Starting phenix.real_space_refine on Sat Feb 24 01:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z30_14469/02_2024/7z30_14469.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z30_14469/02_2024/7z30_14469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z30_14469/02_2024/7z30_14469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z30_14469/02_2024/7z30_14469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z30_14469/02_2024/7z30_14469.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z30_14469/02_2024/7z30_14469.pdb" } resolution = 2.9 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= 0.006 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: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 Mg 2 5.21 5 S 217 5.16 5 C 25784 2.51 5 N 7014 2.21 5 O 7661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 732": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 870": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 965": "OE1" <-> "OE2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A TYR 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1367": "OE1" <-> "OE2" Residue "A GLU 1413": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 742": "OE1" <-> "OE2" Residue "B GLU 786": "OE1" <-> "OE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B GLU 1011": "OE1" <-> "OE2" Residue "B GLU 1064": "OE1" <-> "OE2" Residue "B GLU 1091": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "E GLU 4": "OE1" <-> "OE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "G PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "I GLU 78": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "M GLU 72": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 83": "OE1" <-> "OE2" Residue "M GLU 103": "OE1" <-> "OE2" Residue "M GLU 174": "OE1" <-> "OE2" Residue "M ARG 226": "NH1" <-> "NH2" Residue "M GLU 240": "OE1" <-> "OE2" Residue "M GLU 253": "OE1" <-> "OE2" Residue "M GLU 262": "OE1" <-> "OE2" Residue "M GLU 272": "OE1" <-> "OE2" Residue "N GLU 225": "OE1" <-> "OE2" Residue "N GLU 279": "OE1" <-> "OE2" Residue "N GLU 281": "OE1" <-> "OE2" Residue "N GLU 302": "OE1" <-> "OE2" Residue "N GLU 387": "OE1" <-> "OE2" Residue "O GLU 78": "OE1" <-> "OE2" Residue "O GLU 81": "OE1" <-> "OE2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O GLU 258": "OE1" <-> "OE2" Residue "O GLU 570": "OE1" <-> "OE2" Residue "O GLU 582": "OE1" <-> "OE2" Residue "O GLU 593": "OE1" <-> "OE2" Residue "O GLU 598": "OE1" <-> "OE2" Residue "O GLU 623": "OE1" <-> "OE2" Residue "O GLU 649": "OE1" <-> "OE2" Residue "P GLU 254": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q GLU 51": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40685 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 11123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1419, 11123 Classifications: {'peptide': 1419} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1354} Chain breaks: 3 Chain: "B" Number of atoms: 8701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8701 Classifications: {'peptide': 1102} Link IDs: {'PTRANS': 41, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2655 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 20, 'TRANS': 314} Chain: "D" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1140 Classifications: {'peptide': 145} Incomplete info: {'backbone_only': 11} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1544 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 12, 'TRANS': 178} Chain breaks: 2 Chain: "H" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 549 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 381 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 49} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1492 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 1 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4558 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Chain: "P" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 829 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 8, 'TRANS': 95} Chain breaks: 1 Chain: "W" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 141 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "X" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 492 SG CYS A 67 101.609 117.559 91.454 1.00 90.27 S ATOM 510 SG CYS A 70 99.873 120.622 90.485 1.00 68.08 S ATOM 557 SG CYS A 77 98.898 117.347 91.792 1.00 66.90 S ATOM 795 SG CYS A 107 71.556 94.916 59.682 1.00 91.82 S ATOM 818 SG CYS A 110 71.804 96.359 57.066 1.00 92.83 S ATOM 1184 SG CYS A 154 68.266 96.077 58.181 1.00 92.75 S ATOM 1208 SG CYS A 157 71.776 94.326 56.072 1.00 98.41 S ATOM 19397 SG CYS B1095 85.639 125.393 81.376 1.00 58.28 S ATOM 19420 SG CYS B1098 85.522 121.914 80.112 1.00 57.41 S ATOM 19486 SG CYS B1107 88.361 123.073 80.827 1.00 60.48 S ATOM 19506 SG CYS B1110 88.044 124.993 78.390 1.00 76.25 S ATOM 28735 SG CYS I 5 58.306 36.244 89.124 1.00 78.08 S ATOM 28754 SG CYS I 8 62.061 38.776 88.906 1.00 74.00 S ATOM 28882 SG CYS I 26 59.260 39.580 87.475 1.00 78.20 S ATOM 28905 SG CYS I 29 60.250 37.307 86.657 1.00 82.87 S ATOM 29232 SG CYS I 69 43.006 100.683 129.748 1.00 61.10 S ATOM 29280 SG CYS I 75 39.721 100.316 128.108 1.00 55.27 S ATOM 29482 SG CYS I 100 42.286 97.282 129.296 1.00 53.58 S ATOM 29503 SG CYS I 103 41.830 99.021 126.288 1.00 53.02 S ATOM 29622 SG CYS J 7 87.874 99.702 157.499 1.00 29.32 S ATOM 29645 SG CYS J 10 85.774 101.610 160.052 1.00 42.13 S ATOM 29925 SG CYS J 45 85.105 99.698 159.125 1.00 21.16 S ATOM 29931 SG CYS J 46 87.697 99.137 161.540 1.00 23.43 S ATOM 30982 SG CYS L 31 121.629 86.164 134.581 1.00 54.08 S ATOM 31002 SG CYS L 34 123.592 85.793 136.764 1.00 64.22 S ATOM 31106 SG CYS L 48 125.099 86.550 133.931 1.00 56.30 S ATOM 31129 SG CYS L 51 123.662 82.779 134.645 1.00 65.72 S Time building chain proxies: 21.74, per 1000 atoms: 0.53 Number of scatterers: 40685 At special positions: 0 Unit cell: (138.86, 192.92, 199.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 217 16.00 Mg 2 11.99 O 7661 8.00 N 7014 7.00 C 25784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 16.27 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 67 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 157 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 154 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1107 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1095 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1110 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1098 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb=" ZN I 203 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 69 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 203 " - pdb=" SG CYS I 100 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 46 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 39 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9656 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 46 sheets defined 41.1% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 22 through 29 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.788A pdb=" N ARG A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 191 through 206 Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.349A pdb=" N TYR A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.338A pdb=" N GLU A 240 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 241 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 283 through 304 removed outlier: 3.596A pdb=" N ASP A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 412 through 423 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.884A pdb=" N LEU A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 504 through 509 removed outlier: 4.148A pdb=" N TYR A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.100A pdb=" N LEU A 541 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.480A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 720 through 748 removed outlier: 3.614A pdb=" N GLN A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 784 removed outlier: 3.880A pdb=" N LEU A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 Processing helix chain 'A' and resid 802 through 811 Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.696A pdb=" N GLY A 846 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 874 through 894 removed outlier: 4.333A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 922 through 926 removed outlier: 3.715A pdb=" N MET A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 955 through 967 removed outlier: 3.689A pdb=" N MET A 960 " --> pdb=" O PRO A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 973 Processing helix chain 'A' and resid 998 through 1026 Processing helix chain 'A' and resid 1037 through 1042 removed outlier: 4.612A pdb=" N GLY A1041 " --> pdb=" O GLU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1060 Processing helix chain 'A' and resid 1063 through 1081 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1100 through 1103 Processing helix chain 'A' and resid 1122 through 1132 Processing helix chain 'A' and resid 1153 through 1161 removed outlier: 4.157A pdb=" N VAL A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1171 removed outlier: 4.548A pdb=" N PHE A1171 " --> pdb=" O SER A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1196 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1254 through 1267 Processing helix chain 'A' and resid 1268 through 1270 No H-bonds generated for 'chain 'A' and resid 1268 through 1270' Processing helix chain 'A' and resid 1299 through 1306 removed outlier: 3.813A pdb=" N VAL A1303 " --> pdb=" O GLY A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1345 Processing helix chain 'A' and resid 1351 through 1364 removed outlier: 3.965A pdb=" N ILE A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1377 removed outlier: 3.601A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1423 through 1427 Processing helix chain 'A' and resid 1447 through 1456 removed outlier: 3.712A pdb=" N ALA A1456 " --> pdb=" O SER A1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.889A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 80 removed outlier: 5.025A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 266 through 274 Processing helix chain 'B' and resid 276 through 294 removed outlier: 3.772A pdb=" N GLN B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 321 through 322 No H-bonds generated for 'chain 'B' and resid 321 through 322' Processing helix chain 'B' and resid 323 through 331 removed outlier: 3.716A pdb=" N ILE B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 362 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 379 through 408 Processing helix chain 'B' and resid 419 through 426 Processing helix chain 'B' and resid 426 through 440 removed outlier: 3.815A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.605A pdb=" N ARG B 487 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.614A pdb=" N SER B 548 " --> pdb=" O ASP B 545 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N HIS B 550 " --> pdb=" O ALA B 547 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN B 552 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 581 Processing helix chain 'B' and resid 624 through 633 Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.762A pdb=" N PHE B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 removed outlier: 3.952A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 Processing helix chain 'B' and resid 684 through 688 Processing helix chain 'B' and resid 690 through 694 Processing helix chain 'B' and resid 695 through 706 removed outlier: 3.519A pdb=" N ASN B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 removed outlier: 3.786A pdb=" N GLU B 742 " --> pdb=" O THR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 822 Processing helix chain 'B' and resid 927 through 931 Processing helix chain 'B' and resid 947 through 953 removed outlier: 4.704A pdb=" N SER B 951 " --> pdb=" O HIS B 947 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 971 removed outlier: 3.725A pdb=" N MET B 958 " --> pdb=" O THR B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1075 through 1084 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 60 through 74 Processing helix chain 'C' and resid 93 through 104 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.040A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.712A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 309 through 331 Processing helix chain 'D' and resid 14 through 27 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.894A pdb=" N VAL D 63 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 119 through 124 removed outlier: 4.364A pdb=" N ILE D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 151 through 158 Processing helix chain 'E' and resid 2 through 26 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.763A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.089A pdb=" N HIS G 19 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.639A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 51 through 54 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.607A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 142 Processing helix chain 'M' and resid 132 through 140 Processing helix chain 'M' and resid 183 through 195 Processing helix chain 'M' and resid 229 through 240 Processing helix chain 'M' and resid 252 through 265 Processing helix chain 'M' and resid 273 through 281 removed outlier: 3.827A pdb=" N ASP M 279 " --> pdb=" O GLU M 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 210 No H-bonds generated for 'chain 'N' and resid 208 through 210' Processing helix chain 'N' and resid 211 through 223 removed outlier: 3.538A pdb=" N VAL N 215 " --> pdb=" O ASP N 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG N 217 " --> pdb=" O GLU N 213 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLU N 221 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 297 Processing helix chain 'N' and resid 367 through 369 No H-bonds generated for 'chain 'N' and resid 367 through 369' Processing helix chain 'O' and resid 43 through 57 removed outlier: 3.751A pdb=" N TYR O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 71 Processing helix chain 'O' and resid 75 through 83 Processing helix chain 'O' and resid 87 through 101 Processing helix chain 'O' and resid 126 through 132 removed outlier: 4.250A pdb=" N LEU O 130 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.729A pdb=" N MET O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 167 Processing helix chain 'O' and resid 171 through 178 removed outlier: 4.103A pdb=" N SER O 176 " --> pdb=" O GLU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 197 removed outlier: 3.596A pdb=" N THR O 186 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE O 187 " --> pdb=" O MET O 183 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN O 193 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 208 Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.900A pdb=" N LYS O 221 " --> pdb=" O PHE O 217 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 260 through 265 removed outlier: 4.456A pdb=" N VAL O 265 " --> pdb=" O GLN O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 304 Processing helix chain 'O' and resid 305 through 316 removed outlier: 4.416A pdb=" N VAL O 311 " --> pdb=" O VAL O 307 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR O 312 " --> pdb=" O THR O 308 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE O 314 " --> pdb=" O GLN O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 323 removed outlier: 4.351A pdb=" N GLU O 320 " --> pdb=" O ARG O 317 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN O 321 " --> pdb=" O LEU O 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 356 Processing helix chain 'O' and resid 362 through 368 removed outlier: 3.758A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 449 through 463 Processing helix chain 'O' and resid 483 through 500 Processing helix chain 'O' and resid 501 through 514 Processing helix chain 'O' and resid 520 through 527 Processing helix chain 'O' and resid 529 through 542 removed outlier: 4.035A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) Processing helix chain 'O' and resid 569 through 599 removed outlier: 3.928A pdb=" N SER O 573 " --> pdb=" O LYS O 569 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG O 578 " --> pdb=" O TYR O 574 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 620 through 645 Processing helix chain 'O' and resid 646 through 647 No H-bonds generated for 'chain 'O' and resid 646 through 647' Processing helix chain 'O' and resid 648 through 652 Processing helix chain 'P' and resid 171 through 190 removed outlier: 3.626A pdb=" N SER P 177 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG P 184 " --> pdb=" O THR P 180 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE P 185 " --> pdb=" O ILE P 181 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE P 186 " --> pdb=" O VAL P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 199 Processing helix chain 'P' and resid 201 through 205 removed outlier: 4.130A pdb=" N ASN P 205 " --> pdb=" O PRO P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 228 Processing helix chain 'P' and resid 236 through 247 Processing helix chain 'P' and resid 265 through 271 Processing helix chain 'Q' and resid 48 through 68 removed outlier: 4.491A pdb=" N GLY Q 62 " --> pdb=" O TYR Q 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 111 Processing helix chain 'Q' and resid 128 through 132 Processing helix chain 'Q' and resid 133 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 17 removed outlier: 6.869A pdb=" N ARG B1142 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 16 " --> pdb=" O ARG B1140 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG B1140 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 33 removed outlier: 7.778A pdb=" N HIS A 83 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LYS A 85 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 11.864A pdb=" N LEU A 86 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 11.795A pdb=" N LEU A 88 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N TYR A 260 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 107 removed outlier: 3.638A pdb=" N ALA A 112 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.884A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.919A pdb=" N LEU B1060 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.578A pdb=" N THR A 379 " --> pdb=" O MET A 517 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL A 392 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG A 493 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL A 394 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE A 498 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 380 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A 500 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER A 382 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.651A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'A' and resid 597 through 599 removed outlier: 5.952A pdb=" N VAL H 96 " --> pdb=" O MET A 598 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 626 through 629 removed outlier: 6.163A pdb=" N ILE A 653 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 817 through 818 Processing sheet with id=AB3, first strand: chain 'A' and resid 897 through 898 removed outlier: 6.839A pdb=" N VAL A 904 " --> pdb=" O VAL A 912 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1278 through 1285 removed outlier: 4.433A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ARG A1291 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU A1145 " --> pdb=" O ARG A1291 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A1144 " --> pdb=" O ARG A1313 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A1313 " --> pdb=" O VAL A1144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1176 through 1177 Processing sheet with id=AB6, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AB7, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.323A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 100 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 378 Processing sheet with id=AC1, first strand: chain 'B' and resid 220 through 222 Processing sheet with id=AC2, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AC3, first strand: chain 'B' and resid 442 through 444 removed outlier: 3.911A pdb=" N ARG B 451 " --> pdb=" O TRP B 442 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 444 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 449 " --> pdb=" O LEU B 444 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 619 through 620 current: chain 'B' and resid 672 through 673 Processing sheet with id=AC5, first strand: chain 'B' and resid 539 through 540 removed outlier: 5.546A pdb=" N LEU B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 557 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 563 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR B 553 " --> pdb=" O ILE B 565 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 725 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 785 through 795 current: chain 'B' and resid 879 through 888 removed outlier: 7.920A pdb=" N SER B 879 " --> pdb=" O ASN B 903 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN B 903 " --> pdb=" O SER B 879 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 883 " --> pdb=" O LEU B 899 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 894 through 904 current: chain 'L' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AC8, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 6.845A pdb=" N LEU B 771 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE B 925 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 773 " --> pdb=" O ILE B 925 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE B 942 " --> pdb=" O ASN B 754 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B 756 " --> pdb=" O ILE B 942 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET B 944 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 758 " --> pdb=" O MET B 944 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 841 through 843 removed outlier: 3.810A pdb=" N ILE B 843 " --> pdb=" O VAL B 871 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 846 through 848 Processing sheet with id=AD2, first strand: chain 'B' and resid 1101 through 1102 removed outlier: 4.051A pdb=" N ASP B1093 " --> pdb=" O GLY B1102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 13 current: chain 'C' and resid 51 through 57 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 57 current: chain 'C' and resid 289 through 304 Processing sheet with id=AD4, first strand: chain 'C' and resid 167 through 169 removed outlier: 7.199A pdb=" N LYS C 205 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE C 85 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N HIS C 207 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL C 83 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 209 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU C 81 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY C 211 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA C 79 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AD6, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AD8, first strand: chain 'D' and resid 3 through 5 removed outlier: 7.285A pdb=" N LYS G 6 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN G 69 " --> pdb=" O VAL G 54 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL G 54 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL G 75 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE G 48 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.491A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.590A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 15 through 16 removed outlier: 4.413A pdb=" N TYR I 31 " --> pdb=" O CYS I 26 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 80 through 85 Processing sheet with id=AE5, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.516A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 72 through 78 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 72 through 78 current: chain 'M' and resid 118 through 124 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 145 through 153 current: chain 'M' and resid 168 through 172 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 168 through 172 current: chain 'N' and resid 371 through 374 removed outlier: 6.137A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 380 through 383 current: chain 'N' and resid 404 through 420 Processing sheet with id=AE7, first strand: chain 'O' and resid 106 through 109 removed outlier: 4.324A pdb=" N GLU O 109 " --> pdb=" O THR O 117 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR O 117 " --> pdb=" O GLU O 109 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 168 through 170 removed outlier: 3.747A pdb=" N THR O 281 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 469 through 472 removed outlier: 4.085A pdb=" N THR O 471 " --> pdb=" O VAL O 475 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL O 475 " --> pdb=" O THR O 471 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 547 through 548 1558 hydrogen bonds defined for protein. 4317 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: 17.03 Time building geometry restraints manager: 17.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12638 1.34 - 1.46: 7254 1.46 - 1.58: 21168 1.58 - 1.70: 1 1.70 - 1.82: 352 Bond restraints: 41413 Sorted by residual: bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.73e+01 bond pdb=" N VAL B 233 " pdb=" CA VAL B 233 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N LEU C 120 " pdb=" CA LEU C 120 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.11e-02 8.12e+03 1.10e+01 bond pdb=" C TYR B 690 " pdb=" O TYR B 690 " ideal model delta sigma weight residual 1.235 1.221 0.014 4.70e-03 4.53e+04 9.34e+00 bond pdb=" N ILE B 234 " pdb=" CA ILE B 234 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.12e+00 ... (remaining 41408 not shown) Histogram of bond angle deviations from ideal: 97.35 - 104.70: 692 104.70 - 112.04: 20126 112.04 - 119.39: 14634 119.39 - 126.74: 20017 126.74 - 134.09: 439 Bond angle restraints: 55908 Sorted by residual: angle pdb=" N ILE A1371 " pdb=" CA ILE A1371 " pdb=" C ILE A1371 " ideal model delta sigma weight residual 112.17 105.99 6.18 9.50e-01 1.11e+00 4.24e+01 angle pdb=" N VAL G 42 " pdb=" CA VAL G 42 " pdb=" C VAL G 42 " ideal model delta sigma weight residual 113.71 108.15 5.56 9.50e-01 1.11e+00 3.43e+01 angle pdb=" N VAL L 46 " pdb=" CA VAL L 46 " pdb=" C VAL L 46 " ideal model delta sigma weight residual 113.20 108.60 4.60 9.60e-01 1.09e+00 2.29e+01 angle pdb=" CA VAL A 873 " pdb=" C VAL A 873 " pdb=" O VAL A 873 " ideal model delta sigma weight residual 122.13 117.42 4.71 1.11e+00 8.12e-01 1.80e+01 angle pdb=" N ASP A 513 " pdb=" CA ASP A 513 " pdb=" C ASP A 513 " ideal model delta sigma weight residual 112.41 107.27 5.14 1.30e+00 5.92e-01 1.56e+01 ... (remaining 55903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 21397 17.93 - 35.86: 2921 35.86 - 53.79: 844 53.79 - 71.72: 174 71.72 - 89.65: 63 Dihedral angle restraints: 25399 sinusoidal: 10470 harmonic: 14929 Sorted by residual: dihedral pdb=" CD ARG C 174 " pdb=" NE ARG C 174 " pdb=" CZ ARG C 174 " pdb=" NH1 ARG C 174 " ideal model delta sinusoidal sigma weight residual 0.00 86.59 -86.59 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CD ARG A 869 " pdb=" NE ARG A 869 " pdb=" CZ ARG A 869 " pdb=" NH1 ARG A 869 " ideal model delta sinusoidal sigma weight residual 0.00 -62.22 62.22 1 1.00e+01 1.00e-02 5.13e+01 dihedral pdb=" CD ARG M 226 " pdb=" NE ARG M 226 " pdb=" CZ ARG M 226 " pdb=" NH1 ARG M 226 " ideal model delta sinusoidal sigma weight residual 0.00 53.15 -53.15 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 25396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5313 0.064 - 0.128: 907 0.128 - 0.193: 65 0.193 - 0.257: 7 0.257 - 0.321: 2 Chirality restraints: 6294 Sorted by residual: chirality pdb=" CB ILE E 127 " pdb=" CA ILE E 127 " pdb=" CG1 ILE E 127 " pdb=" CG2 ILE E 127 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE A 350 " pdb=" CA ILE A 350 " pdb=" CG1 ILE A 350 " pdb=" CG2 ILE A 350 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CG LEU O 589 " pdb=" CB LEU O 589 " pdb=" CD1 LEU O 589 " pdb=" CD2 LEU O 589 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 6291 not shown) Planarity restraints: 7205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 174 " -1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG C 174 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 174 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 174 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG C 174 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 869 " -0.968 9.50e-02 1.11e+02 4.34e-01 1.14e+02 pdb=" NE ARG A 869 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 869 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 869 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 869 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 226 " 0.874 9.50e-02 1.11e+02 3.92e-01 9.32e+01 pdb=" NE ARG M 226 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG M 226 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG M 226 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG M 226 " 0.024 2.00e-02 2.50e+03 ... (remaining 7202 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 246 2.51 - 3.10: 29629 3.10 - 3.70: 65173 3.70 - 4.30: 93949 4.30 - 4.90: 152311 Nonbonded interactions: 341308 Sorted by model distance: nonbonded pdb=" OD2 ASP A 513 " pdb="MG MG I 201 " model vdw 1.908 2.170 nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A1503 " model vdw 2.017 2.170 nonbonded pdb=" O UNK X1008 " pdb=" N UNK X1010 " model vdw 2.035 2.520 nonbonded pdb=" O LEU B 271 " pdb=" NE2 HIS B 550 " model vdw 2.198 2.520 nonbonded pdb=" O LEU A 613 " pdb=" NH1 ARG A 696 " model vdw 2.199 2.520 ... (remaining 341303 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.370 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: 0.030 Extract box with map and model: 8.260 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 113.540 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.150 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.004 0.093 41413 Z= 0.261 Angle : 0.734 10.606 55908 Z= 0.423 Chirality : 0.047 0.321 6294 Planarity : 0.011 0.492 7205 Dihedral : 18.287 89.648 15743 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.80 % Allowed : 29.21 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -1.03 (0.11), residues: 5039 helix: 0.18 (0.12), residues: 1805 sheet: -0.70 (0.21), residues: 609 loop : -1.29 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 79 HIS 0.008 0.001 HIS A 427 PHE 0.021 0.002 PHE P 224 TYR 0.023 0.002 TYR A 943 ARG 0.012 0.001 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 566 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.3057 (OUTLIER) cc_final: 0.2761 (ptm) REVERT: A 325 MET cc_start: 0.4932 (pmm) cc_final: 0.4126 (mpp) REVERT: A 739 ASP cc_start: 0.8075 (p0) cc_final: 0.7856 (p0) REVERT: A 884 TYR cc_start: 0.4670 (t80) cc_final: 0.3887 (t80) REVERT: A 890 MET cc_start: 0.8579 (tpp) cc_final: 0.8248 (tpp) REVERT: A 1060 TYR cc_start: 0.7626 (m-80) cc_final: 0.7425 (m-80) REVERT: A 1343 MET cc_start: 0.8436 (ptp) cc_final: 0.7930 (ptp) REVERT: B 269 MET cc_start: 0.7823 (ttp) cc_final: 0.7556 (tmm) REVERT: B 289 GLU cc_start: 0.6499 (pp20) cc_final: 0.6226 (tm-30) REVERT: B 393 LYS cc_start: 0.6936 (mttt) cc_final: 0.6717 (mtpt) REVERT: B 638 ASP cc_start: 0.7268 (m-30) cc_final: 0.6725 (m-30) REVERT: B 1054 ARG cc_start: 0.6822 (ttt90) cc_final: 0.6271 (ptp-110) REVERT: B 1114 GLU cc_start: 0.6912 (tp30) cc_final: 0.6517 (tp30) REVERT: B 1120 THR cc_start: 0.8998 (t) cc_final: 0.8745 (m) REVERT: C 145 ASP cc_start: 0.5499 (OUTLIER) cc_final: 0.4628 (p0) REVERT: C 150 SER cc_start: 0.4114 (OUTLIER) cc_final: 0.3577 (m) REVERT: C 151 THR cc_start: 0.5196 (OUTLIER) cc_final: 0.4990 (m) REVERT: E 56 LYS cc_start: 0.6566 (mmmm) cc_final: 0.5948 (mmtt) REVERT: E 58 MET cc_start: 0.6781 (ptp) cc_final: 0.6578 (ptp) REVERT: E 121 MET cc_start: 0.4376 (ppp) cc_final: 0.3682 (tpp) REVERT: G 56 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7605 (mm-30) REVERT: H 77 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6668 (mmp-170) REVERT: N 374 LYS cc_start: 0.7299 (ttmp) cc_final: 0.6958 (tttm) REVERT: N 387 GLU cc_start: 0.5509 (pm20) cc_final: 0.4329 (mm-30) REVERT: O 528 MET cc_start: 0.3285 (mpp) cc_final: 0.3045 (mpp) REVERT: O 577 MET cc_start: 0.5527 (mmm) cc_final: 0.5275 (mmm) outliers start: 126 outliers final: 58 residues processed: 661 average time/residue: 1.4586 time to fit residues: 1183.5781 Evaluate side-chains 568 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 505 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1282 VAL Chi-restraints excluded: chain A residue 1312 SER Chi-restraints excluded: chain A residue 1395 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 669 SER Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 182 CYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 304 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 279 SER Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 THR Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain Q residue 121 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 204 optimal weight: 0.2980 chunk 395 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 458 optimal weight: 0.0570 overall best weight: 2.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 455 ASN A 619 ASN ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A 948 ASN A1356 GLN A1395 HIS A1453 ASN ** B 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN B 423 ASN B 519 HIS B 695 GLN ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1149 GLN C 58 ASN C 87 ASN C 143 ASN C 172 GLN D 8 ASN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 71 ASN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 115 ASN E 136 ASN E 179 GLN G 32 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 83 GLN H 137 GLN I 71 ASN L 66 GLN ** M 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 178 GLN M 190 ASN M 225 ASN N 377 ASN N 392 GLN O 295 GLN O 298 ASN O 310 GLN O 549 GLN O 579 GLN P 176 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 41413 Z= 0.234 Angle : 0.607 9.015 55908 Z= 0.315 Chirality : 0.045 0.241 6294 Planarity : 0.005 0.106 7205 Dihedral : 6.159 76.663 5657 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 5.26 % Allowed : 26.06 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.82 (0.12), residues: 5039 helix: 0.40 (0.12), residues: 1845 sheet: -0.61 (0.21), residues: 597 loop : -1.22 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 201 HIS 0.008 0.001 HIS A 427 PHE 0.022 0.002 PHE E 60 TYR 0.026 0.002 TYR O 494 ARG 0.007 0.000 ARG C 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 548 time to evaluate : 5.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.4306 (OUTLIER) cc_final: 0.3668 (ptm) REVERT: A 1060 TYR cc_start: 0.7501 (m-80) cc_final: 0.7254 (m-80) REVERT: A 1065 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8075 (ttmm) REVERT: A 1187 ARG cc_start: 0.6035 (tmt170) cc_final: 0.5383 (tmt-80) REVERT: A 1190 LEU cc_start: 0.6618 (mt) cc_final: 0.5702 (pt) REVERT: B 249 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: B 299 GLN cc_start: 0.5988 (OUTLIER) cc_final: 0.5759 (pt0) REVERT: B 389 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: B 393 LYS cc_start: 0.6913 (mttt) cc_final: 0.6641 (mtpt) REVERT: B 989 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8377 (ttpt) REVERT: B 1114 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: C 37 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8353 (tppt) REVERT: C 245 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7571 (mpt180) REVERT: D 153 MET cc_start: 0.2421 (mmt) cc_final: 0.1317 (mtp) REVERT: E 96 PHE cc_start: 0.5284 (t80) cc_final: 0.5054 (t80) REVERT: E 121 MET cc_start: 0.4361 (ppp) cc_final: 0.3614 (tmt) REVERT: G 20 ARG cc_start: 0.7430 (mtp85) cc_final: 0.6695 (mtp85) REVERT: G 46 ILE cc_start: 0.7077 (mp) cc_final: 0.6840 (mm) REVERT: G 58 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: G 73 ARG cc_start: 0.7333 (mtm180) cc_final: 0.7075 (mtm180) REVERT: G 124 GLU cc_start: 0.3877 (pp20) cc_final: 0.2835 (tt0) REVERT: H 35 GLN cc_start: 0.6856 (mt0) cc_final: 0.6605 (mp10) REVERT: H 77 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6630 (mmp-170) REVERT: I 60 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7194 (t0) REVERT: J 32 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7522 (mt-10) REVERT: K 100 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8422 (mp) REVERT: K 129 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: M 112 TYR cc_start: 0.6515 (t80) cc_final: 0.5784 (t80) REVERT: N 302 GLU cc_start: 0.4624 (tp30) cc_final: 0.4354 (tt0) REVERT: N 387 GLU cc_start: 0.5503 (pm20) cc_final: 0.4642 (mm-30) REVERT: N 407 GLU cc_start: 0.5049 (mp0) cc_final: 0.4663 (tt0) REVERT: O 224 LYS cc_start: 0.3548 (ttpt) cc_final: 0.3088 (mttt) REVERT: O 577 MET cc_start: 0.6054 (mmm) cc_final: 0.5709 (mmm) outliers start: 237 outliers final: 86 residues processed: 716 average time/residue: 1.5036 time to fit residues: 1320.9914 Evaluate side-chains 598 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 497 time to evaluate : 4.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 32 GLU Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 370 LYS Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain Q residue 121 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 254 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 381 optimal weight: 0.0370 chunk 312 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 459 optimal weight: 30.0000 chunk 496 optimal weight: 9.9990 chunk 409 optimal weight: 0.0570 chunk 455 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN L 66 GLN N 377 ASN ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN O 549 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 41413 Z= 0.185 Angle : 0.561 9.148 55908 Z= 0.290 Chirality : 0.043 0.239 6294 Planarity : 0.004 0.103 7205 Dihedral : 5.215 55.159 5598 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 5.15 % Allowed : 26.68 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.63 (0.12), residues: 5039 helix: 0.65 (0.12), residues: 1841 sheet: -0.61 (0.21), residues: 612 loop : -1.15 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 201 HIS 0.006 0.001 HIS A 427 PHE 0.020 0.001 PHE P 224 TYR 0.027 0.001 TYR O 494 ARG 0.009 0.000 ARG H 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 552 time to evaluate : 5.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.4171 (OUTLIER) cc_final: 0.3528 (ptm) REVERT: A 269 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7074 (ppt170) REVERT: A 312 MET cc_start: 0.4554 (pp-130) cc_final: 0.3520 (ttt) REVERT: A 313 MET cc_start: 0.6716 (tpp) cc_final: 0.6413 (tpp) REVERT: A 739 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7747 (p0) REVERT: A 870 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7458 (pp20) REVERT: A 890 MET cc_start: 0.8729 (tpp) cc_final: 0.8256 (tpp) REVERT: A 931 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7844 (mp10) REVERT: A 1060 TYR cc_start: 0.7581 (m-80) cc_final: 0.7250 (m-80) REVERT: A 1190 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6446 (mp) REVERT: A 1287 ASP cc_start: 0.3743 (OUTLIER) cc_final: 0.2804 (m-30) REVERT: B 75 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7734 (mttm) REVERT: B 204 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7614 (tpp-160) REVERT: B 217 GLN cc_start: 0.6093 (OUTLIER) cc_final: 0.5755 (pt0) REVERT: B 249 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6751 (pt0) REVERT: B 299 GLN cc_start: 0.5912 (OUTLIER) cc_final: 0.5711 (pt0) REVERT: B 389 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: B 393 LYS cc_start: 0.6810 (mttt) cc_final: 0.6572 (mtpt) REVERT: B 1054 ARG cc_start: 0.6796 (ttt90) cc_final: 0.6119 (ptp-110) REVERT: B 1084 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8356 (ttp) REVERT: B 1114 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6342 (tp30) REVERT: C 37 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8284 (tppt) REVERT: C 112 MET cc_start: 0.8014 (mtp) cc_final: 0.7636 (mtp) REVERT: C 245 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7575 (mpt180) REVERT: D 52 HIS cc_start: 0.2471 (m-70) cc_final: 0.2231 (m170) REVERT: E 121 MET cc_start: 0.4260 (ppp) cc_final: 0.3570 (tmt) REVERT: G 20 ARG cc_start: 0.7429 (mtp85) cc_final: 0.6725 (mtp85) REVERT: G 58 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: G 114 MET cc_start: 0.3068 (OUTLIER) cc_final: 0.2741 (pp-130) REVERT: G 124 GLU cc_start: 0.3946 (pp20) cc_final: 0.2947 (tt0) REVERT: H 77 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6537 (mmp-170) REVERT: I 10 ASN cc_start: 0.7416 (m-40) cc_final: 0.7122 (m-40) REVERT: I 32 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: I 60 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7261 (t0) REVERT: J 19 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: K 100 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8361 (mp) REVERT: M 112 TYR cc_start: 0.6368 (t80) cc_final: 0.5682 (t80) REVERT: M 240 GLU cc_start: 0.4300 (OUTLIER) cc_final: 0.4035 (tm-30) REVERT: M 272 GLU cc_start: 0.2835 (OUTLIER) cc_final: 0.2374 (tt0) REVERT: N 387 GLU cc_start: 0.5475 (pm20) cc_final: 0.4676 (mm-30) REVERT: O 117 THR cc_start: 0.3608 (OUTLIER) cc_final: 0.3295 (m) REVERT: O 224 LYS cc_start: 0.3561 (ttpt) cc_final: 0.3105 (mttt) REVERT: O 288 MET cc_start: 0.3896 (ppp) cc_final: 0.3661 (ppp) REVERT: O 627 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3969 (mp) outliers start: 232 outliers final: 88 residues processed: 717 average time/residue: 1.4554 time to fit residues: 1293.7693 Evaluate side-chains 627 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 511 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 5.9990 chunk 345 optimal weight: 0.0770 chunk 238 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 461 optimal weight: 9.9990 chunk 488 optimal weight: 20.0000 chunk 240 optimal weight: 0.9990 chunk 436 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 HIS C 161 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN L 66 GLN M 86 HIS M 92 ASN M 144 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN N 392 GLN O 298 ASN Q 60 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 41413 Z= 0.348 Angle : 0.653 10.866 55908 Z= 0.338 Chirality : 0.047 0.260 6294 Planarity : 0.005 0.098 7205 Dihedral : 5.558 53.518 5591 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.85 % Favored : 94.07 % Rotamer: Outliers : 6.81 % Allowed : 25.73 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.84 (0.12), residues: 5039 helix: 0.44 (0.12), residues: 1846 sheet: -0.71 (0.21), residues: 604 loop : -1.25 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 201 HIS 0.010 0.001 HIS A 427 PHE 0.027 0.002 PHE N 390 TYR 0.028 0.002 TYR O 494 ARG 0.006 0.001 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 540 time to evaluate : 4.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.3412 (OUTLIER) cc_final: 0.2991 (mpt180) REVERT: A 269 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.5488 (ppt-90) REVERT: A 517 MET cc_start: 0.9285 (mtp) cc_final: 0.9055 (mtm) REVERT: A 739 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7748 (p0) REVERT: A 890 MET cc_start: 0.8765 (tpp) cc_final: 0.8372 (tpp) REVERT: A 991 LYS cc_start: 0.5727 (OUTLIER) cc_final: 0.5461 (tptt) REVERT: A 1065 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8026 (ttmm) REVERT: A 1174 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.5597 (mt0) REVERT: A 1187 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5561 (ttt90) REVERT: A 1190 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6675 (mp) REVERT: A 1204 ASP cc_start: 0.5660 (OUTLIER) cc_final: 0.5383 (p0) REVERT: A 1287 ASP cc_start: 0.3976 (OUTLIER) cc_final: 0.3124 (m-30) REVERT: A 1373 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6477 (ptp90) REVERT: B 72 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7236 (m-30) REVERT: B 204 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7902 (tpp-160) REVERT: B 394 LYS cc_start: 0.7310 (mttt) cc_final: 0.6977 (mmtt) REVERT: B 719 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8299 (mmmt) REVERT: B 989 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8387 (ttpt) REVERT: B 1054 ARG cc_start: 0.6850 (ttt90) cc_final: 0.6145 (ptp-110) REVERT: B 1114 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6344 (tp30) REVERT: B 1142 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7160 (mmt180) REVERT: C 37 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8263 (tppt) REVERT: C 145 ASP cc_start: 0.5842 (OUTLIER) cc_final: 0.4939 (p0) REVERT: C 245 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7592 (mpt180) REVERT: C 319 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8100 (tpp-160) REVERT: D 98 MET cc_start: 0.2471 (OUTLIER) cc_final: 0.2248 (mpp) REVERT: D 150 ILE cc_start: 0.3286 (OUTLIER) cc_final: 0.3047 (mp) REVERT: D 153 MET cc_start: 0.2403 (mmt) cc_final: 0.1292 (mtp) REVERT: E 101 GLN cc_start: 0.5765 (OUTLIER) cc_final: 0.5424 (pt0) REVERT: E 121 MET cc_start: 0.4274 (ppp) cc_final: 0.3541 (tmt) REVERT: G 20 ARG cc_start: 0.7538 (mtp85) cc_final: 0.6805 (mtp85) REVERT: G 44 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6997 (tp) REVERT: G 58 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: G 110 ILE cc_start: 0.2472 (OUTLIER) cc_final: 0.2024 (pp) REVERT: G 114 MET cc_start: 0.3411 (OUTLIER) cc_final: 0.3067 (pp-130) REVERT: G 124 GLU cc_start: 0.4080 (pp20) cc_final: 0.3085 (tt0) REVERT: H 35 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6373 (mt0) REVERT: I 10 ASN cc_start: 0.7625 (m-40) cc_final: 0.7389 (m-40) REVERT: I 32 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6467 (tt0) REVERT: I 44 LYS cc_start: 0.6547 (pptt) cc_final: 0.6321 (ptpt) REVERT: I 60 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7263 (t0) REVERT: I 106 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7071 (mmm160) REVERT: J 19 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7572 (mt-10) REVERT: K 100 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8461 (mp) REVERT: L 57 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8832 (mt) REVERT: M 112 TYR cc_start: 0.6337 (t80) cc_final: 0.5515 (t80) REVERT: M 174 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.5322 (tm-30) REVERT: M 240 GLU cc_start: 0.4273 (OUTLIER) cc_final: 0.4020 (tm-30) REVERT: M 272 GLU cc_start: 0.2799 (OUTLIER) cc_final: 0.2347 (tt0) REVERT: N 387 GLU cc_start: 0.5463 (pm20) cc_final: 0.4749 (mm-30) REVERT: N 407 GLU cc_start: 0.4952 (OUTLIER) cc_final: 0.4709 (pm20) REVERT: O 224 LYS cc_start: 0.3768 (ttpt) cc_final: 0.3118 (mttt) REVERT: O 332 GLN cc_start: 0.2839 (mt0) cc_final: 0.2564 (mt0) REVERT: O 627 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.3953 (mt) outliers start: 307 outliers final: 150 residues processed: 764 average time/residue: 1.4144 time to fit residues: 1334.9096 Evaluate side-chains 694 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 505 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1174 GLN Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1373 ARG Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 719 LYS Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1045 VAL Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain B residue 1142 ARG Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 240 GLU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 407 GLU Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain O residue 217 PHE Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 298 ASN Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 195 PHE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 5.9990 chunk 277 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 201 optimal weight: 0.9990 chunk 416 optimal weight: 30.0000 chunk 337 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 438 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 83 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN A1254 ASN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 27 HIS ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 105 HIS ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN N 392 GLN Q 31 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 41413 Z= 0.390 Angle : 0.692 15.021 55908 Z= 0.357 Chirality : 0.048 0.272 6294 Planarity : 0.005 0.094 7205 Dihedral : 5.751 59.859 5587 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 7.21 % Allowed : 26.24 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -1.05 (0.11), residues: 5039 helix: 0.25 (0.12), residues: 1837 sheet: -0.85 (0.20), residues: 605 loop : -1.35 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 201 HIS 0.011 0.002 HIS A 427 PHE 0.028 0.002 PHE N 390 TYR 0.024 0.002 TYR O 494 ARG 0.007 0.001 ARG G 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 542 time to evaluate : 4.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.3257 (OUTLIER) cc_final: 0.2845 (mpt180) REVERT: A 269 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.5294 (ppt-90) REVERT: A 296 SER cc_start: 0.7042 (OUTLIER) cc_final: 0.6825 (p) REVERT: A 312 MET cc_start: 0.4849 (OUTLIER) cc_final: 0.3862 (ttt) REVERT: A 313 MET cc_start: 0.6741 (tpp) cc_final: 0.6394 (ttp) REVERT: A 365 ARG cc_start: 0.7305 (mtp85) cc_final: 0.6860 (ttm-80) REVERT: A 517 MET cc_start: 0.9295 (mtp) cc_final: 0.9051 (mtm) REVERT: A 639 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7148 (tppt) REVERT: A 739 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7629 (p0) REVERT: A 870 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: A 890 MET cc_start: 0.8770 (tpp) cc_final: 0.8416 (tpp) REVERT: A 999 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7445 (t0) REVERT: A 1060 TYR cc_start: 0.7605 (m-80) cc_final: 0.7300 (m-80) REVERT: A 1065 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8028 (ttmm) REVERT: A 1174 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.5798 (mt0) REVERT: A 1187 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5508 (ttt-90) REVERT: A 1190 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6836 (mp) REVERT: A 1204 ASP cc_start: 0.5785 (OUTLIER) cc_final: 0.5559 (p0) REVERT: A 1255 ASP cc_start: 0.4973 (OUTLIER) cc_final: 0.4716 (t0) REVERT: A 1287 ASP cc_start: 0.4037 (OUTLIER) cc_final: 0.3155 (m-30) REVERT: B 78 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6907 (tttt) REVERT: B 204 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7883 (tpp-160) REVERT: B 217 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6444 (pt0) REVERT: B 394 LYS cc_start: 0.7336 (mttt) cc_final: 0.6995 (mmtt) REVERT: B 420 LEU cc_start: 0.3911 (OUTLIER) cc_final: 0.3606 (mt) REVERT: B 719 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8275 (mmmt) REVERT: B 890 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.4920 (t70) REVERT: B 1054 ARG cc_start: 0.6787 (ttt90) cc_final: 0.6137 (ptp-110) REVERT: B 1084 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (ttp) REVERT: B 1114 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6397 (tp30) REVERT: B 1142 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7144 (mmt180) REVERT: C 37 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8243 (tppt) REVERT: C 154 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7855 (mmtp) REVERT: C 245 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7657 (mpt180) REVERT: D 23 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5546 (tm) REVERT: D 52 HIS cc_start: 0.3101 (m-70) cc_final: 0.2870 (m170) REVERT: D 150 ILE cc_start: 0.3227 (OUTLIER) cc_final: 0.3016 (mp) REVERT: E 101 GLN cc_start: 0.5625 (OUTLIER) cc_final: 0.5238 (pt0) REVERT: E 115 ASN cc_start: 0.5674 (p0) cc_final: 0.5406 (p0) REVERT: E 121 MET cc_start: 0.4224 (ppp) cc_final: 0.3516 (tmt) REVERT: E 172 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6711 (mt-10) REVERT: F 127 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: G 20 ARG cc_start: 0.7554 (mtp85) cc_final: 0.6892 (mtp85) REVERT: G 44 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7019 (tp) REVERT: G 58 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: G 97 ILE cc_start: 0.3273 (tt) cc_final: 0.2697 (mt) REVERT: G 124 GLU cc_start: 0.4211 (pp20) cc_final: 0.3212 (tt0) REVERT: G 151 GLU cc_start: 0.3040 (OUTLIER) cc_final: 0.2434 (mp0) REVERT: I 27 ARG cc_start: 0.6616 (mtt-85) cc_final: 0.6347 (ttm110) REVERT: I 44 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6796 (ptpt) REVERT: I 60 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7126 (t0) REVERT: I 106 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7070 (mmm160) REVERT: J 19 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7631 (mt-10) REVERT: K 100 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8500 (mp) REVERT: K 142 MET cc_start: 0.6661 (mtp) cc_final: 0.6251 (mtp) REVERT: L 37 LYS cc_start: 0.7690 (mppt) cc_final: 0.6973 (pttt) REVERT: L 57 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (mt) REVERT: M 272 GLU cc_start: 0.2850 (OUTLIER) cc_final: 0.2433 (tt0) REVERT: N 370 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6418 (mtpt) REVERT: N 375 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7672 (mm) REVERT: N 387 GLU cc_start: 0.5443 (pm20) cc_final: 0.5072 (mm-30) REVERT: O 148 ASP cc_start: 0.3344 (OUTLIER) cc_final: 0.1939 (t0) REVERT: O 224 LYS cc_start: 0.3899 (ttpt) cc_final: 0.3092 (mttt) REVERT: O 534 ARG cc_start: 0.1641 (OUTLIER) cc_final: 0.1427 (ptp-110) REVERT: O 627 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.3979 (mt) outliers start: 325 outliers final: 160 residues processed: 788 average time/residue: 1.4435 time to fit residues: 1403.5348 Evaluate side-chains 719 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 513 time to evaluate : 4.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1174 GLN Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1279 SER Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 369 ARG Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 719 LYS Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain B residue 1142 ARG Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 154 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 108 LYS Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 370 LYS Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 534 ARG Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 195 PHE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 0.9980 chunk 439 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 286 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 488 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 226 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 787 ASN B 81 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN G 69 ASN H 137 GLN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN N 392 GLN O 295 GLN O 298 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 41413 Z= 0.340 Angle : 0.665 11.076 55908 Z= 0.342 Chirality : 0.047 0.334 6294 Planarity : 0.005 0.092 7205 Dihedral : 5.677 55.297 5586 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer: Outliers : 6.77 % Allowed : 27.35 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -1.05 (0.11), residues: 5039 helix: 0.28 (0.12), residues: 1839 sheet: -0.88 (0.20), residues: 610 loop : -1.36 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 201 HIS 0.010 0.001 HIS A 427 PHE 0.055 0.002 PHE O 217 TYR 0.026 0.002 TYR O 494 ARG 0.015 0.001 ARG P 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 540 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.3308 (OUTLIER) cc_final: 0.2861 (mpt180) REVERT: A 269 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.5354 (ppt-90) REVERT: A 296 SER cc_start: 0.6789 (OUTLIER) cc_final: 0.6572 (p) REVERT: A 312 MET cc_start: 0.5005 (OUTLIER) cc_final: 0.3981 (ttt) REVERT: A 313 MET cc_start: 0.6721 (tpp) cc_final: 0.6418 (ttp) REVERT: A 365 ARG cc_start: 0.7292 (mtp85) cc_final: 0.6817 (ttm-80) REVERT: A 639 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7160 (tppt) REVERT: A 739 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7678 (p0) REVERT: A 870 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: A 890 MET cc_start: 0.8802 (tpp) cc_final: 0.8432 (mmm) REVERT: A 999 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7579 (t0) REVERT: A 1060 TYR cc_start: 0.7590 (m-80) cc_final: 0.7256 (m-80) REVERT: A 1065 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8011 (ttmm) REVERT: A 1187 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5499 (ttt90) REVERT: A 1190 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6844 (mp) REVERT: A 1204 ASP cc_start: 0.5778 (OUTLIER) cc_final: 0.5555 (p0) REVERT: A 1255 ASP cc_start: 0.5018 (OUTLIER) cc_final: 0.4667 (t0) REVERT: A 1275 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8094 (mt) REVERT: A 1287 ASP cc_start: 0.4036 (OUTLIER) cc_final: 0.3149 (m-30) REVERT: A 1307 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7403 (t0) REVERT: B 72 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: B 204 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7955 (tpp-160) REVERT: B 217 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6542 (pt0) REVERT: B 239 LYS cc_start: 0.7586 (mttp) cc_final: 0.7186 (mmtp) REVERT: B 315 GLN cc_start: 0.2993 (OUTLIER) cc_final: 0.2621 (pm20) REVERT: B 394 LYS cc_start: 0.7337 (mttt) cc_final: 0.6960 (mmtt) REVERT: B 420 LEU cc_start: 0.3961 (OUTLIER) cc_final: 0.3657 (mt) REVERT: B 890 ASP cc_start: 0.5808 (OUTLIER) cc_final: 0.4878 (t70) REVERT: B 1054 ARG cc_start: 0.6838 (ttt90) cc_final: 0.6148 (ptp-110) REVERT: B 1114 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6373 (tp30) REVERT: C 37 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8244 (tppt) REVERT: C 145 ASP cc_start: 0.5892 (OUTLIER) cc_final: 0.4991 (p0) REVERT: C 245 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7598 (mpt180) REVERT: D 1 MET cc_start: 0.5080 (tpt) cc_final: 0.4665 (tpt) REVERT: D 134 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5061 (tm) REVERT: D 150 ILE cc_start: 0.3225 (OUTLIER) cc_final: 0.3003 (mp) REVERT: E 101 GLN cc_start: 0.5783 (OUTLIER) cc_final: 0.5318 (pt0) REVERT: E 115 ASN cc_start: 0.5798 (p0) cc_final: 0.5508 (p0) REVERT: E 121 MET cc_start: 0.4175 (ppp) cc_final: 0.3540 (tmt) REVERT: G 20 ARG cc_start: 0.7548 (mtp85) cc_final: 0.6913 (mtp85) REVERT: G 58 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: G 101 LEU cc_start: 0.3679 (OUTLIER) cc_final: 0.3171 (tt) REVERT: G 124 GLU cc_start: 0.4015 (pp20) cc_final: 0.3114 (tt0) REVERT: G 151 GLU cc_start: 0.3049 (OUTLIER) cc_final: 0.2472 (mp0) REVERT: H 103 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8047 (ttpt) REVERT: I 60 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7081 (t0) REVERT: I 106 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7070 (mmm160) REVERT: K 100 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8475 (mp) REVERT: K 129 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: L 37 LYS cc_start: 0.7702 (mppt) cc_final: 0.7003 (pttt) REVERT: L 57 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8908 (mt) REVERT: M 112 TYR cc_start: 0.6483 (t80) cc_final: 0.5948 (t80) REVERT: M 135 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5698 (tttp) REVERT: M 231 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.6011 (mt) REVERT: M 272 GLU cc_start: 0.2717 (OUTLIER) cc_final: 0.2268 (tt0) REVERT: N 275 GLU cc_start: 0.4488 (OUTLIER) cc_final: 0.3647 (pt0) REVERT: N 375 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7661 (mm) REVERT: N 407 GLU cc_start: 0.5445 (pm20) cc_final: 0.4987 (pm20) REVERT: O 148 ASP cc_start: 0.3368 (OUTLIER) cc_final: 0.1994 (t0) REVERT: O 224 LYS cc_start: 0.3886 (ttpt) cc_final: 0.3072 (mttt) REVERT: O 244 ASN cc_start: 0.4609 (m-40) cc_final: 0.4320 (m-40) REVERT: O 288 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.3799 (ppp) REVERT: O 316 LEU cc_start: 0.4154 (OUTLIER) cc_final: 0.3944 (tp) REVERT: O 534 ARG cc_start: 0.1657 (pmm-80) cc_final: 0.1441 (ptp-110) REVERT: O 543 TYR cc_start: 0.5748 (m-80) cc_final: 0.5378 (m-10) REVERT: O 549 GLN cc_start: 0.5300 (OUTLIER) cc_final: 0.5032 (tp40) REVERT: O 627 LEU cc_start: 0.4683 (OUTLIER) cc_final: 0.4222 (mt) outliers start: 305 outliers final: 150 residues processed: 778 average time/residue: 1.4348 time to fit residues: 1377.4690 Evaluate side-chains 703 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 505 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1187 ARG Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1279 SER Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1341 TYR Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 THR Chi-restraints excluded: chain B residue 889 SER Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1111 LYS Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 283 LEU Chi-restraints excluded: chain N residue 297 MET Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 356 LEU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 117 THR Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 169 LEU Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 288 MET Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 549 GLN Chi-restraints excluded: chain O residue 601 THR Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 195 PHE Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 278 optimal weight: 10.0000 chunk 356 optimal weight: 5.9990 chunk 276 optimal weight: 0.0980 chunk 411 optimal weight: 10.0000 chunk 272 optimal weight: 0.1980 chunk 486 optimal weight: 30.0000 chunk 304 optimal weight: 1.9990 chunk 296 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A1261 GLN B 42 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 ASN ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN H 137 GLN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN O 298 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 41413 Z= 0.212 Angle : 0.599 10.199 55908 Z= 0.308 Chirality : 0.044 0.282 6294 Planarity : 0.004 0.091 7205 Dihedral : 5.350 50.286 5586 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.44 % Favored : 94.48 % Rotamer: Outliers : 5.68 % Allowed : 28.77 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.80 (0.12), residues: 5039 helix: 0.55 (0.12), residues: 1819 sheet: -0.85 (0.20), residues: 609 loop : -1.22 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 197 HIS 0.006 0.001 HIS A 427 PHE 0.038 0.001 PHE O 217 TYR 0.022 0.002 TYR B 296 ARG 0.007 0.000 ARG N 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 539 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5527 (mp0) cc_final: 0.5278 (mp0) REVERT: A 217 ARG cc_start: 0.3251 (OUTLIER) cc_final: 0.2813 (mpt180) REVERT: A 283 ASP cc_start: 0.5958 (OUTLIER) cc_final: 0.5754 (p0) REVERT: A 296 SER cc_start: 0.6639 (OUTLIER) cc_final: 0.6426 (p) REVERT: A 312 MET cc_start: 0.5059 (OUTLIER) cc_final: 0.3914 (ttt) REVERT: A 313 MET cc_start: 0.6711 (tpp) cc_final: 0.6439 (ttp) REVERT: A 365 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6832 (ttm-80) REVERT: A 739 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 776 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7630 (tp30) REVERT: A 870 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7475 (pp20) REVERT: A 890 MET cc_start: 0.8784 (tpp) cc_final: 0.8431 (tpp) REVERT: A 1065 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7989 (ttmm) REVERT: A 1174 GLN cc_start: 0.6851 (mm110) cc_final: 0.6492 (tp40) REVERT: A 1190 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6904 (mp) REVERT: A 1204 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5549 (p0) REVERT: A 1255 ASP cc_start: 0.4708 (OUTLIER) cc_final: 0.4478 (t0) REVERT: A 1287 ASP cc_start: 0.3932 (OUTLIER) cc_final: 0.3063 (m-30) REVERT: A 1307 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7425 (t0) REVERT: A 1373 ARG cc_start: 0.6551 (ptp90) cc_final: 0.6208 (ptt-90) REVERT: B 72 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: B 204 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7841 (tpp-160) REVERT: B 239 LYS cc_start: 0.7439 (mttp) cc_final: 0.7095 (mmtp) REVERT: B 269 MET cc_start: 0.8043 (ttp) cc_final: 0.7527 (tpp) REVERT: B 351 MET cc_start: 0.8069 (mmm) cc_final: 0.7724 (mpm) REVERT: B 394 LYS cc_start: 0.7298 (mttt) cc_final: 0.6943 (mmtt) REVERT: B 1054 ARG cc_start: 0.6844 (ttt90) cc_final: 0.6194 (ptp-110) REVERT: B 1114 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6245 (tp30) REVERT: C 37 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8227 (tppt) REVERT: C 145 ASP cc_start: 0.5985 (OUTLIER) cc_final: 0.5056 (p0) REVERT: C 319 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7997 (tpp-160) REVERT: D 23 LEU cc_start: 0.5765 (OUTLIER) cc_final: 0.5442 (tm) REVERT: D 134 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5097 (tm) REVERT: D 150 ILE cc_start: 0.3350 (OUTLIER) cc_final: 0.3099 (mp) REVERT: E 101 GLN cc_start: 0.5965 (OUTLIER) cc_final: 0.5469 (pt0) REVERT: E 115 ASN cc_start: 0.5851 (p0) cc_final: 0.5569 (p0) REVERT: E 121 MET cc_start: 0.3945 (ppp) cc_final: 0.3488 (tmt) REVERT: F 127 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: G 20 ARG cc_start: 0.7494 (mtp85) cc_final: 0.6870 (mtp85) REVERT: G 58 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: G 81 LEU cc_start: 0.5088 (OUTLIER) cc_final: 0.4771 (tt) REVERT: G 101 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.2885 (tt) REVERT: G 124 GLU cc_start: 0.4092 (pp20) cc_final: 0.3179 (tt0) REVERT: H 35 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6413 (mt0) REVERT: H 103 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8014 (ttpt) REVERT: I 106 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7069 (mmm160) REVERT: K 100 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8412 (mp) REVERT: K 129 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: L 37 LYS cc_start: 0.7607 (mppt) cc_final: 0.6947 (pttt) REVERT: L 57 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8866 (mt) REVERT: M 83 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5437 (tt0) REVERT: M 112 TYR cc_start: 0.6428 (t80) cc_final: 0.5888 (t80) REVERT: M 135 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5643 (tttp) REVERT: M 272 GLU cc_start: 0.2691 (OUTLIER) cc_final: 0.2235 (tt0) REVERT: N 375 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7673 (mm) REVERT: N 407 GLU cc_start: 0.5628 (pm20) cc_final: 0.5077 (pm20) REVERT: O 49 TYR cc_start: 0.6135 (m-10) cc_final: 0.5701 (m-80) REVERT: O 65 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6934 (mt) REVERT: O 121 TYR cc_start: 0.4496 (m-10) cc_final: 0.4059 (m-10) REVERT: O 224 LYS cc_start: 0.3787 (ttpt) cc_final: 0.3043 (mttt) REVERT: O 288 MET cc_start: 0.4184 (ppp) cc_final: 0.3810 (ppp) REVERT: O 316 LEU cc_start: 0.4107 (OUTLIER) cc_final: 0.3772 (tp) REVERT: O 627 LEU cc_start: 0.4750 (OUTLIER) cc_final: 0.4280 (mt) outliers start: 256 outliers final: 123 residues processed: 732 average time/residue: 1.4636 time to fit residues: 1318.5236 Evaluate side-chains 667 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 506 time to evaluate : 4.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1279 SER Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 65 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 216 GLN Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 238 SER Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 290 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 331 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS ** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN B 42 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN H 137 GLN L 66 GLN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN M 234 HIS ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 377 ASN O 298 ASN P 239 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 41413 Z= 0.307 Angle : 0.646 10.146 55908 Z= 0.333 Chirality : 0.046 0.282 6294 Planarity : 0.005 0.088 7205 Dihedral : 5.485 48.895 5582 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.15 % Favored : 93.77 % Rotamer: Outliers : 5.77 % Allowed : 28.79 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.85 (0.12), residues: 5039 helix: 0.48 (0.12), residues: 1823 sheet: -0.82 (0.20), residues: 609 loop : -1.25 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 201 HIS 0.009 0.001 HIS A 427 PHE 0.036 0.002 PHE O 217 TYR 0.021 0.002 TYR A 256 ARG 0.008 0.001 ARG A1229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 513 time to evaluate : 4.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.3328 (OUTLIER) cc_final: 0.2864 (mpt180) REVERT: A 269 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7310 (ppt-90) REVERT: A 283 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5697 (p0) REVERT: A 312 MET cc_start: 0.5024 (OUTLIER) cc_final: 0.3941 (ttt) REVERT: A 313 MET cc_start: 0.6603 (tpp) cc_final: 0.6342 (ttp) REVERT: A 365 ARG cc_start: 0.7279 (mtp85) cc_final: 0.6867 (ttm-80) REVERT: A 639 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7177 (tppt) REVERT: A 739 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7570 (p0) REVERT: A 776 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7635 (tp30) REVERT: A 870 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7647 (pp20) REVERT: A 890 MET cc_start: 0.8748 (tpp) cc_final: 0.8500 (tpp) REVERT: A 999 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7600 (t0) REVERT: A 1065 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8017 (ttmm) REVERT: A 1204 ASP cc_start: 0.5470 (OUTLIER) cc_final: 0.5252 (p0) REVERT: A 1255 ASP cc_start: 0.5018 (OUTLIER) cc_final: 0.4683 (t0) REVERT: A 1275 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8072 (mt) REVERT: A 1287 ASP cc_start: 0.3961 (OUTLIER) cc_final: 0.3078 (m-30) REVERT: A 1373 ARG cc_start: 0.6635 (ptp90) cc_final: 0.6250 (ptt-90) REVERT: B 72 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7210 (m-30) REVERT: B 204 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7926 (tpp-160) REVERT: B 239 LYS cc_start: 0.7546 (mttp) cc_final: 0.7077 (mmtp) REVERT: B 269 MET cc_start: 0.8040 (ttp) cc_final: 0.7538 (tpp) REVERT: B 351 MET cc_start: 0.8079 (mmm) cc_final: 0.7699 (mpm) REVERT: B 394 LYS cc_start: 0.7293 (mttt) cc_final: 0.6984 (mmtt) REVERT: B 420 LEU cc_start: 0.3375 (OUTLIER) cc_final: 0.3141 (mt) REVERT: B 566 ARG cc_start: 0.6843 (mmm-85) cc_final: 0.6545 (mtp85) REVERT: B 890 ASP cc_start: 0.5811 (OUTLIER) cc_final: 0.4863 (t70) REVERT: B 1054 ARG cc_start: 0.6796 (ttt90) cc_final: 0.6160 (ptp-110) REVERT: B 1114 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6216 (tp30) REVERT: B 1142 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7033 (mmt180) REVERT: C 37 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8241 (tppt) REVERT: C 145 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5118 (p0) REVERT: D 1 MET cc_start: 0.5218 (tpt) cc_final: 0.4720 (tpt) REVERT: D 23 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5398 (tm) REVERT: D 134 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5099 (tm) REVERT: D 150 ILE cc_start: 0.3361 (OUTLIER) cc_final: 0.3085 (mp) REVERT: E 101 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5528 (pt0) REVERT: E 115 ASN cc_start: 0.5846 (p0) cc_final: 0.5539 (p0) REVERT: E 121 MET cc_start: 0.4055 (ppp) cc_final: 0.3550 (tmt) REVERT: F 127 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: G 44 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6897 (tp) REVERT: G 58 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: G 81 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4891 (tt) REVERT: G 101 LEU cc_start: 0.3639 (OUTLIER) cc_final: 0.3116 (tt) REVERT: G 124 GLU cc_start: 0.4013 (pp20) cc_final: 0.3058 (tt0) REVERT: H 35 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6374 (mt0) REVERT: H 103 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8025 (ttpt) REVERT: I 60 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7045 (t0) REVERT: I 106 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7056 (mmm160) REVERT: K 100 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8481 (mp) REVERT: L 37 LYS cc_start: 0.7767 (mppt) cc_final: 0.7050 (pttt) REVERT: L 57 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8895 (mt) REVERT: M 112 TYR cc_start: 0.6486 (t80) cc_final: 0.5871 (t80) REVERT: M 122 ASP cc_start: 0.6529 (m-30) cc_final: 0.6180 (m-30) REVERT: M 135 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5739 (tttp) REVERT: M 231 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6110 (mt) REVERT: M 272 GLU cc_start: 0.2848 (OUTLIER) cc_final: 0.2370 (tt0) REVERT: N 375 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7705 (mm) REVERT: O 49 TYR cc_start: 0.6094 (m-10) cc_final: 0.5583 (m-80) REVERT: O 148 ASP cc_start: 0.3150 (OUTLIER) cc_final: 0.1935 (t0) REVERT: O 224 LYS cc_start: 0.3765 (ttpt) cc_final: 0.3019 (mttt) REVERT: O 237 LYS cc_start: 0.2647 (ptpp) cc_final: 0.2384 (ptmm) REVERT: O 244 ASN cc_start: 0.5046 (m-40) cc_final: 0.4477 (m-40) REVERT: O 316 LEU cc_start: 0.4124 (OUTLIER) cc_final: 0.3638 (tp) REVERT: O 627 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.4209 (mt) outliers start: 260 outliers final: 140 residues processed: 720 average time/residue: 1.4689 time to fit residues: 1306.5775 Evaluate side-chains 682 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 499 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1279 SER Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain B residue 1142 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 265 VAL Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 298 ASN Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain Q residue 110 ASP Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 442 optimal weight: 9.9990 chunk 466 optimal weight: 4.9990 chunk 425 optimal weight: 8.9990 chunk 453 optimal weight: 9.9990 chunk 273 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 409 optimal weight: 0.2980 chunk 428 optimal weight: 10.0000 chunk 451 optimal weight: 20.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS A 753 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 41413 Z= 0.346 Angle : 0.680 11.056 55908 Z= 0.350 Chirality : 0.047 0.280 6294 Planarity : 0.005 0.087 7205 Dihedral : 5.631 51.508 5582 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 5.22 % Allowed : 29.59 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.97 (0.11), residues: 5039 helix: 0.35 (0.12), residues: 1829 sheet: -0.82 (0.20), residues: 618 loop : -1.32 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 201 HIS 0.010 0.001 HIS A 427 PHE 0.035 0.002 PHE O 217 TYR 0.025 0.002 TYR O 494 ARG 0.009 0.001 ARG A1229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 517 time to evaluate : 5.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5554 (mp0) cc_final: 0.5308 (mp0) REVERT: A 140 ILE cc_start: 0.6827 (mp) cc_final: 0.6600 (mt) REVERT: A 217 ARG cc_start: 0.3410 (OUTLIER) cc_final: 0.2952 (mpt180) REVERT: A 312 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.3990 (ttt) REVERT: A 313 MET cc_start: 0.6628 (tpp) cc_final: 0.6391 (ttp) REVERT: A 365 ARG cc_start: 0.7265 (mtp85) cc_final: 0.6841 (ttm-80) REVERT: A 639 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7217 (tppt) REVERT: A 739 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7579 (p0) REVERT: A 776 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7673 (tp30) REVERT: A 870 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: A 890 MET cc_start: 0.8738 (tpp) cc_final: 0.8432 (mmm) REVERT: A 999 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7629 (t0) REVERT: A 1065 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7975 (ttmm) REVERT: A 1204 ASP cc_start: 0.5491 (OUTLIER) cc_final: 0.5279 (p0) REVERT: A 1255 ASP cc_start: 0.5038 (OUTLIER) cc_final: 0.4721 (t70) REVERT: A 1275 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8037 (mt) REVERT: A 1287 ASP cc_start: 0.4064 (OUTLIER) cc_final: 0.3190 (m-30) REVERT: B 72 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: B 204 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7960 (tpp-160) REVERT: B 239 LYS cc_start: 0.7668 (mttp) cc_final: 0.7131 (mmtp) REVERT: B 269 MET cc_start: 0.7952 (ttp) cc_final: 0.7530 (tpp) REVERT: B 351 MET cc_start: 0.8024 (mmm) cc_final: 0.7652 (mpm) REVERT: B 420 LEU cc_start: 0.3396 (OUTLIER) cc_final: 0.3159 (mt) REVERT: B 890 ASP cc_start: 0.5720 (OUTLIER) cc_final: 0.4793 (t70) REVERT: B 1054 ARG cc_start: 0.6839 (ttt90) cc_final: 0.6109 (ptp-110) REVERT: B 1114 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: C 37 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8240 (tppt) REVERT: C 145 ASP cc_start: 0.6127 (OUTLIER) cc_final: 0.5137 (p0) REVERT: C 319 ARG cc_start: 0.8530 (tpp80) cc_final: 0.8077 (tpp-160) REVERT: D 1 MET cc_start: 0.5243 (tpt) cc_final: 0.4895 (tpt) REVERT: D 23 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5505 (tm) REVERT: D 134 LEU cc_start: 0.5985 (OUTLIER) cc_final: 0.5060 (tm) REVERT: D 150 ILE cc_start: 0.3230 (OUTLIER) cc_final: 0.2990 (mp) REVERT: E 101 GLN cc_start: 0.5983 (OUTLIER) cc_final: 0.5525 (pt0) REVERT: E 115 ASN cc_start: 0.5959 (p0) cc_final: 0.5663 (p0) REVERT: E 121 MET cc_start: 0.4089 (ppp) cc_final: 0.3587 (tmt) REVERT: F 127 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: G 58 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8079 (pt0) REVERT: G 81 LEU cc_start: 0.5107 (OUTLIER) cc_final: 0.4837 (tt) REVERT: G 101 LEU cc_start: 0.3717 (OUTLIER) cc_final: 0.3248 (tt) REVERT: G 124 GLU cc_start: 0.4049 (pp20) cc_final: 0.3085 (tt0) REVERT: G 169 GLU cc_start: 0.4200 (mm-30) cc_final: 0.3829 (tm-30) REVERT: H 11 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8122 (tp40) REVERT: H 35 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6400 (mt0) REVERT: H 103 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8060 (ttpt) REVERT: I 106 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7021 (mmm160) REVERT: K 100 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8505 (mp) REVERT: L 37 LYS cc_start: 0.7793 (mppt) cc_final: 0.7047 (pttt) REVERT: L 57 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8894 (mt) REVERT: M 112 TYR cc_start: 0.6443 (t80) cc_final: 0.5882 (t80) REVERT: M 122 ASP cc_start: 0.6536 (m-30) cc_final: 0.6174 (m-30) REVERT: M 135 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5711 (tttp) REVERT: M 174 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5625 (tm-30) REVERT: M 231 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6274 (mt) REVERT: M 272 GLU cc_start: 0.3079 (OUTLIER) cc_final: 0.2586 (tt0) REVERT: N 375 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7739 (mm) REVERT: N 407 GLU cc_start: 0.5420 (pm20) cc_final: 0.4747 (pm20) REVERT: O 49 TYR cc_start: 0.6103 (m-10) cc_final: 0.5589 (m-80) REVERT: O 121 TYR cc_start: 0.4478 (m-10) cc_final: 0.3916 (m-10) REVERT: O 148 ASP cc_start: 0.3172 (OUTLIER) cc_final: 0.1936 (t0) REVERT: O 224 LYS cc_start: 0.3694 (ttpt) cc_final: 0.2939 (mttt) REVERT: O 237 LYS cc_start: 0.2840 (ptpp) cc_final: 0.2543 (ptmm) REVERT: O 244 ASN cc_start: 0.5057 (m-40) cc_final: 0.4479 (m-40) REVERT: O 316 LEU cc_start: 0.4222 (OUTLIER) cc_final: 0.3794 (tp) REVERT: O 332 GLN cc_start: 0.2100 (mp10) cc_final: 0.1838 (mp10) REVERT: O 627 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4358 (mt) outliers start: 235 outliers final: 147 residues processed: 703 average time/residue: 1.4989 time to fit residues: 1301.5641 Evaluate side-chains 679 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 492 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 639 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1279 SER Chi-restraints excluded: chain A residue 1287 ASP Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1361 VAL Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 890 ASP Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1060 LEU Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 11 GLN Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 83 ILE Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 478 VAL Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 535 SER Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 297 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 333 optimal weight: 0.4980 chunk 503 optimal weight: 20.0000 chunk 463 optimal weight: 2.9990 chunk 400 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 309 optimal weight: 0.5980 chunk 245 optimal weight: 7.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS A 229 ASN A 760 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN B 42 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN H 137 GLN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 41413 Z= 0.230 Angle : 0.622 10.256 55908 Z= 0.319 Chirality : 0.045 0.265 6294 Planarity : 0.004 0.086 7205 Dihedral : 5.372 52.714 5582 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 4.13 % Allowed : 30.79 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.90 % 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: -0.77 (0.12), residues: 5039 helix: 0.56 (0.12), residues: 1818 sheet: -0.81 (0.20), residues: 604 loop : -1.21 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 197 HIS 0.008 0.001 HIS N 287 PHE 0.034 0.002 PHE O 217 TYR 0.029 0.002 TYR O 494 ARG 0.009 0.000 ARG A1229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10078 Ramachandran restraints generated. 5039 Oldfield, 0 Emsley, 5039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 517 time to evaluate : 4.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5524 (mp0) cc_final: 0.5289 (mp0) REVERT: A 217 ARG cc_start: 0.3258 (OUTLIER) cc_final: 0.2828 (mpt180) REVERT: A 283 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5672 (p0) REVERT: A 312 MET cc_start: 0.4983 (OUTLIER) cc_final: 0.3862 (ttt) REVERT: A 313 MET cc_start: 0.6492 (tpp) cc_final: 0.6207 (ttp) REVERT: A 365 ARG cc_start: 0.7230 (mtp85) cc_final: 0.6836 (ttm-80) REVERT: A 739 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7541 (p0) REVERT: A 776 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7581 (tp30) REVERT: A 870 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: A 890 MET cc_start: 0.8746 (tpp) cc_final: 0.8496 (tpp) REVERT: A 1065 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7975 (ttmm) REVERT: A 1105 THR cc_start: 0.6573 (p) cc_final: 0.6289 (p) REVERT: A 1255 ASP cc_start: 0.4983 (OUTLIER) cc_final: 0.4705 (t70) REVERT: B 72 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: B 204 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7846 (tpp-160) REVERT: B 239 LYS cc_start: 0.7445 (mttp) cc_final: 0.6942 (mmtp) REVERT: B 269 MET cc_start: 0.7943 (ttp) cc_final: 0.7576 (tpp) REVERT: B 351 MET cc_start: 0.7954 (mmm) cc_final: 0.7578 (mpm) REVERT: B 369 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7251 (ttt180) REVERT: B 420 LEU cc_start: 0.3395 (OUTLIER) cc_final: 0.3141 (mt) REVERT: B 1054 ARG cc_start: 0.6777 (ttt90) cc_final: 0.6114 (ptp-110) REVERT: B 1114 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6295 (tp30) REVERT: B 1147 PHE cc_start: 0.7473 (m-80) cc_final: 0.7061 (m-80) REVERT: C 145 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.5229 (p0) REVERT: C 319 ARG cc_start: 0.8406 (tpp80) cc_final: 0.8029 (tpp-160) REVERT: D 1 MET cc_start: 0.5151 (tpt) cc_final: 0.4896 (tpt) REVERT: D 23 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5497 (tm) REVERT: D 134 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5140 (tm) REVERT: D 150 ILE cc_start: 0.3353 (OUTLIER) cc_final: 0.3084 (mp) REVERT: E 101 GLN cc_start: 0.6066 (OUTLIER) cc_final: 0.5615 (pt0) REVERT: E 115 ASN cc_start: 0.6068 (p0) cc_final: 0.5736 (p0) REVERT: E 121 MET cc_start: 0.3969 (ppp) cc_final: 0.3578 (tmt) REVERT: F 127 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: G 58 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: G 101 LEU cc_start: 0.3701 (OUTLIER) cc_final: 0.3205 (tt) REVERT: G 124 GLU cc_start: 0.4039 (pp20) cc_final: 0.3083 (tt0) REVERT: G 169 GLU cc_start: 0.4383 (mm-30) cc_final: 0.3945 (tm-30) REVERT: H 35 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6438 (mt0) REVERT: H 103 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8000 (ttpt) REVERT: I 106 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7015 (mmm160) REVERT: K 100 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8423 (mp) REVERT: K 129 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: L 37 LYS cc_start: 0.7722 (mppt) cc_final: 0.7000 (pttt) REVERT: L 57 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8865 (mt) REVERT: M 112 TYR cc_start: 0.6234 (t80) cc_final: 0.5862 (t80) REVERT: M 122 ASP cc_start: 0.6574 (m-30) cc_final: 0.6217 (m-30) REVERT: M 135 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5745 (tttp) REVERT: M 166 MET cc_start: 0.6027 (mmt) cc_final: 0.5210 (mpt) REVERT: M 231 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6300 (mt) REVERT: M 272 GLU cc_start: 0.2868 (OUTLIER) cc_final: 0.2383 (tt0) REVERT: N 375 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7671 (mm) REVERT: N 407 GLU cc_start: 0.5419 (pm20) cc_final: 0.4846 (pm20) REVERT: O 49 TYR cc_start: 0.6069 (m-10) cc_final: 0.5646 (m-80) REVERT: O 121 TYR cc_start: 0.4513 (m-10) cc_final: 0.4042 (m-10) REVERT: O 148 ASP cc_start: 0.3121 (OUTLIER) cc_final: 0.1972 (t0) REVERT: O 224 LYS cc_start: 0.3859 (ttpt) cc_final: 0.3109 (mttt) REVERT: O 237 LYS cc_start: 0.2613 (ptpp) cc_final: 0.2390 (ptmm) REVERT: O 244 ASN cc_start: 0.5064 (m-40) cc_final: 0.4460 (m-40) REVERT: O 316 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.3693 (tp) REVERT: O 332 GLN cc_start: 0.2081 (mp10) cc_final: 0.1871 (mp10) REVERT: O 627 LEU cc_start: 0.4690 (OUTLIER) cc_final: 0.4259 (mt) outliers start: 186 outliers final: 123 residues processed: 663 average time/residue: 1.5571 time to fit residues: 1273.2158 Evaluate side-chains 659 residues out of total 4516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 504 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 107 CYS Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 ASP Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 781 CYS Chi-restraints excluded: chain A residue 870 GLU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 897 SER Chi-restraints excluded: chain A residue 931 GLN Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1065 LYS Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1185 GLN Chi-restraints excluded: chain A residue 1201 THR Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1255 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1279 SER Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1304 MET Chi-restraints excluded: chain A residue 1383 VAL Chi-restraints excluded: chain A residue 1393 THR Chi-restraints excluded: chain A residue 1422 SER Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 713 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 800 ASN Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 901 ARG Chi-restraints excluded: chain B residue 908 LEU Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 1008 ILE Chi-restraints excluded: chain B residue 1114 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 58 GLN Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 40 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain K residue 52 GLN Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 93 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 272 GLU Chi-restraints excluded: chain N residue 290 ILE Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 363 ILE Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 375 ILE Chi-restraints excluded: chain N residue 390 PHE Chi-restraints excluded: chain N residue 395 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 32 MET Chi-restraints excluded: chain O residue 57 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 148 ASP Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 191 PHE Chi-restraints excluded: chain O residue 257 ASN Chi-restraints excluded: chain O residue 282 ILE Chi-restraints excluded: chain O residue 298 ASN Chi-restraints excluded: chain O residue 299 LEU Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 319 THR Chi-restraints excluded: chain O residue 344 SER Chi-restraints excluded: chain O residue 486 VAL Chi-restraints excluded: chain O residue 516 LEU Chi-restraints excluded: chain O residue 627 LEU Chi-restraints excluded: chain O residue 637 VAL Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain Q residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 0.5980 chunk 426 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 369 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 401 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 412 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 83 HIS ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 32 ASN ** M 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 ASN ** N 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.195762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143086 restraints weight = 49349.432| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.72 r_work: 0.3285 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.353 41413 Z= 0.275 Angle : 0.740 59.185 55908 Z= 0.412 Chirality : 0.045 0.293 6294 Planarity : 0.005 0.178 7205 Dihedral : 5.368 52.763 5582 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 3.91 % Allowed : 31.10 % Favored : 64.99 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.90 % 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: -0.77 (0.12), residues: 5039 helix: 0.56 (0.12), residues: 1818 sheet: -0.80 (0.20), residues: 604 loop : -1.20 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 197 HIS 0.007 0.001 HIS N 287 PHE 0.047 0.002 PHE P 312 TYR 0.025 0.002 TYR O 494 ARG 0.008 0.000 ARG O 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18493.93 seconds wall clock time: 328 minutes 27.45 seconds (19707.45 seconds total)