.7848 (tpp) cc_final: 0.7628 (tpp) REVERT: A 224 THR cc_start: 0.7231 (m) cc_final: 0.7018 (t) REVERT: A 248 SER cc_start: 0.8598 (m) cc_final: 0.8135 (p) REVERT: A 255 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6357 (pp) REVERT: A 275 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6795 (pp) REVERT: A 308 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 57 GLN cc_start: 0.6628 (pt0) cc_final: 0.6163 (tp40) REVERT: C 80 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6124 (mm) REVERT: C 99 ASP cc_start: 0.6694 (m-30) cc_final: 0.6209 (m-30) REVERT: C 192 ARG cc_start: 0.5033 (OUTLIER) cc_final: 0.4203 (mtt90) REVERT: C 195 ARG cc_start: 0.7119 (mmm-85) cc_final: 0.5784 (mmm160) REVERT: C 209 MET cc_start: 0.6619 (ttm) cc_final: 0.6312 (ttm) REVERT: C 217 MET cc_start: 0.8321 (mtm) cc_final: 0.7963 (mtp) REVERT: C 248 SER cc_start: 0.8509 (m) cc_final: 0.7998 (p) REVERT: C 275 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6908 (pp) REVERT: C 280 ASP cc_start: 0.8049 (t70) cc_final: 0.7520 (t0) REVERT: C 308 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 321 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6190 (tm-30) REVERT: B 48 ASN cc_start: 0.6790 (m-40) cc_final: 0.6493 (m110) REVERT: B 57 GLN cc_start: 0.6423 (pt0) cc_final: 0.5881 (tp40) REVERT: B 80 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6164 (mm) REVERT: B 99 ASP cc_start: 0.6938 (m-30) cc_final: 0.6401 (m-30) REVERT: B 108 GLU cc_start: 0.7447 (tt0) cc_final: 0.7243 (tt0) REVERT: B 195 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.5720 (mmm160) REVERT: B 248 SER cc_start: 0.8614 (m) cc_final: 0.8162 (p) REVERT: B 255 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6300 (pp) REVERT: B 275 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7065 (pp) REVERT: B 308 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7340 (mt-10) REVERT: B 325 ARG cc_start: 0.6814 (mtm-85) cc_final: 0.6317 (ttp-110) REVERT: D 57 GLN cc_start: 0.6692 (pt0) cc_final: 0.6182 (tm-30) REVERT: D 66 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6641 (mt) REVERT: D 99 ASP cc_start: 0.7577 (t70) cc_final: 0.7358 (m-30) REVERT: D 195 ARG cc_start: 0.6998 (mmm-85) cc_final: 0.5614 (mmm160) REVERT: D 229 GLU cc_start: 0.7228 (pt0) cc_final: 0.6724 (tt0) REVERT: D 248 SER cc_start: 0.8540 (m) cc_final: 0.8008 (p) REVERT: D 275 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6915 (pp) REVERT: D 280 ASP cc_start: 0.8101 (t70) cc_final: 0.7588 (t0) REVERT: D 288 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: D 321 GLU cc_start: 0.6307 (tm-30) cc_final: 0.5971 (tm-30) REVERT: D 350 ASP cc_start: 0.6616 (m-30) cc_final: 0.6414 (m-30) REVERT: E 32 ASN cc_start: 0.7868 (t0) cc_final: 0.7230 (m-40) REVERT: E 74 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5473 (ttp-170) REVERT: E 108 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.7191 (ttp) REVERT: E 312 LEU cc_start: 0.6652 (tp) cc_final: 0.6172 (mp) REVERT: E 357 VAL cc_start: 0.7080 (t) cc_final: 0.6794 (m) REVERT: E 361 LEU cc_start: 0.6587 (tp) cc_final: 0.6320 (mt) REVERT: E 378 TYR cc_start: 0.5987 (t80) cc_final: 0.5433 (t80) REVERT: E 411 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6357 (pm20) REVERT: E 732 LYS cc_start: 0.7394 (pttm) cc_final: 0.7056 (pttp) REVERT: E 827 ILE cc_start: 0.6834 (tt) cc_final: 0.6413 (pt) REVERT: E 861 ILE cc_start: 0.5641 (mm) cc_final: 0.4902 (mp) REVERT: E 865 ASP cc_start: 0.6721 (m-30) cc_final: 0.5971 (m-30) REVERT: E 1024 MET cc_start: 0.6805 (ttt) cc_final: 0.6466 (tpt) REVERT: E 1065 MET cc_start: 0.6294 (tpt) cc_final: 0.5349 (ttt) REVERT: E 1098 ARG cc_start: 0.6261 (tpp80) cc_final: 0.5839 (ttm-80) REVERT: E 1110 ARG cc_start: 0.7300 (mmm160) cc_final: 0.6875 (mmp-170) REVERT: E 1145 SER cc_start: 0.6889 (m) cc_final: 0.6558 (p) REVERT: E 1208 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: E 1244 ASN cc_start: 0.7486 (m-40) cc_final: 0.7175 (m-40) REVERT: E 1273 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5756 (ttt90) REVERT: E 1275 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5473 (pp) REVERT: E 1352 ARG cc_start: 0.5415 (ptt180) cc_final: 0.4551 (ptt-90) REVERT: E 1427 ASP cc_start: 0.8061 (m-30) cc_final: 0.7773 (m-30) REVERT: E 1470 LEU cc_start: 0.7210 (pp) cc_final: 0.6786 (tt) REVERT: E 1569 LYS cc_start: 0.8764 (tmtp) cc_final: 0.8288 (tmmt) REVERT: H 114 PHE cc_start: 0.8166 (t80) cc_final: 0.7902 (t80) REVERT: H 152 ILE cc_start: 0.7043 (mm) cc_final: 0.6816 (mt) REVERT: H 175 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6918 (mm) REVERT: H 298 ARG cc_start: 0.6824 (mtp-110) cc_final: 0.6057 (ttp80) REVERT: H 378 TYR cc_start: 0.5960 (t80) cc_final: 0.5492 (t80) REVERT: H 433 PHE cc_start: 0.5504 (m-80) cc_final: 0.5290 (m-80) REVERT: H 441 MET cc_start: 0.5052 (ttt) cc_final: 0.4599 (tmm) REVERT: H 827 ILE cc_start: 0.6739 (tt) cc_final: 0.6259 (pt) REVERT: H 846 HIS cc_start: 0.7000 (t-90) cc_final: 0.5992 (m-70) REVERT: H 885 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6159 (pt) REVERT: H 1012 LEU cc_start: 0.6667 (mm) cc_final: 0.6366 (mm) REVERT: H 1124 PHE cc_start: 0.8149 (m-80) cc_final: 0.7925 (m-80) REVERT: H 1125 SER cc_start: 0.7321 (t) cc_final: 0.7045 (m) REVERT: H 1226 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5398 (tp) REVERT: H 1275 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5226 (pp) REVERT: H 1293 TYR cc_start: 0.5918 (m-80) cc_final: 0.5403 (m-80) REVERT: H 1297 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6675 (tpp) REVERT: H 1485 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.5124 (mp10) REVERT: H 1497 ARG cc_start: 0.7034 (mtt180) cc_final: 0.6823 (mtt180) REVERT: H 1542 ILE cc_start: 0.7268 (tt) cc_final: 0.7056 (tt) REVERT: H 1569 LYS cc_start: 0.8641 (tppt) cc_final: 0.8343 (ttpt) REVERT: G 298 ARG cc_start: 0.6119 (mtt-85) cc_final: 0.5727 (tpt-90) REVERT: G 394 LYS cc_start: 0.5907 (tppp) cc_final: 0.5629 (tttp) REVERT: G 411 GLU cc_start: 0.7742 (pm20) cc_final: 0.7432 (pm20) REVERT: G 612 GLU cc_start: 0.7039 (tt0) cc_final: 0.6173 (mt-10) REVERT: G 800 MET cc_start: 0.6828 (ttp) cc_final: 0.5831 (ptp) REVERT: G 827 ILE cc_start: 0.6751 (tt) cc_final: 0.6328 (pt) REVERT: G 846 HIS cc_start: 0.6856 (t-90) cc_final: 0.5977 (m-70) REVERT: G 865 ASP cc_start: 0.6787 (m-30) cc_final: 0.6117 (m-30) REVERT: G 1011 LEU cc_start: 0.5790 (mt) cc_final: 0.5419 (mt) REVERT: G 1012 LEU cc_start: 0.6869 (mm) cc_final: 0.6562 (mm) REVERT: G 1020 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6553 (mm) REVERT: G 1024 MET cc_start: 0.6828 (ttt) cc_final: 0.6496 (tpt) REVERT: G 1038 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5698 (p0) REVERT: G 1125 SER cc_start: 0.7644 (t) cc_final: 0.7288 (m) REVERT: G 1145 SER cc_start: 0.6984 (m) cc_final: 0.6619 (p) REVERT: G 1226 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5874 (tp) REVERT: G 1272 HIS cc_start: 0.6707 (m170) cc_final: 0.6485 (m-70) REVERT: G 1275 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5431 (pp) REVERT: G 1284 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.5011 (pp) REVERT: G 1293 TYR cc_start: 0.6065 (m-80) cc_final: 0.5615 (m-80) REVERT: G 1362 LYS cc_start: 0.6533 (ptpt) cc_final: 0.6319 (pttm) REVERT: G 1459 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5713 (mt) REVERT: G 1470 LEU cc_start: 0.7646 (pp) cc_final: 0.7433 (pp) REVERT: G 1540 HIS cc_start: 0.7803 (t-90) cc_final: 0.7574 (t-90) REVERT: F 175 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6905 (mm) REVERT: F 181 MET cc_start: 0.6805 (mmt) cc_final: 0.6410 (mmt) REVERT: F 298 ARG cc_start: 0.6402 (mtt-85) cc_final: 0.6027 (tpt-90) REVERT: F 369 GLN cc_start: 0.5145 (OUTLIER) cc_final: 0.4867 (tp-100) REVERT: F 502 MET cc_start: 0.5758 (tpp) cc_final: 0.5018 (mtt) REVERT: F 577 PHE cc_start: 0.4306 (OUTLIER) cc_final: 0.3910 (m-80) REVERT: F 703 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5846 (mp) REVERT: F 803 GLU cc_start: 0.6943 (pp20) cc_final: 0.6583 (pp20) REVERT: F 827 ILE cc_start: 0.6631 (tt) cc_final: 0.6183 (pt) REVERT: F 845 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6596 (tm-30) REVERT: F 846 HIS cc_start: 0.6762 (t-90) cc_final: 0.5950 (m170) REVERT: F 885 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6205 (pt) REVERT: F 1012 LEU cc_start: 0.6796 (mm) cc_final: 0.6496 (mm) REVERT: F 1065 MET cc_start: 0.6071 (tpt) cc_final: 0.5109 (ttt) REVERT: F 1110 ARG cc_start: 0.7343 (mmm160) cc_final: 0.6679 (mmp-170) REVERT: F 1121 LEU cc_start: 0.6718 (tp) cc_final: 0.6419 (tp) REVERT: F 1125 SER cc_start: 0.7171 (t) cc_final: 0.6888 (p) REVERT: F 1275 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5805 (pp) REVERT: F 1284 LEU cc_start: 0.5249 (OUTLIER) cc_final: 0.5032 (pp) REVERT: F 1399 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6589 (mm-30) REVERT: F 1458 GLN cc_start: 0.6407 (mp10) cc_final: 0.6155 (mp10) REVERT: F 1470 LEU cc_start: 0.7861 (pp) cc_final: 0.7593 (tt) outliers start: 241 outliers final: 183 residues processed: 1254 average time/residue: 0.5657 time to fit residues: 1211.7427 Evaluate side-chains 1308 residues out of total 5580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1088 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 68 TRP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 125 HIS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 411 GLU Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 489 LEU Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 778 LEU Chi-restraints excluded: chain E residue 782 THR Chi-restraints excluded: chain E residue 813 ILE Chi-restraints excluded: chain E residue 874 GLU Chi-restraints excluded: chain E residue 897 ASP Chi-restraints excluded: chain E residue 902 MET Chi-restraints excluded: chain E residue 1082 SER Chi-restraints excluded: chain E residue 1087 TRP Chi-restraints excluded: chain E residue 1121 LEU Chi-restraints excluded: chain E residue 1128 CYS Chi-restraints excluded: chain E residue 1130 THR Chi-restraints excluded: chain E residue 1142 LEU Chi-restraints excluded: chain E residue 1183 VAL Chi-restraints excluded: chain E residue 1208 GLU Chi-restraints excluded: chain E residue 1211 THR Chi-restraints excluded: chain E residue 1273 ARG Chi-restraints excluded: chain E residue 1275 LEU Chi-restraints excluded: chain E residue 1294 LEU Chi-restraints excluded: chain E residue 1301 LEU Chi-restraints excluded: chain E residue 1389 LEU Chi-restraints excluded: chain E residue 1402 ILE Chi-restraints excluded: chain E residue 1409 ILE Chi-restraints excluded: chain E residue 1475 THR Chi-restraints excluded: chain E residue 1501 ILE Chi-restraints excluded: chain E residue 1529 ASP Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 293 HIS Chi-restraints excluded: chain H residue 314 PHE Chi-restraints excluded: chain H residue 401 HIS Chi-restraints excluded: chain H residue 413 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 446 ILE Chi-restraints excluded: chain H residue 479 THR Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 579 SER Chi-restraints excluded: chain H residue 582 LEU Chi-restraints excluded: chain H residue 607 VAL Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 682 MET Chi-restraints excluded: chain H residue 778 LEU Chi-restraints excluded: chain H residue 782 THR Chi-restraints excluded: chain H residue 802 ILE Chi-restraints excluded: chain H residue 857 SER Chi-restraints excluded: chain H residue 885 LEU Chi-restraints excluded: chain H residue 891 GLN Chi-restraints excluded: chain H residue 1025 VAL Chi-restraints excluded: chain H residue 1080 VAL Chi-restraints excluded: chain H residue 1082 SER Chi-restraints excluded: chain H residue 1121 LEU Chi-restraints excluded: chain H residue 1142 LEU Chi-restraints excluded: chain H residue 1183 VAL Chi-restraints excluded: chain H residue 1226 LEU Chi-restraints excluded: chain H residue 1275 LEU Chi-restraints excluded: chain H residue 1284 LEU Chi-restraints excluded: chain H residue 1290 VAL Chi-restraints excluded: chain H residue 1294 LEU Chi-restraints excluded: chain H residue 1297 MET Chi-restraints excluded: chain H residue 1298 VAL Chi-restraints excluded: chain H residue 1301 LEU Chi-restraints excluded: chain H residue 1314 ILE Chi-restraints excluded: chain H residue 1318 LEU Chi-restraints excluded: chain H residue 1402 ILE Chi-restraints excluded: chain H residue 1409 ILE Chi-restraints excluded: chain H residue 1475 THR Chi-restraints excluded: chain H residue 1485 GLN Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 125 HIS Chi-restraints excluded: chain G residue 172 THR Chi-restraints excluded: chain G residue 293 HIS Chi-restraints excluded: chain G residue 369 GLN Chi-restraints excluded: chain G residue 401 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 579 SER Chi-restraints excluded: chain G residue 582 LEU Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 614 LEU Chi-restraints excluded: chain G residue 778 LEU Chi-restraints excluded: chain G residue 782 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 897 ASP Chi-restraints excluded: chain G residue 1020 LEU Chi-restraints excluded: chain G residue 1038 ASP Chi-restraints excluded: chain G residue 1087 TRP Chi-restraints excluded: chain G residue 1121 LEU Chi-restraints excluded: chain G residue 1128 CYS Chi-restraints excluded: chain G residue 1142 LEU Chi-restraints excluded: chain G residue 1183 VAL Chi-restraints excluded: chain G residue 1226 LEU Chi-restraints excluded: chain G residue 1271 LEU Chi-restraints excluded: chain G residue 1275 LEU Chi-restraints excluded: chain G residue 1284 LEU Chi-restraints excluded: chain G residue 1294 LEU Chi-restraints excluded: chain G residue 1301 LEU Chi-restraints excluded: chain G residue 1306 LEU Chi-restraints excluded: chain G residue 1314 ILE Chi-restraints excluded: chain G residue 1368 ILE Chi-restraints excluded: chain G residue 1376 ILE Chi-restraints excluded: chain G residue 1402 ILE Chi-restraints excluded: chain G residue 1409 ILE Chi-restraints excluded: chain G residue 1459 LEU Chi-restraints excluded: chain G residue 1501 ILE Chi-restraints excluded: chain G residue 1503 ILE Chi-restraints excluded: chain G residue 1531 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 293 HIS Chi-restraints excluded: chain F residue 314 PHE Chi-restraints excluded: chain F residue 369 GLN Chi-restraints excluded: chain F residue 401 HIS Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 496 LEU Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 550 ILE Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 577 PHE Chi-restraints excluded: chain F residue 579 SER Chi-restraints excluded: chain F residue 582 LEU Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 703 ILE Chi-restraints excluded: chain F residue 715 VAL Chi-restraints excluded: chain F residue 778 LEU Chi-restraints excluded: chain F residue 843 LEU Chi-restraints excluded: chain F residue 885 LEU Chi-restraints excluded: chain F residue 887 THR Chi-restraints excluded: chain F residue 895 HIS Chi-restraints excluded: chain F residue 1142 LEU Chi-restraints excluded: chain F residue 1183 VAL Chi-restraints excluded: chain F residue 1188 LEU Chi-restraints excluded: chain F residue 1226 LEU Chi-restraints excluded: chain F residue 1275 LEU Chi-restraints excluded: chain F residue 1284 LEU Chi-restraints excluded: chain F residue 1290 VAL Chi-restraints excluded: chain F residue 1294 LEU Chi-restraints excluded: chain F residue 1298 VAL Chi-restraints excluded: chain F residue 1301 LEU Chi-restraints excluded: chain F residue 1314 ILE Chi-restraints excluded: chain F residue 1409 ILE Chi-restraints excluded: chain F residue 1447 ASP Chi-restraints excluded: chain F residue 1475 THR Chi-restraints excluded: chain F residue 1501 ILE Chi-restraints excluded: chain F residue 1503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 405 optimal weight: 0.0270 chunk 544 optimal weight: 0.0060 chunk 156 optimal weight: 4.9990 chunk 471 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 511 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 525 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.0170 overall best weight: 0.3892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 103 HIS ** E1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1426 GLN H 103 HIS ** H 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 888 HIS F1097 HIS ** F1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.203030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.198760 restraints weight = 49208.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.196902 restraints weight = 56460.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.195771 restraints weight = 50264.517| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 50056 Z= 0.179 Angle : 0.669 13.276 68280 Z= 0.326 Chirality : 0.043 0.339 8356 Planarity : 0.005 0.064 8388 Dihedral : 7.809 108.753 7156 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.02 % Allowed : 23.22 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6384 helix: 1.34 (0.08), residues: 3884 sheet: -0.66 (0.23), residues: 492 loop : -1.71 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 430 HIS 0.011 0.001 HIS H 103 PHE 0.072 0.002 PHE E 433 TYR 0.021 0.001 TYR G 123 ARG 0.016 0.001 ARG G 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17387.75 seconds wall clock time: 314 minutes 3.01 seconds (18843.01 seconds total)