Starting phenix.real_space_refine on Tue Aug 26 14:30:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x9w_38186/08_2025/8x9w_38186.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x9w_38186/08_2025/8x9w_38186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x9w_38186/08_2025/8x9w_38186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x9w_38186/08_2025/8x9w_38186.map" model { file = "/net/cci-nas-00/data/ceres_data/8x9w_38186/08_2025/8x9w_38186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x9w_38186/08_2025/8x9w_38186.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 193 5.16 5 C 23541 2.51 5 N 6726 2.21 5 O 6884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37344 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 10392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1347, 10392 Classifications: {'peptide': 1347} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 1263} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 13, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'CIS': 3, 'TRANS': 83} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 9888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1287, 9888 Classifications: {'peptide': 1287} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 80, 'TRANS': 1205} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 11, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "F" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 8, 'PTRANS': 21, 'TRANS': 267} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "H" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'CIS': 3, 'TRANS': 83} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'CIS': 3, 'TRANS': 83} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'CIS': 3, 'TRANS': 83} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "K" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 380 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'CIS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'UNK:plan-1': 76} Unresolved non-hydrogen planarities: 76 Chain: "L" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 380 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'CIS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'UNK:plan-1': 76} Unresolved non-hydrogen planarities: 76 Chain: "O" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2279 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 14, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 272} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 63 Chain: "Q" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 380 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'CIS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'UNK:plan-1': 76} Unresolved non-hydrogen planarities: 76 Chain: "R" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 380 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'CIS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'UNK:plan-1': 76} Unresolved non-hydrogen planarities: 76 Chain: "S" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 380 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'CIS': 4, 'TRANS': 71} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'UNK:plan-1': 76} Unresolved non-hydrogen planarities: 76 Chain: "T" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 435 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'CIS': 3, 'TRANS': 83} Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'UNK:plan-1': 87} Unresolved non-hydrogen planarities: 87 Chain: "X" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2198 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 22, 'PTRANS': 10, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "k" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4206 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 509} Chain breaks: 7 Chain: "l" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 8, 'TRANS': 85} Chain: "m" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 384 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "o" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 384 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Time building chain proxies: 7.91, per 1000 atoms: 0.21 Number of scatterers: 37344 At special positions: 0 Unit cell: (203.85, 224.1, 198.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 193 16.00 O 6884 8.00 N 6726 7.00 C 23541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 846 " - pdb=" SG CYS A 985 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 985 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.13 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9774 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 42 sheets defined 53.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.672A pdb=" N ARG A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 4.049A pdb=" N ARG A 45 " --> pdb=" O CYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 90 removed outlier: 4.403A pdb=" N ALA A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 163 through 204 removed outlier: 3.573A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Proline residue: A 212 - end of helix removed outlier: 3.926A pdb=" N LYS A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.580A pdb=" N ARG A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 4.514A pdb=" N ILE A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.396A pdb=" N GLY A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 329 through 336 removed outlier: 3.935A pdb=" N VAL A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.039A pdb=" N VAL A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.950A pdb=" N GLY A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.534A pdb=" N LEU A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 516 through 530 removed outlier: 3.964A pdb=" N ASP A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 removed outlier: 3.598A pdb=" N VAL A 538 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 539 " --> pdb=" O HIS A 536 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 535 through 539' Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.635A pdb=" N LEU A 555 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 623 through 635 Processing helix chain 'A' and resid 640 through 651 removed outlier: 4.279A pdb=" N TYR A 644 " --> pdb=" O PRO A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 660 through 676 removed outlier: 3.742A pdb=" N GLN A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'A' and resid 700 through 724 removed outlier: 3.620A pdb=" N ILE A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 756 through 766 removed outlier: 3.534A pdb=" N ALA A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 842 removed outlier: 4.306A pdb=" N GLY A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 851 through 859 Proline residue: A 857 - end of helix Processing helix chain 'A' and resid 885 through 889 Processing helix chain 'A' and resid 893 through 901 removed outlier: 3.794A pdb=" N ALA A 901 " --> pdb=" O TYR A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 917 removed outlier: 3.886A pdb=" N LEU A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 996 through 1004 removed outlier: 3.794A pdb=" N ARG A1000 " --> pdb=" O THR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1014 Processing helix chain 'A' and resid 1022 through 1032 removed outlier: 3.631A pdb=" N ALA A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1047 Processing helix chain 'A' and resid 1051 through 1062 Processing helix chain 'A' and resid 1147 through 1151 removed outlier: 3.963A pdb=" N PHE A1150 " --> pdb=" O ASN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1172 removed outlier: 3.636A pdb=" N THR A1163 " --> pdb=" O HIS A1159 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1219 removed outlier: 4.100A pdb=" N PHE A1218 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1247 Processing helix chain 'A' and resid 1270 through 1277 Processing helix chain 'A' and resid 1292 through 1296 Processing helix chain 'A' and resid 1306 through 1315 removed outlier: 3.764A pdb=" N ARG A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1363 removed outlier: 3.742A pdb=" N ARG A1363 " --> pdb=" O ALA A1359 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 238 through 250 removed outlier: 3.632A pdb=" N UNK B 242 " --> pdb=" O UNK B 238 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N UNK B 250 " --> pdb=" O UNK B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 306 removed outlier: 3.987A pdb=" N UNK B 262 " --> pdb=" O UNK B 258 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N UNK B 283 " --> pdb=" O UNK B 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.811A pdb=" N VAL C 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 100 removed outlier: 4.432A pdb=" N ALA C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 100' Processing helix chain 'C' and resid 148 through 156 Processing helix chain 'C' and resid 167 through 203 removed outlier: 3.941A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 223 through 241 removed outlier: 3.582A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.528A pdb=" N HIS C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 4.389A pdb=" N ILE C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 removed outlier: 3.536A pdb=" N GLN C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.807A pdb=" N VAL C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 4.468A pdb=" N VAL C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 removed outlier: 4.160A pdb=" N GLY C 476 " --> pdb=" O ARG C 472 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N THR C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 485 through 493 removed outlier: 4.549A pdb=" N THR C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 529 removed outlier: 3.521A pdb=" N PHE C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 552 through 558 removed outlier: 3.684A pdb=" N LEU C 555 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 556 " --> pdb=" O PRO C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 598 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 604 through 616 Processing helix chain 'C' and resid 623 through 635 removed outlier: 4.018A pdb=" N ASP C 632 " --> pdb=" O LYS C 628 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 651 Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 660 through 671 Processing helix chain 'C' and resid 683 through 694 removed outlier: 3.960A pdb=" N LEU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET C 688 " --> pdb=" O PHE C 684 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N TYR C 689 " --> pdb=" O HIS C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 724 removed outlier: 3.893A pdb=" N ILE C 704 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 740 Processing helix chain 'C' and resid 756 through 767 removed outlier: 4.393A pdb=" N ARG C 767 " --> pdb=" O ASP C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 835 removed outlier: 4.213A pdb=" N GLY C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 827 " --> pdb=" O ARG C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 842 Processing helix chain 'C' and resid 851 through 860 Proline residue: C 857 - end of helix Processing helix chain 'C' and resid 909 through 917 removed outlier: 4.014A pdb=" N LEU C 913 " --> pdb=" O ALA C 909 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLN C 914 " --> pdb=" O LEU C 910 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 943 removed outlier: 3.640A pdb=" N ARG C 943 " --> pdb=" O ALA C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1014 Processing helix chain 'C' and resid 1015 through 1019 Processing helix chain 'C' and resid 1022 through 1031 removed outlier: 3.897A pdb=" N ALA C1026 " --> pdb=" O ARG C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1047 Processing helix chain 'C' and resid 1051 through 1061 removed outlier: 3.942A pdb=" N HIS C1057 " --> pdb=" O ILE C1053 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C1058 " --> pdb=" O SER C1054 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C1059 " --> pdb=" O LEU C1055 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C1060 " --> pdb=" O THR C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1172 removed outlier: 3.511A pdb=" N THR C1163 " --> pdb=" O HIS C1159 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C1172 " --> pdb=" O ARG C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1214 through 1219 Processing helix chain 'C' and resid 1239 through 1247 removed outlier: 3.868A pdb=" N ALA C1243 " --> pdb=" O ALA C1239 " (cutoff:3.500A) Processing helix chain 'C' and resid 1270 through 1277 Processing helix chain 'C' and resid 1278 through 1281 Processing helix chain 'C' and resid 1290 through 1296 removed outlier: 3.638A pdb=" N LYS C1294 " --> pdb=" O PRO C1291 " (cutoff:3.500A) Processing helix chain 'C' and resid 1306 through 1314 removed outlier: 3.642A pdb=" N ARG C1310 " --> pdb=" O ASN C1306 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 27 removed outlier: 3.896A pdb=" N ALA F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 removed outlier: 3.551A pdb=" N TYR F 52 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 68 Processing helix chain 'F' and resid 153 through 162 removed outlier: 3.903A pdb=" N GLU F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 162 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 208 removed outlier: 3.720A pdb=" N LEU F 203 " --> pdb=" O ALA F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 216 removed outlier: 3.610A pdb=" N GLY F 214 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 243 removed outlier: 3.613A pdb=" N SER F 243 " --> pdb=" O LEU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.765A pdb=" N GLN F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) Proline residue: F 254 - end of helix Processing helix chain 'F' and resid 268 through 273 removed outlier: 4.578A pdb=" N THR F 272 " --> pdb=" O PRO F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 287 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 238 through 250 removed outlier: 3.707A pdb=" N UNK H 242 " --> pdb=" O UNK H 238 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N UNK H 250 " --> pdb=" O UNK H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 306 removed outlier: 3.945A pdb=" N UNK H 262 " --> pdb=" O UNK H 258 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N UNK H 283 " --> pdb=" O UNK H 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 238 through 250 removed outlier: 3.653A pdb=" N UNK I 242 " --> pdb=" O UNK I 238 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK I 250 " --> pdb=" O UNK I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 306 removed outlier: 3.979A pdb=" N UNK I 262 " --> pdb=" O UNK I 258 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N UNK I 283 " --> pdb=" O UNK I 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 231 Processing helix chain 'J' and resid 238 through 250 removed outlier: 3.612A pdb=" N UNK J 242 " --> pdb=" O UNK J 238 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N UNK J 250 " --> pdb=" O UNK J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 306 removed outlier: 3.967A pdb=" N UNK J 262 " --> pdb=" O UNK J 258 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N UNK J 283 " --> pdb=" O UNK J 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 215 removed outlier: 3.817A pdb=" N UNK K 204 " --> pdb=" O UNK K 200 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N UNK K 215 " --> pdb=" O UNK K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 256 Processing helix chain 'L' and resid 198 through 215 removed outlier: 3.835A pdb=" N UNK L 204 " --> pdb=" O UNK L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 256 Processing helix chain 'O' and resid 17 through 27 Processing helix chain 'O' and resid 59 through 69 Processing helix chain 'O' and resid 152 through 159 Processing helix chain 'O' and resid 198 through 207 Processing helix chain 'O' and resid 213 through 217 Processing helix chain 'O' and resid 222 through 229 Processing helix chain 'O' and resid 261 through 265 removed outlier: 4.101A pdb=" N HIS O 264 " --> pdb=" O GLN O 261 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG O 265 " --> pdb=" O ASP O 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 261 through 265' Processing helix chain 'O' and resid 271 through 276 removed outlier: 3.637A pdb=" N SER O 275 " --> pdb=" O GLU O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 288 Processing helix chain 'Q' and resid 198 through 215 removed outlier: 3.841A pdb=" N UNK Q 204 " --> pdb=" O UNK Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 217 through 256 Processing helix chain 'R' and resid 198 through 215 removed outlier: 3.823A pdb=" N UNK R 204 " --> pdb=" O UNK R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 256 Processing helix chain 'S' and resid 198 through 215 removed outlier: 3.825A pdb=" N UNK S 204 " --> pdb=" O UNK S 200 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N UNK S 215 " --> pdb=" O UNK S 211 " (cutoff:3.500A) Processing helix chain 'S' and resid 217 through 256 Processing helix chain 'T' and resid 222 through 231 Processing helix chain 'T' and resid 238 through 250 removed outlier: 3.703A pdb=" N UNK T 242 " --> pdb=" O UNK T 238 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 306 removed outlier: 3.996A pdb=" N UNK T 262 " --> pdb=" O UNK T 258 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N UNK T 283 " --> pdb=" O UNK T 279 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 146 Processing helix chain 'X' and resid 153 through 168 removed outlier: 4.442A pdb=" N LEU X 157 " --> pdb=" O GLN X 153 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 194 Processing helix chain 'X' and resid 201 through 207 Processing helix chain 'X' and resid 209 through 216 Processing helix chain 'X' and resid 223 through 237 removed outlier: 3.502A pdb=" N GLN X 236 " --> pdb=" O ARG X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 339 through 345 Processing helix chain 'k' and resid 2 through 12 Processing helix chain 'k' and resid 29 through 37 removed outlier: 3.546A pdb=" N LEU k 33 " --> pdb=" O SER k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 44 Processing helix chain 'k' and resid 84 through 91 removed outlier: 3.587A pdb=" N GLU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU k 89 " --> pdb=" O ALA k 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 101 removed outlier: 4.127A pdb=" N LEU k 101 " --> pdb=" O PRO k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 139 through 143 removed outlier: 3.506A pdb=" N CYS k 142 " --> pdb=" O GLY k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 150 through 154 Processing helix chain 'k' and resid 159 through 162 Processing helix chain 'k' and resid 163 through 182 removed outlier: 3.732A pdb=" N ILE k 167 " --> pdb=" O ASP k 163 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET k 168 " --> pdb=" O SER k 164 " (cutoff:3.500A) Processing helix chain 'k' and resid 183 through 185 No H-bonds generated for 'chain 'k' and resid 183 through 185' Processing helix chain 'k' and resid 186 through 198 removed outlier: 3.696A pdb=" N MET k 198 " --> pdb=" O ALA k 194 " (cutoff:3.500A) Processing helix chain 'k' and resid 243 through 266 removed outlier: 3.734A pdb=" N VAL k 251 " --> pdb=" O ALA k 247 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER k 252 " --> pdb=" O ALA k 248 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU k 256 " --> pdb=" O SER k 252 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASN k 257 " --> pdb=" O ILE k 253 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN k 265 " --> pdb=" O LEU k 261 " (cutoff:3.500A) Processing helix chain 'k' and resid 356 through 370 removed outlier: 3.513A pdb=" N TRP k 360 " --> pdb=" O SER k 356 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY k 364 " --> pdb=" O TRP k 360 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA k 367 " --> pdb=" O ARG k 363 " (cutoff:3.500A) Processing helix chain 'k' and resid 373 through 380 removed outlier: 3.740A pdb=" N LEU k 377 " --> pdb=" O ARG k 373 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP k 378 " --> pdb=" O PRO k 374 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER k 379 " --> pdb=" O ASP k 375 " (cutoff:3.500A) Processing helix chain 'k' and resid 421 through 432 removed outlier: 3.647A pdb=" N CYS k 430 " --> pdb=" O LEU k 426 " (cutoff:3.500A) Processing helix chain 'k' and resid 437 through 441 removed outlier: 3.674A pdb=" N GLN k 440 " --> pdb=" O ARG k 437 " (cutoff:3.500A) Processing helix chain 'k' and resid 442 through 453 Processing helix chain 'k' and resid 454 through 457 removed outlier: 3.591A pdb=" N GLU k 457 " --> pdb=" O PRO k 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 454 through 457' Processing helix chain 'k' and resid 473 through 498 Processing helix chain 'k' and resid 516 through 540 removed outlier: 3.746A pdb=" N LEU k 520 " --> pdb=" O GLN k 516 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR k 524 " --> pdb=" O LEU k 520 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG k 525 " --> pdb=" O GLY k 521 " (cutoff:3.500A) Proline residue: k 528 - end of helix removed outlier: 3.854A pdb=" N MET k 535 " --> pdb=" O LEU k 531 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG k 536 " --> pdb=" O GLU k 532 " (cutoff:3.500A) Processing helix chain 'k' and resid 542 through 547 removed outlier: 3.815A pdb=" N PHE k 547 " --> pdb=" O PRO k 543 " (cutoff:3.500A) Processing helix chain 'k' and resid 549 through 561 removed outlier: 3.918A pdb=" N GLY k 561 " --> pdb=" O ALA k 557 " (cutoff:3.500A) Processing helix chain 'k' and resid 635 through 640 Processing helix chain 'k' and resid 680 through 691 Processing helix chain 'l' and resid 47 through 74 Processing helix chain 'l' and resid 75 through 94 removed outlier: 3.976A pdb=" N ARG l 85 " --> pdb=" O GLU l 81 " (cutoff:3.500A) Proline residue: l 86 - end of helix removed outlier: 3.691A pdb=" N ILE l 94 " --> pdb=" O ASN l 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 73 removed outlier: 4.069A pdb=" N GLN m 51 " --> pdb=" O THR m 47 " (cutoff:3.500A) Processing helix chain 'm' and resid 75 through 92 removed outlier: 4.297A pdb=" N ARG m 83 " --> pdb=" O ASP m 79 " (cutoff:3.500A) Proline residue: m 86 - end of helix Processing helix chain 'n' and resid 3094 through 3138 removed outlier: 3.827A pdb=" N VAL n3101 " --> pdb=" O SER n3097 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU n3102 " --> pdb=" O ALA n3098 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN n3111 " --> pdb=" O TYR n3107 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU n3113 " --> pdb=" O LEU n3109 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN n3114 " --> pdb=" O GLN n3110 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS n3122 " --> pdb=" O ARG n3118 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL n3127 " --> pdb=" O HIS n3123 " (cutoff:3.500A) Processing helix chain 'o' and resid 3094 through 3138 removed outlier: 3.949A pdb=" N ALA o3100 " --> pdb=" O ARG o3096 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL o3101 " --> pdb=" O SER o3097 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU o3102 " --> pdb=" O ALA o3098 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG o3108 " --> pdb=" O ARG o3104 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN o3111 " --> pdb=" O TYR o3107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU o3113 " --> pdb=" O LEU o3109 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN o3114 " --> pdb=" O GLN o3110 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS o3122 " --> pdb=" O ARG o3118 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS o3123 " --> pdb=" O ALA o3119 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER o3124 " --> pdb=" O LEU o3120 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP o3125 " --> pdb=" O LEU o3121 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA o3126 " --> pdb=" O HIS o3122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 95 removed outlier: 6.294A pdb=" N ILE A 92 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A1094 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 94 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 143 removed outlier: 3.830A pdb=" N HIS A 137 " --> pdb=" O HIS A1118 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 141 " --> pdb=" O GLN A1114 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A1114 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 143 " --> pdb=" O LEU A1112 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A1112 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 135 removed outlier: 3.618A pdb=" N LYS A 134 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 40 " --> pdb=" O GLN A 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 314 removed outlier: 3.584A pdb=" N ASP A 307 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 384 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR A 309 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ASP A 383 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 289 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A1083 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1128 through 1134 removed outlier: 6.178A pdb=" N GLU A1080 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU A1134 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ALA A1078 " --> pdb=" O LEU A1134 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASN A 414 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A1340 " --> pdb=" O VAL A1318 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A1318 " --> pdb=" O THR A1340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 456 through 460 Processing sheet with id=AA7, first strand: chain 'A' and resid 563 through 569 Processing sheet with id=AA8, first strand: chain 'A' and resid 752 through 753 Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 958 Processing sheet with id=AB1, first strand: chain 'A' and resid 1355 through 1356 removed outlier: 3.652A pdb=" N CYS A1355 " --> pdb=" O ILE A1382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 36 through 37 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.334A pdb=" N ILE C 92 " --> pdb=" O TYR C1092 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL C1094 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR C 94 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.334A pdb=" N ILE C 92 " --> pdb=" O TYR C1092 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL C1094 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR C 94 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AB6, first strand: chain 'C' and resid 306 through 313 removed outlier: 6.357A pdb=" N LEU C 384 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR C 309 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP C 383 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 394 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY C 287 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLU C 395 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU C 289 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA C1078 " --> pdb=" O LEU C1134 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU C1134 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU C1080 " --> pdb=" O ALA C1132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 414 through 422 Processing sheet with id=AB8, first strand: chain 'C' and resid 469 through 470 Processing sheet with id=AB9, first strand: chain 'C' and resid 563 through 569 removed outlier: 3.608A pdb=" N THR C 590 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 752 through 753 Processing sheet with id=AC2, first strand: chain 'C' and resid 956 through 958 Processing sheet with id=AC3, first strand: chain 'F' and resid 31 through 34 Processing sheet with id=AC4, first strand: chain 'F' and resid 99 through 100 Processing sheet with id=AC5, first strand: chain 'F' and resid 112 through 115 Processing sheet with id=AC6, first strand: chain 'F' and resid 127 through 128 Processing sheet with id=AC7, first strand: chain 'F' and resid 177 through 179 removed outlier: 3.953A pdb=" N TYR F 179 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 182 " --> pdb=" O TYR F 179 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 31 through 34 removed outlier: 6.901A pdb=" N LEU O 84 " --> pdb=" O THR O 76 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA O 41 " --> pdb=" O GLU O 7 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU O 9 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 99 through 100 Processing sheet with id=AD1, first strand: chain 'O' and resid 139 through 142 removed outlier: 3.720A pdb=" N LEU O 293 " --> pdb=" O ILE O 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 111 through 116 Processing sheet with id=AD3, first strand: chain 'X' and resid 184 through 186 removed outlier: 6.903A pdb=" N VAL X 131 " --> pdb=" O PHE X 248 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 269 through 270 Processing sheet with id=AD5, first strand: chain 'X' and resid 288 through 289 removed outlier: 3.528A pdb=" N ILE X 288 " --> pdb=" O LEU X 452 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 327 through 328 Processing sheet with id=AD7, first strand: chain 'X' and resid 327 through 328 removed outlier: 6.487A pdb=" N LEU X 312 " --> pdb=" O LEU X 424 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU X 424 " --> pdb=" O LEU X 312 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE X 314 " --> pdb=" O TYR X 422 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR X 422 " --> pdb=" O PHE X 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR X 422 " --> pdb=" O ASN X 464 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN X 464 " --> pdb=" O TYR X 422 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 439 through 440 removed outlier: 4.286A pdb=" N GLU X 440 " --> pdb=" O VAL X 447 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL X 447 " --> pdb=" O GLU X 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'k' and resid 79 through 80 removed outlier: 3.548A pdb=" N VAL k 112 " --> pdb=" O VAL k 26 " (cutoff:3.500A) removed outlier: 11.799A pdb=" N LEU k 23 " --> pdb=" O TYR k 402 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N TYR k 402 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS k 25 " --> pdb=" O VAL k 400 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'k' and resid 74 through 76 Processing sheet with id=AE2, first strand: chain 'k' and resid 504 through 505 Processing sheet with id=AE3, first strand: chain 'k' and resid 570 through 571 removed outlier: 3.742A pdb=" N VAL k 570 " --> pdb=" O ARG k 693 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'k' and resid 586 through 589 removed outlier: 3.943A pdb=" N ILE k 606 " --> pdb=" O PHE k 589 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'k' and resid 591 through 592 Processing sheet with id=AE6, first strand: chain 'l' and resid 10 through 14 removed outlier: 3.697A pdb=" N VAL l 12 " --> pdb=" O ARG m 16 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG m 16 " --> pdb=" O VAL l 12 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU m 14 " --> pdb=" O GLU l 14 " (cutoff:3.500A) 1687 hydrogen bonds defined for protein. 4725 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: 8.41 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12713 1.34 - 1.46: 6837 1.46 - 1.58: 18228 1.58 - 1.70: 3 1.70 - 1.82: 295 Bond restraints: 38076 Sorted by residual: bond pdb=" N ILE C 68 " pdb=" CA ILE C 68 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.31e+00 bond pdb=" N TYR C 62 " pdb=" CA TYR C 62 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.31e-02 5.83e+03 7.84e+00 bond pdb=" N VAL C 184 " pdb=" CA VAL C 184 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.04e+00 bond pdb=" C GLN C 176 " pdb=" O GLN C 176 " ideal model delta sigma weight residual 1.236 1.267 -0.030 1.15e-02 7.56e+03 6.88e+00 bond pdb=" N LEU C 181 " pdb=" CA LEU C 181 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.71e+00 ... (remaining 38071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 51474 3.49 - 6.98: 472 6.98 - 10.47: 49 10.47 - 13.97: 18 13.97 - 17.46: 2 Bond angle restraints: 52015 Sorted by residual: angle pdb=" C LEU O 217 " pdb=" N ILE O 218 " pdb=" CA ILE O 218 " ideal model delta sigma weight residual 121.70 139.16 -17.46 1.80e+00 3.09e-01 9.41e+01 angle pdb=" C ILE F 277 " pdb=" N SER F 278 " pdb=" CA SER F 278 " ideal model delta sigma weight residual 121.70 136.47 -14.77 1.80e+00 3.09e-01 6.73e+01 angle pdb=" C UNK B 255 " pdb=" N UNK B 256 " pdb=" CA UNK B 256 " ideal model delta sigma weight residual 121.70 134.28 -12.58 1.80e+00 3.09e-01 4.89e+01 angle pdb=" C UNK I 255 " pdb=" N UNK I 256 " pdb=" CA UNK I 256 " ideal model delta sigma weight residual 121.70 134.28 -12.58 1.80e+00 3.09e-01 4.88e+01 angle pdb=" C UNK H 255 " pdb=" N UNK H 256 " pdb=" CA UNK H 256 " ideal model delta sigma weight residual 121.70 134.23 -12.53 1.80e+00 3.09e-01 4.85e+01 ... (remaining 52010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 21072 17.70 - 35.41: 1459 35.41 - 53.11: 224 53.11 - 70.82: 50 70.82 - 88.52: 29 Dihedral angle restraints: 22834 sinusoidal: 7807 harmonic: 15027 Sorted by residual: dihedral pdb=" CB CYS C 846 " pdb=" SG CYS C 846 " pdb=" SG CYS C 985 " pdb=" CB CYS C 985 " ideal model delta sinusoidal sigma weight residual -86.00 -13.27 -72.73 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS A 846 " pdb=" SG CYS A 846 " pdb=" SG CYS A 985 " pdb=" CB CYS A 985 " ideal model delta sinusoidal sigma weight residual -86.00 -16.30 -69.70 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CD ARG C 45 " pdb=" NE ARG C 45 " pdb=" CZ ARG C 45 " pdb=" NH1 ARG C 45 " ideal model delta sinusoidal sigma weight residual 0.00 -68.05 68.05 1 1.00e+01 1.00e-02 6.01e+01 ... (remaining 22831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4966 0.056 - 0.112: 1032 0.112 - 0.168: 132 0.168 - 0.224: 19 0.224 - 0.280: 8 Chirality restraints: 6157 Sorted by residual: chirality pdb=" CB ILE A 92 " pdb=" CA ILE A 92 " pdb=" CG1 ILE A 92 " pdb=" CG2 ILE A 92 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA LEU F 63 " pdb=" N LEU F 63 " pdb=" C LEU F 63 " pdb=" CB LEU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE X 450 " pdb=" CA ILE X 450 " pdb=" CG1 ILE X 450 " pdb=" CG2 ILE X 450 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 6154 not shown) Planarity restraints: 6855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 45 " -1.011 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG C 45 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 45 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 45 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 45 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY X 269 " 0.092 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO X 270 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO X 270 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO X 270 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP l 2 " -0.068 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO l 3 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO l 3 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO l 3 " -0.054 5.00e-02 4.00e+02 ... (remaining 6852 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 249 2.43 - 3.05: 26460 3.05 - 3.67: 60098 3.67 - 4.28: 80315 4.28 - 4.90: 126095 Nonbonded interactions: 293217 Sorted by model distance: nonbonded pdb=" CG2 VAL C 337 " pdb=" CD2 LEU C 340 " model vdw 1.816 3.880 nonbonded pdb=" O VAL A 681 " pdb=" OH TYR A 832 " model vdw 2.045 3.040 nonbonded pdb=" OG1 THR A1144 " pdb=" O SER A1202 " model vdw 2.062 3.040 nonbonded pdb=" OH TYR A1092 " pdb=" NH1 ARG A1116 " model vdw 2.107 3.120 nonbonded pdb=" O ALA A1085 " pdb=" OG SER A1089 " model vdw 2.121 3.040 ... (remaining 293212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 45 or resid 61 through 156 or resi \ d 166 through 181 or (resid 182 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD )) or resid 183 through 636 or (resid 637 through 63 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 671 or resid 678 through 853 or (resid 854 and (name N or name CA or name C or n \ ame O or name CB )) or resid 855 through 856 or (resid 857 through 858 and (name \ N or name CA or name C or name O or name CB )) or resid 859 through 860 or resi \ d 908 through 960 or resid 971 through 972 or (resid 973 and (name N or name CA \ or name C or name O or name CB )) or resid 974 through 990 or resid 1004 through \ 1231 or (resid 1232 through 1234 and (name N or name CA or name C or name O or \ name CB )) or resid 1235 through 1394)) selection = (chain 'C' and (resid 14 through 317 or (resid 321 through 323 and (name N or na \ me CA or name C or name O or name CB )) or (resid 324 through 333 and (name N or \ name CA or name C or name O or name CB )) or resid 334 or (resid 335 through 34 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 344 or resid \ 376 through 1394)) } ncs_group { reference = (chain 'B' and resid 231 through 306) selection = (chain 'H' and resid 231 through 306) selection = (chain 'I' and resid 231 through 306) selection = (chain 'J' and resid 231 through 306) selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = (chain 'T' and resid 231 through 306) } ncs_group { reference = (chain 'l' and (resid 13 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 92)) selection = chain 'm' } ncs_group { reference = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.770 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.005 0.108 38078 Z= 0.233 Angle : 0.926 17.457 52019 Z= 0.498 Chirality : 0.047 0.280 6157 Planarity : 0.008 0.453 6855 Dihedral : 12.901 88.524 13054 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 23.07 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.52 % Favored : 88.82 % Rotamer: Outliers : 0.43 % Allowed : 0.52 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.13), residues: 4277 helix: -0.15 (0.14), residues: 1315 sheet: -1.33 (0.22), residues: 497 loop : -1.69 (0.13), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 767 TYR 0.034 0.002 TYR A 409 PHE 0.039 0.002 PHE A 244 TRP 0.028 0.002 TRP k 376 HIS 0.007 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00456 (38076) covalent geometry : angle 0.92555 (52015) SS BOND : bond 0.00330 ( 2) SS BOND : angle 1.77854 ( 4) hydrogen bonds : bond 0.15841 ( 1681) hydrogen bonds : angle 6.43500 ( 4725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 853 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.7598 (m-10) cc_final: 0.6982 (m-10) REVERT: A 166 ASP cc_start: 0.9079 (t70) cc_final: 0.8854 (t0) REVERT: A 200 LEU cc_start: 0.9536 (tp) cc_final: 0.9280 (tp) REVERT: A 295 LEU cc_start: 0.9648 (mm) cc_final: 0.9380 (mm) REVERT: A 298 GLN cc_start: 0.9032 (pp30) cc_final: 0.8665 (pp30) REVERT: A 301 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 421 MET cc_start: 0.8718 (tpp) cc_final: 0.8500 (tpp) REVERT: A 431 MET cc_start: 0.7199 (tpt) cc_final: 0.6429 (tpp) REVERT: A 468 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8486 (tm-30) REVERT: A 559 LEU cc_start: 0.9403 (mt) cc_final: 0.9128 (mt) REVERT: A 560 ASN cc_start: 0.9283 (t0) cc_final: 0.8921 (t0) REVERT: A 605 ILE cc_start: 0.9404 (mp) cc_final: 0.8891 (tt) REVERT: A 631 LYS cc_start: 0.9453 (mmpt) cc_final: 0.9103 (mmmt) REVERT: A 645 MET cc_start: 0.9270 (mtt) cc_final: 0.8988 (mtp) REVERT: A 686 MET cc_start: 0.9251 (ptp) cc_final: 0.9010 (ptt) REVERT: A 687 LEU cc_start: 0.9484 (pt) cc_final: 0.9211 (pp) REVERT: A 753 LEU cc_start: 0.9194 (mt) cc_final: 0.8985 (mt) REVERT: A 793 ASN cc_start: 0.8590 (t0) cc_final: 0.8302 (t0) REVERT: A 797 ARG cc_start: 0.8690 (mpt90) cc_final: 0.8414 (mmt180) REVERT: A 832 TYR cc_start: 0.8602 (t80) cc_final: 0.8150 (t80) REVERT: A 872 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7615 (pm20) REVERT: A 983 PHE cc_start: 0.9122 (m-80) cc_final: 0.8847 (m-80) REVERT: A 1055 LEU cc_start: 0.9697 (tp) cc_final: 0.9353 (tp) REVERT: A 1059 LEU cc_start: 0.9436 (mt) cc_final: 0.9110 (mt) REVERT: A 1097 ILE cc_start: 0.8856 (tp) cc_final: 0.8169 (tp) REVERT: A 1138 LEU cc_start: 0.9035 (pp) cc_final: 0.8745 (pp) REVERT: A 1160 ASP cc_start: 0.9033 (p0) cc_final: 0.8594 (p0) REVERT: A 1245 MET cc_start: 0.9212 (tpt) cc_final: 0.8959 (tpp) REVERT: A 1351 TYR cc_start: 0.8519 (m-10) cc_final: 0.8267 (m-10) REVERT: C 85 LEU cc_start: 0.9324 (mt) cc_final: 0.9088 (mt) REVERT: C 186 ASP cc_start: 0.9337 (OUTLIER) cc_final: 0.9070 (t0) REVERT: C 188 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8778 (t80) REVERT: C 242 MET cc_start: 0.8346 (tpt) cc_final: 0.7949 (tpp) REVERT: C 243 PHE cc_start: 0.8913 (m-80) cc_final: 0.8503 (m-80) REVERT: C 262 MET cc_start: 0.9103 (tpt) cc_final: 0.8765 (tmm) REVERT: C 320 MET cc_start: 0.8366 (tmm) cc_final: 0.8002 (tmm) REVERT: C 416 ASP cc_start: 0.8093 (m-30) cc_final: 0.7795 (m-30) REVERT: C 419 PHE cc_start: 0.8871 (m-80) cc_final: 0.8627 (m-80) REVERT: C 429 ASN cc_start: 0.8878 (m-40) cc_final: 0.8610 (t0) REVERT: C 534 HIS cc_start: 0.9056 (t70) cc_final: 0.8627 (t70) REVERT: C 608 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8236 (ttm110) REVERT: C 680 PHE cc_start: 0.8422 (m-80) cc_final: 0.8038 (m-80) REVERT: C 688 MET cc_start: 0.9141 (ppp) cc_final: 0.8861 (ppp) REVERT: C 689 TYR cc_start: 0.9000 (m-80) cc_final: 0.8312 (m-80) REVERT: C 759 LEU cc_start: 0.9746 (tt) cc_final: 0.9449 (tt) REVERT: C 983 PHE cc_start: 0.9190 (m-80) cc_final: 0.8816 (m-80) REVERT: C 1005 MET cc_start: 0.9229 (ttt) cc_final: 0.8580 (tpp) REVERT: C 1057 HIS cc_start: 0.8937 (m-70) cc_final: 0.8313 (m-70) REVERT: C 1126 THR cc_start: 0.8752 (p) cc_final: 0.8421 (t) REVERT: C 1131 THR cc_start: 0.8725 (p) cc_final: 0.7813 (p) REVERT: C 1223 ASN cc_start: 0.9278 (t0) cc_final: 0.8258 (p0) REVERT: C 1242 GLU cc_start: 0.9193 (mp0) cc_final: 0.8946 (mp0) REVERT: C 1245 MET cc_start: 0.9041 (ppp) cc_final: 0.8697 (ppp) REVERT: C 1275 LEU cc_start: 0.9157 (tp) cc_final: 0.8546 (tp) REVERT: C 1276 TYR cc_start: 0.7920 (m-10) cc_final: 0.7474 (m-10) REVERT: C 1289 TYR cc_start: 0.8951 (t80) cc_final: 0.8550 (t80) REVERT: C 1361 MET cc_start: 0.8538 (ptt) cc_final: 0.8242 (pmm) REVERT: F 46 ILE cc_start: 0.9331 (pt) cc_final: 0.9046 (pt) REVERT: F 141 ILE cc_start: 0.9134 (mm) cc_final: 0.8640 (mm) REVERT: O 7 GLU cc_start: 0.8376 (pm20) cc_final: 0.8138 (pm20) REVERT: O 112 TYR cc_start: 0.8488 (m-10) cc_final: 0.8215 (m-10) REVERT: O 137 PHE cc_start: 0.8246 (m-80) cc_final: 0.7610 (m-80) REVERT: O 290 ARG cc_start: 0.7655 (pmt170) cc_final: 0.7201 (pmt170) REVERT: O 313 ILE cc_start: 0.9522 (tp) cc_final: 0.9238 (tp) REVERT: O 314 GLN cc_start: 0.9287 (pm20) cc_final: 0.8816 (pm20) REVERT: X 268 LYS cc_start: 0.9080 (pttp) cc_final: 0.8854 (pttm) REVERT: X 336 GLU cc_start: 0.8744 (tt0) cc_final: 0.8122 (tp30) REVERT: X 457 TRP cc_start: 0.7360 (m-90) cc_final: 0.6735 (m-90) REVERT: k 26 VAL cc_start: 0.8319 (m) cc_final: 0.7953 (m) REVERT: k 527 PHE cc_start: 0.8873 (t80) cc_final: 0.8533 (t80) REVERT: k 649 LEU cc_start: 0.9029 (mm) cc_final: 0.8695 (mm) REVERT: l 26 PHE cc_start: 0.4817 (t80) cc_final: 0.4578 (t80) outliers start: 15 outliers final: 2 residues processed: 865 average time/residue: 0.1929 time to fit residues: 277.6545 Evaluate side-chains 686 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 682 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 50.0000 chunk 494 optimal weight: 40.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 180 ASN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 496 GLN A 656 ASN ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS C 112 GLN C 588 ASN C 741 ASN C1057 HIS C1146 GLN C1262 ASN ** C1321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 126 HIS ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN ** m 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.130115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093673 restraints weight = 150054.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095891 restraints weight = 92874.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097340 restraints weight = 65223.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.098658 restraints weight = 51463.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099379 restraints weight = 42886.528| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38078 Z= 0.173 Angle : 0.784 17.589 52019 Z= 0.398 Chirality : 0.044 0.284 6157 Planarity : 0.005 0.081 6855 Dihedral : 5.108 38.322 5553 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.61 % Favored : 89.85 % Rotamer: Outliers : 0.14 % Allowed : 5.60 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.04 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.13), residues: 4277 helix: 0.01 (0.14), residues: 1357 sheet: -1.21 (0.22), residues: 520 loop : -1.65 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1310 TYR 0.020 0.002 TYR A 409 PHE 0.020 0.002 PHE F 98 TRP 0.019 0.002 TRP k 376 HIS 0.007 0.001 HIS C 821 Details of bonding type rmsd covalent geometry : bond 0.00362 (38076) covalent geometry : angle 0.78416 (52015) SS BOND : bond 0.00461 ( 2) SS BOND : angle 1.13502 ( 4) hydrogen bonds : bond 0.03896 ( 1681) hydrogen bonds : angle 5.07533 ( 4725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 866 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8828 (mppt) cc_final: 0.8152 (mmtm) REVERT: A 166 ASP cc_start: 0.9131 (t70) cc_final: 0.8873 (t0) REVERT: A 188 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: A 200 LEU cc_start: 0.9688 (tp) cc_final: 0.9479 (tp) REVERT: A 233 ASP cc_start: 0.9408 (t70) cc_final: 0.9094 (t0) REVERT: A 236 ARG cc_start: 0.9275 (ttp-110) cc_final: 0.8302 (mtm110) REVERT: A 296 LYS cc_start: 0.9360 (tppp) cc_final: 0.8726 (mmtp) REVERT: A 298 GLN cc_start: 0.9154 (pp30) cc_final: 0.8817 (pp30) REVERT: A 301 GLN cc_start: 0.9269 (tm-30) cc_final: 0.9033 (tm-30) REVERT: A 421 MET cc_start: 0.8720 (tpp) cc_final: 0.8370 (tpp) REVERT: A 431 MET cc_start: 0.8001 (tpt) cc_final: 0.7195 (tpp) REVERT: A 469 LEU cc_start: 0.9179 (mm) cc_final: 0.8791 (mm) REVERT: A 559 LEU cc_start: 0.9627 (mt) cc_final: 0.9365 (mt) REVERT: A 560 ASN cc_start: 0.9301 (t0) cc_final: 0.8941 (t0) REVERT: A 605 ILE cc_start: 0.9407 (mp) cc_final: 0.8810 (tt) REVERT: A 631 LYS cc_start: 0.9368 (mmpt) cc_final: 0.9152 (mmmt) REVERT: A 645 MET cc_start: 0.9278 (mtt) cc_final: 0.9013 (mtp) REVERT: A 687 LEU cc_start: 0.9294 (pt) cc_final: 0.9035 (pp) REVERT: A 688 MET cc_start: 0.8811 (ptp) cc_final: 0.8538 (ptp) REVERT: A 797 ARG cc_start: 0.8554 (mpt90) cc_final: 0.8346 (mmt180) REVERT: A 872 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7973 (pm20) REVERT: A 923 ARG cc_start: 0.8155 (ppt170) cc_final: 0.7480 (ppt170) REVERT: A 949 ASP cc_start: 0.9105 (t0) cc_final: 0.8896 (t0) REVERT: A 959 MET cc_start: 0.8312 (mmp) cc_final: 0.7014 (mmm) REVERT: A 983 PHE cc_start: 0.8824 (m-80) cc_final: 0.8493 (m-80) REVERT: A 1005 MET cc_start: 0.7626 (ppp) cc_final: 0.7385 (ppp) REVERT: A 1055 LEU cc_start: 0.9607 (tp) cc_final: 0.9134 (tp) REVERT: A 1059 LEU cc_start: 0.9380 (mt) cc_final: 0.9118 (mt) REVERT: A 1086 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 1097 ILE cc_start: 0.9128 (tp) cc_final: 0.8512 (tp) REVERT: A 1147 ASN cc_start: 0.9514 (t0) cc_final: 0.9185 (t0) REVERT: A 1160 ASP cc_start: 0.8942 (p0) cc_final: 0.8278 (p0) REVERT: A 1245 MET cc_start: 0.9588 (tpt) cc_final: 0.9167 (tpp) REVERT: A 1247 ASP cc_start: 0.9182 (t0) cc_final: 0.8773 (t0) REVERT: A 1250 GLN cc_start: 0.9066 (pt0) cc_final: 0.8598 (pt0) REVERT: A 1281 ASN cc_start: 0.9360 (p0) cc_final: 0.9136 (p0) REVERT: A 1309 ASP cc_start: 0.9187 (m-30) cc_final: 0.8892 (t0) REVERT: A 1313 MET cc_start: 0.9267 (mtm) cc_final: 0.8396 (mtt) REVERT: A 1373 ASP cc_start: 0.8308 (t0) cc_final: 0.7732 (t0) REVERT: C 44 HIS cc_start: 0.7220 (m90) cc_final: 0.6913 (m90) REVERT: C 85 LEU cc_start: 0.9458 (mt) cc_final: 0.9254 (mt) REVERT: C 197 LEU cc_start: 0.9704 (tt) cc_final: 0.9459 (tt) REVERT: C 201 LEU cc_start: 0.9494 (mm) cc_final: 0.9201 (mm) REVERT: C 242 MET cc_start: 0.8557 (tpt) cc_final: 0.8083 (tpp) REVERT: C 243 PHE cc_start: 0.9208 (m-80) cc_final: 0.8714 (m-10) REVERT: C 245 MET cc_start: 0.9529 (mmp) cc_final: 0.9307 (mmp) REVERT: C 320 MET cc_start: 0.8691 (tmm) cc_final: 0.8242 (tmm) REVERT: C 327 LEU cc_start: 0.9579 (mt) cc_final: 0.9333 (mt) REVERT: C 331 LEU cc_start: 0.9261 (mm) cc_final: 0.8991 (mm) REVERT: C 383 ASP cc_start: 0.8271 (p0) cc_final: 0.8017 (p0) REVERT: C 395 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8764 (tm-30) REVERT: C 416 ASP cc_start: 0.8437 (m-30) cc_final: 0.8093 (m-30) REVERT: C 429 ASN cc_start: 0.9348 (m-40) cc_final: 0.8865 (t0) REVERT: C 534 HIS cc_start: 0.9059 (t70) cc_final: 0.8485 (t-90) REVERT: C 680 PHE cc_start: 0.8476 (m-80) cc_final: 0.8050 (m-80) REVERT: C 688 MET cc_start: 0.9161 (ppp) cc_final: 0.8815 (ppp) REVERT: C 689 TYR cc_start: 0.9096 (m-80) cc_final: 0.8048 (m-80) REVERT: C 718 ARG cc_start: 0.9459 (tmt-80) cc_final: 0.8984 (tpt90) REVERT: C 764 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8764 (pm20) REVERT: C 983 PHE cc_start: 0.9206 (m-80) cc_final: 0.8765 (m-80) REVERT: C 1005 MET cc_start: 0.9232 (ttt) cc_final: 0.8533 (tpp) REVERT: C 1050 PHE cc_start: 0.8729 (t80) cc_final: 0.8305 (t80) REVERT: C 1084 TYR cc_start: 0.9309 (t80) cc_final: 0.8869 (t80) REVERT: C 1126 THR cc_start: 0.8786 (p) cc_final: 0.8480 (t) REVERT: C 1131 THR cc_start: 0.8843 (p) cc_final: 0.8163 (p) REVERT: C 1157 MET cc_start: 0.9601 (mmm) cc_final: 0.9293 (mmm) REVERT: C 1188 LEU cc_start: 0.9455 (mp) cc_final: 0.9221 (mp) REVERT: C 1223 ASN cc_start: 0.9461 (t0) cc_final: 0.8985 (t0) REVERT: C 1231 MET cc_start: 0.8826 (ppp) cc_final: 0.8611 (ppp) REVERT: C 1242 GLU cc_start: 0.9490 (mp0) cc_final: 0.9162 (mp0) REVERT: C 1258 ARG cc_start: 0.8705 (ptt-90) cc_final: 0.8384 (ptt-90) REVERT: F 46 ILE cc_start: 0.9337 (pt) cc_final: 0.9048 (pt) REVERT: F 115 LEU cc_start: 0.9256 (mm) cc_final: 0.8958 (mm) REVERT: F 139 LEU cc_start: 0.8900 (tp) cc_final: 0.8590 (tp) REVERT: F 141 ILE cc_start: 0.9277 (mm) cc_final: 0.9025 (mm) REVERT: F 200 ILE cc_start: 0.9558 (pt) cc_final: 0.9340 (tt) REVERT: F 209 PHE cc_start: 0.9068 (p90) cc_final: 0.8844 (p90) REVERT: O 7 GLU cc_start: 0.8734 (pm20) cc_final: 0.8225 (tm-30) REVERT: O 112 TYR cc_start: 0.8681 (m-10) cc_final: 0.8450 (m-10) REVERT: O 137 PHE cc_start: 0.8472 (m-80) cc_final: 0.7409 (m-80) REVERT: O 289 THR cc_start: 0.8432 (m) cc_final: 0.7811 (t) REVERT: O 313 ILE cc_start: 0.9500 (tp) cc_final: 0.9282 (tp) REVERT: O 314 GLN cc_start: 0.9173 (pm20) cc_final: 0.8695 (pm20) REVERT: X 183 TYR cc_start: 0.8446 (m-10) cc_final: 0.7801 (m-10) REVERT: X 336 GLU cc_start: 0.8703 (tt0) cc_final: 0.7971 (tp30) REVERT: X 337 GLN cc_start: 0.7399 (pm20) cc_final: 0.7068 (pm20) REVERT: X 422 TYR cc_start: 0.6887 (p90) cc_final: 0.6088 (p90) REVERT: k 28 ILE cc_start: 0.5645 (mp) cc_final: 0.5256 (mp) REVERT: k 483 HIS cc_start: 0.8597 (t-90) cc_final: 0.8351 (t-90) REVERT: k 527 PHE cc_start: 0.9242 (t80) cc_final: 0.8782 (t80) REVERT: k 535 MET cc_start: 0.9188 (ppp) cc_final: 0.8650 (ppp) REVERT: k 649 LEU cc_start: 0.9312 (mm) cc_final: 0.9002 (mm) REVERT: l 26 PHE cc_start: 0.4215 (t80) cc_final: 0.3153 (t80) REVERT: m 71 MET cc_start: 0.2298 (ppp) cc_final: 0.1840 (ptp) outliers start: 5 outliers final: 0 residues processed: 870 average time/residue: 0.1987 time to fit residues: 287.5068 Evaluate side-chains 719 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 717 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 392 optimal weight: 50.0000 chunk 435 optimal weight: 30.0000 chunk 184 optimal weight: 4.9990 chunk 459 optimal weight: 40.0000 chunk 239 optimal weight: 6.9990 chunk 424 optimal weight: 10.0000 chunk 411 optimal weight: 8.9990 chunk 36 optimal weight: 0.0170 chunk 470 optimal weight: 50.0000 chunk 389 optimal weight: 60.0000 chunk 398 optimal weight: 50.0000 overall best weight: 6.2028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 GLN k 548 HIS k 619 GLN l 90 ASN ** m 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o3133 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.130063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093303 restraints weight = 151071.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.097710 restraints weight = 93718.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.097991 restraints weight = 53450.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098556 restraints weight = 44754.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.098698 restraints weight = 45880.019| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 38078 Z= 0.164 Angle : 0.767 17.423 52019 Z= 0.388 Chirality : 0.043 0.280 6157 Planarity : 0.005 0.102 6855 Dihedral : 4.995 37.424 5553 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.59 % Favored : 89.90 % Rotamer: Outliers : 0.03 % Allowed : 3.96 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.04 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.13), residues: 4277 helix: 0.12 (0.14), residues: 1362 sheet: -1.17 (0.23), residues: 485 loop : -1.67 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG k 536 TYR 0.024 0.002 TYR k 402 PHE 0.019 0.002 PHE A 748 TRP 0.016 0.002 TRP k 365 HIS 0.006 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00350 (38076) covalent geometry : angle 0.76731 (52015) SS BOND : bond 0.00578 ( 2) SS BOND : angle 1.31487 ( 4) hydrogen bonds : bond 0.03603 ( 1681) hydrogen bonds : angle 4.89615 ( 4725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 865 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9255 (tp30) cc_final: 0.9041 (tp30) REVERT: A 102 VAL cc_start: 0.9002 (t) cc_final: 0.8750 (t) REVERT: A 109 PHE cc_start: 0.8329 (m-10) cc_final: 0.8081 (m-10) REVERT: A 134 LYS cc_start: 0.9036 (mppt) cc_final: 0.8466 (mmtm) REVERT: A 138 LYS cc_start: 0.7873 (tppp) cc_final: 0.6987 (tppp) REVERT: A 200 LEU cc_start: 0.9706 (tp) cc_final: 0.9449 (tp) REVERT: A 233 ASP cc_start: 0.9404 (t70) cc_final: 0.9033 (t0) REVERT: A 236 ARG cc_start: 0.9268 (ttp-110) cc_final: 0.8316 (mtm110) REVERT: A 259 LEU cc_start: 0.9767 (mm) cc_final: 0.9518 (mm) REVERT: A 289 LEU cc_start: 0.9702 (tt) cc_final: 0.9498 (tt) REVERT: A 296 LYS cc_start: 0.9386 (tppp) cc_final: 0.8820 (mmtp) REVERT: A 298 GLN cc_start: 0.9036 (pp30) cc_final: 0.8735 (pp30) REVERT: A 421 MET cc_start: 0.8437 (tpp) cc_final: 0.8133 (tpp) REVERT: A 431 MET cc_start: 0.8066 (tpt) cc_final: 0.7271 (tpp) REVERT: A 560 ASN cc_start: 0.9319 (t0) cc_final: 0.8947 (t0) REVERT: A 573 ASP cc_start: 0.9120 (t0) cc_final: 0.8918 (t0) REVERT: A 605 ILE cc_start: 0.9305 (mp) cc_final: 0.8761 (tt) REVERT: A 631 LYS cc_start: 0.9343 (mmpt) cc_final: 0.9089 (mmmt) REVERT: A 645 MET cc_start: 0.9296 (mtt) cc_final: 0.8955 (mtp) REVERT: A 687 LEU cc_start: 0.9277 (pt) cc_final: 0.8947 (pp) REVERT: A 763 ASP cc_start: 0.8920 (p0) cc_final: 0.8697 (p0) REVERT: A 797 ARG cc_start: 0.8542 (mpt90) cc_final: 0.8250 (mmt180) REVERT: A 824 GLU cc_start: 0.8927 (pm20) cc_final: 0.8555 (pp20) REVERT: A 872 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7976 (pm20) REVERT: A 923 ARG cc_start: 0.8120 (ppt170) cc_final: 0.7525 (ppt170) REVERT: A 949 ASP cc_start: 0.9071 (t0) cc_final: 0.8694 (t0) REVERT: A 959 MET cc_start: 0.8503 (mmp) cc_final: 0.7441 (mmt) REVERT: A 983 PHE cc_start: 0.8869 (m-80) cc_final: 0.8518 (m-80) REVERT: A 1005 MET cc_start: 0.7551 (ppp) cc_final: 0.6482 (ppp) REVERT: A 1055 LEU cc_start: 0.9614 (tp) cc_final: 0.9161 (tp) REVERT: A 1059 LEU cc_start: 0.9368 (mt) cc_final: 0.9060 (mt) REVERT: A 1079 THR cc_start: 0.8636 (t) cc_final: 0.8331 (t) REVERT: A 1083 LEU cc_start: 0.9706 (tt) cc_final: 0.9203 (tt) REVERT: A 1086 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 1097 ILE cc_start: 0.9236 (tp) cc_final: 0.8666 (tp) REVERT: A 1147 ASN cc_start: 0.9539 (t0) cc_final: 0.9186 (t0) REVERT: A 1160 ASP cc_start: 0.8889 (p0) cc_final: 0.8186 (p0) REVERT: A 1245 MET cc_start: 0.9630 (tpt) cc_final: 0.9246 (tpp) REVERT: A 1313 MET cc_start: 0.9301 (mtm) cc_final: 0.8828 (mtt) REVERT: A 1373 ASP cc_start: 0.8624 (t0) cc_final: 0.7907 (t0) REVERT: A 1377 LEU cc_start: 0.9289 (tp) cc_final: 0.9005 (mt) REVERT: C 85 LEU cc_start: 0.9457 (mt) cc_final: 0.9007 (mt) REVERT: C 197 LEU cc_start: 0.9710 (tt) cc_final: 0.9401 (tt) REVERT: C 201 LEU cc_start: 0.9473 (mm) cc_final: 0.9200 (mm) REVERT: C 242 MET cc_start: 0.8601 (tpt) cc_final: 0.8114 (tpp) REVERT: C 243 PHE cc_start: 0.9149 (m-80) cc_final: 0.8681 (m-10) REVERT: C 327 LEU cc_start: 0.9587 (mt) cc_final: 0.9350 (mt) REVERT: C 331 LEU cc_start: 0.9304 (mm) cc_final: 0.9049 (mm) REVERT: C 383 ASP cc_start: 0.8307 (p0) cc_final: 0.8027 (p0) REVERT: C 395 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8681 (tm-30) REVERT: C 416 ASP cc_start: 0.8446 (m-30) cc_final: 0.8112 (m-30) REVERT: C 429 ASN cc_start: 0.9374 (m-40) cc_final: 0.8877 (t0) REVERT: C 461 ASN cc_start: 0.9758 (t0) cc_final: 0.9297 (t0) REVERT: C 463 ASP cc_start: 0.9129 (m-30) cc_final: 0.8873 (m-30) REVERT: C 530 MET cc_start: 0.9190 (tpt) cc_final: 0.8836 (tpt) REVERT: C 534 HIS cc_start: 0.9050 (t70) cc_final: 0.8470 (t-90) REVERT: C 565 PHE cc_start: 0.9051 (m-10) cc_final: 0.8617 (m-10) REVERT: C 605 ILE cc_start: 0.9400 (pt) cc_final: 0.9162 (pt) REVERT: C 608 ARG cc_start: 0.9071 (mtp85) cc_final: 0.8607 (mtp85) REVERT: C 628 LYS cc_start: 0.9694 (ptpp) cc_final: 0.9411 (tppt) REVERT: C 689 TYR cc_start: 0.8982 (m-80) cc_final: 0.8100 (m-80) REVERT: C 718 ARG cc_start: 0.9446 (tmt-80) cc_final: 0.9234 (tpt170) REVERT: C 719 GLN cc_start: 0.9543 (tp-100) cc_final: 0.9340 (tp-100) REVERT: C 722 THR cc_start: 0.9203 (m) cc_final: 0.8383 (m) REVERT: C 983 PHE cc_start: 0.9189 (m-80) cc_final: 0.8710 (m-80) REVERT: C 1005 MET cc_start: 0.9245 (ttt) cc_final: 0.8539 (tpp) REVERT: C 1050 PHE cc_start: 0.8839 (t80) cc_final: 0.8397 (t80) REVERT: C 1084 TYR cc_start: 0.9301 (t80) cc_final: 0.8994 (t80) REVERT: C 1126 THR cc_start: 0.8775 (p) cc_final: 0.8449 (t) REVERT: C 1131 THR cc_start: 0.8903 (p) cc_final: 0.8163 (p) REVERT: C 1157 MET cc_start: 0.9575 (mmm) cc_final: 0.9215 (mmm) REVERT: C 1188 LEU cc_start: 0.9435 (mp) cc_final: 0.9199 (mp) REVERT: C 1223 ASN cc_start: 0.9441 (t0) cc_final: 0.8974 (t0) REVERT: C 1242 GLU cc_start: 0.9462 (mp0) cc_final: 0.9210 (mp0) REVERT: C 1276 TYR cc_start: 0.8757 (m-10) cc_final: 0.8492 (m-10) REVERT: C 1321 GLN cc_start: 0.8043 (tm130) cc_final: 0.7605 (tm-30) REVERT: F 46 ILE cc_start: 0.9425 (pt) cc_final: 0.9092 (pt) REVERT: F 115 LEU cc_start: 0.9312 (mm) cc_final: 0.8951 (mm) REVERT: F 139 LEU cc_start: 0.8992 (tp) cc_final: 0.8598 (tp) REVERT: F 141 ILE cc_start: 0.9321 (mm) cc_final: 0.8852 (mm) REVERT: F 200 ILE cc_start: 0.9481 (pt) cc_final: 0.9235 (tt) REVERT: O 7 GLU cc_start: 0.8793 (pm20) cc_final: 0.8327 (tm-30) REVERT: O 45 ASP cc_start: 0.7818 (t70) cc_final: 0.7508 (t70) REVERT: O 67 TYR cc_start: 0.9469 (m-80) cc_final: 0.9131 (m-10) REVERT: O 112 TYR cc_start: 0.8671 (m-10) cc_final: 0.8454 (m-10) REVERT: O 137 PHE cc_start: 0.8478 (m-80) cc_final: 0.7498 (m-80) REVERT: O 184 TYR cc_start: 0.8822 (m-80) cc_final: 0.8221 (m-80) REVERT: O 289 THR cc_start: 0.8563 (m) cc_final: 0.7564 (t) REVERT: O 313 ILE cc_start: 0.9507 (tp) cc_final: 0.9287 (tp) REVERT: O 314 GLN cc_start: 0.9159 (pm20) cc_final: 0.8689 (pm20) REVERT: X 268 LYS cc_start: 0.8953 (pttm) cc_final: 0.8439 (pptt) REVERT: X 336 GLU cc_start: 0.8698 (tt0) cc_final: 0.7863 (tp30) REVERT: X 422 TYR cc_start: 0.7087 (p90) cc_final: 0.6063 (p90) REVERT: X 457 TRP cc_start: 0.6985 (m-90) cc_final: 0.6525 (m-90) REVERT: k 1 MET cc_start: 0.7027 (tpt) cc_final: 0.6677 (tpp) REVERT: k 28 ILE cc_start: 0.5718 (mp) cc_final: 0.5250 (mp) REVERT: k 483 HIS cc_start: 0.8629 (t-90) cc_final: 0.8420 (t-90) REVERT: k 506 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6271 (pp30) REVERT: k 527 PHE cc_start: 0.9271 (t80) cc_final: 0.8832 (t80) REVERT: k 649 LEU cc_start: 0.9328 (mm) cc_final: 0.9032 (mm) REVERT: l 26 PHE cc_start: 0.4753 (t80) cc_final: 0.3847 (t80) outliers start: 1 outliers final: 0 residues processed: 866 average time/residue: 0.1932 time to fit residues: 278.9668 Evaluate side-chains 722 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 721 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 442 optimal weight: 50.0000 chunk 420 optimal weight: 20.0000 chunk 239 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 488 optimal weight: 50.0000 chunk 274 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 467 optimal weight: 40.0000 chunk 422 optimal weight: 20.0000 chunk 314 optimal weight: 40.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 390 HIS ** k 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN ** m 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n3110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090807 restraints weight = 147963.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.093013 restraints weight = 92002.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.094539 restraints weight = 64832.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095851 restraints weight = 50918.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096400 restraints weight = 42285.310| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 38078 Z= 0.227 Angle : 0.812 17.144 52019 Z= 0.412 Chirality : 0.045 0.320 6157 Planarity : 0.006 0.085 6855 Dihedral : 5.157 37.023 5553 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.47 % Favored : 89.01 % Rotamer: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.04 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.13), residues: 4277 helix: -0.04 (0.14), residues: 1371 sheet: -1.25 (0.23), residues: 503 loop : -1.74 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 70 TYR 0.028 0.002 TYR O 51 PHE 0.020 0.002 PHE A1050 TRP 0.014 0.002 TRP X 161 HIS 0.008 0.001 HIS F 39 Details of bonding type rmsd covalent geometry : bond 0.00472 (38076) covalent geometry : angle 0.81227 (52015) SS BOND : bond 0.00740 ( 2) SS BOND : angle 1.77334 ( 4) hydrogen bonds : bond 0.03624 ( 1681) hydrogen bonds : angle 4.97210 ( 4725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 838 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8578 (m-10) cc_final: 0.8096 (m-10) REVERT: A 138 LYS cc_start: 0.8042 (tppp) cc_final: 0.7137 (tppp) REVERT: A 166 ASP cc_start: 0.9077 (t0) cc_final: 0.8713 (t0) REVERT: A 200 LEU cc_start: 0.9688 (tp) cc_final: 0.9446 (tp) REVERT: A 236 ARG cc_start: 0.9272 (ttp-110) cc_final: 0.8866 (ttp80) REVERT: A 254 LEU cc_start: 0.9758 (pp) cc_final: 0.9505 (pp) REVERT: A 258 TYR cc_start: 0.8432 (p90) cc_final: 0.7954 (p90) REVERT: A 259 LEU cc_start: 0.9812 (mm) cc_final: 0.9537 (mm) REVERT: A 295 LEU cc_start: 0.9736 (mm) cc_final: 0.9485 (mm) REVERT: A 296 LYS cc_start: 0.9370 (tppp) cc_final: 0.9111 (tppp) REVERT: A 298 GLN cc_start: 0.9164 (pp30) cc_final: 0.8900 (pp30) REVERT: A 417 ILE cc_start: 0.9272 (mm) cc_final: 0.9004 (mm) REVERT: A 421 MET cc_start: 0.8496 (tpp) cc_final: 0.8207 (tpp) REVERT: A 431 MET cc_start: 0.8168 (tpt) cc_final: 0.7273 (tpp) REVERT: A 459 PHE cc_start: 0.8741 (p90) cc_final: 0.8287 (p90) REVERT: A 547 PHE cc_start: 0.9426 (t80) cc_final: 0.9124 (t80) REVERT: A 560 ASN cc_start: 0.9272 (t0) cc_final: 0.8950 (t0) REVERT: A 573 ASP cc_start: 0.9103 (t0) cc_final: 0.8880 (t0) REVERT: A 631 LYS cc_start: 0.9436 (mmpt) cc_final: 0.9122 (mmmt) REVERT: A 645 MET cc_start: 0.9353 (mtt) cc_final: 0.9114 (mtp) REVERT: A 737 GLU cc_start: 0.9049 (tp30) cc_final: 0.8790 (tp30) REVERT: A 797 ARG cc_start: 0.8639 (mpt90) cc_final: 0.8338 (mmt180) REVERT: A 832 TYR cc_start: 0.9055 (t80) cc_final: 0.8475 (t80) REVERT: A 872 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8012 (pm20) REVERT: A 949 ASP cc_start: 0.9181 (t0) cc_final: 0.8744 (t0) REVERT: A 959 MET cc_start: 0.8756 (mmp) cc_final: 0.7759 (tpp) REVERT: A 983 PHE cc_start: 0.8962 (m-80) cc_final: 0.8584 (m-80) REVERT: A 1005 MET cc_start: 0.7716 (ppp) cc_final: 0.6566 (ppp) REVERT: A 1055 LEU cc_start: 0.9600 (tp) cc_final: 0.9140 (tp) REVERT: A 1059 LEU cc_start: 0.9418 (mt) cc_final: 0.9110 (mt) REVERT: A 1083 LEU cc_start: 0.9710 (tt) cc_final: 0.9278 (tt) REVERT: A 1147 ASN cc_start: 0.9587 (t0) cc_final: 0.9261 (t0) REVERT: A 1160 ASP cc_start: 0.8931 (p0) cc_final: 0.8147 (p0) REVERT: A 1164 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9165 (mm-30) REVERT: A 1168 ARG cc_start: 0.9487 (mtm110) cc_final: 0.9187 (ptp-110) REVERT: A 1245 MET cc_start: 0.9614 (tpt) cc_final: 0.9242 (tpp) REVERT: A 1268 LYS cc_start: 0.9415 (tptp) cc_final: 0.8875 (tppt) REVERT: A 1281 ASN cc_start: 0.9369 (p0) cc_final: 0.9126 (p0) REVERT: A 1313 MET cc_start: 0.9274 (mtm) cc_final: 0.8739 (mtt) REVERT: A 1373 ASP cc_start: 0.8528 (t0) cc_final: 0.7783 (t0) REVERT: A 1377 LEU cc_start: 0.9314 (tp) cc_final: 0.8986 (mt) REVERT: A 1381 LEU cc_start: 0.8946 (mp) cc_final: 0.8738 (mp) REVERT: C 84 GLU cc_start: 0.9420 (mp0) cc_final: 0.9168 (mp0) REVERT: C 197 LEU cc_start: 0.9803 (tt) cc_final: 0.9534 (tt) REVERT: C 201 LEU cc_start: 0.9470 (mm) cc_final: 0.9186 (mm) REVERT: C 242 MET cc_start: 0.8723 (tpt) cc_final: 0.8157 (tpp) REVERT: C 243 PHE cc_start: 0.9217 (m-80) cc_final: 0.8691 (m-10) REVERT: C 245 MET cc_start: 0.9546 (mmp) cc_final: 0.9285 (mmp) REVERT: C 383 ASP cc_start: 0.8496 (p0) cc_final: 0.8216 (p0) REVERT: C 416 ASP cc_start: 0.8500 (m-30) cc_final: 0.8164 (m-30) REVERT: C 429 ASN cc_start: 0.9313 (m-40) cc_final: 0.8827 (t0) REVERT: C 461 ASN cc_start: 0.9748 (t0) cc_final: 0.9204 (t0) REVERT: C 463 ASP cc_start: 0.9125 (m-30) cc_final: 0.8820 (m-30) REVERT: C 530 MET cc_start: 0.9180 (tpt) cc_final: 0.8886 (tpt) REVERT: C 531 MET cc_start: 0.9041 (pmm) cc_final: 0.8758 (mpp) REVERT: C 534 HIS cc_start: 0.8947 (t70) cc_final: 0.8379 (t-90) REVERT: C 608 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8762 (mtp85) REVERT: C 680 PHE cc_start: 0.8458 (m-80) cc_final: 0.7911 (m-80) REVERT: C 685 HIS cc_start: 0.8903 (m-70) cc_final: 0.8661 (m170) REVERT: C 689 TYR cc_start: 0.8971 (m-80) cc_final: 0.8130 (m-80) REVERT: C 718 ARG cc_start: 0.9534 (tmt-80) cc_final: 0.9199 (tpt170) REVERT: C 719 GLN cc_start: 0.9558 (tp-100) cc_final: 0.9331 (tp-100) REVERT: C 722 THR cc_start: 0.9271 (m) cc_final: 0.7967 (m) REVERT: C 763 ASP cc_start: 0.9263 (t0) cc_final: 0.8978 (t0) REVERT: C 767 ARG cc_start: 0.8968 (mmt180) cc_final: 0.8745 (mmt180) REVERT: C 959 MET cc_start: 0.9028 (ttt) cc_final: 0.8486 (tpp) REVERT: C 983 PHE cc_start: 0.9243 (m-80) cc_final: 0.8765 (m-80) REVERT: C 1005 MET cc_start: 0.9268 (ttt) cc_final: 0.8480 (tpp) REVERT: C 1035 ASP cc_start: 0.8205 (t0) cc_final: 0.7900 (t0) REVERT: C 1050 PHE cc_start: 0.8899 (t80) cc_final: 0.8490 (t80) REVERT: C 1063 PHE cc_start: 0.9185 (t80) cc_final: 0.8887 (t80) REVERT: C 1131 THR cc_start: 0.8963 (p) cc_final: 0.8178 (p) REVERT: C 1188 LEU cc_start: 0.9395 (mp) cc_final: 0.9194 (mp) REVERT: C 1223 ASN cc_start: 0.9470 (t0) cc_final: 0.9109 (t0) REVERT: C 1231 MET cc_start: 0.8886 (ppp) cc_final: 0.8616 (ppp) REVERT: C 1242 GLU cc_start: 0.9409 (mp0) cc_final: 0.9146 (mp0) REVERT: C 1275 LEU cc_start: 0.9389 (tp) cc_final: 0.8829 (tp) REVERT: C 1276 TYR cc_start: 0.8993 (m-10) cc_final: 0.8559 (m-10) REVERT: F 46 ILE cc_start: 0.9414 (pt) cc_final: 0.9070 (pt) REVERT: F 115 LEU cc_start: 0.9243 (mm) cc_final: 0.8931 (mm) REVERT: F 139 LEU cc_start: 0.9203 (tp) cc_final: 0.8832 (tp) REVERT: F 141 ILE cc_start: 0.9444 (mm) cc_final: 0.8941 (mm) REVERT: F 200 ILE cc_start: 0.9512 (pt) cc_final: 0.9269 (tt) REVERT: O 7 GLU cc_start: 0.8859 (pm20) cc_final: 0.8397 (tm-30) REVERT: O 34 PHE cc_start: 0.8305 (m-80) cc_final: 0.8094 (m-80) REVERT: O 65 GLU cc_start: 0.9457 (tp30) cc_final: 0.9148 (tp30) REVERT: O 137 PHE cc_start: 0.8599 (m-80) cc_final: 0.7822 (m-80) REVERT: O 184 TYR cc_start: 0.8667 (m-80) cc_final: 0.8111 (m-80) REVERT: O 313 ILE cc_start: 0.9535 (tp) cc_final: 0.9258 (tp) REVERT: O 314 GLN cc_start: 0.9145 (pm20) cc_final: 0.8848 (pm20) REVERT: X 336 GLU cc_start: 0.8663 (tt0) cc_final: 0.7857 (tp30) REVERT: X 422 TYR cc_start: 0.7850 (p90) cc_final: 0.6558 (p90) REVERT: k 1 MET cc_start: 0.7196 (tpt) cc_final: 0.6905 (tpp) REVERT: k 28 ILE cc_start: 0.5757 (mp) cc_final: 0.5223 (mp) REVERT: k 483 HIS cc_start: 0.8618 (t-90) cc_final: 0.8373 (t-90) REVERT: k 527 PHE cc_start: 0.9283 (t80) cc_final: 0.8870 (t80) REVERT: k 592 TYR cc_start: 0.9506 (m-10) cc_final: 0.9062 (m-80) REVERT: k 649 LEU cc_start: 0.9373 (mm) cc_final: 0.9111 (mm) REVERT: l 26 PHE cc_start: 0.5258 (t80) cc_final: 0.4449 (t80) outliers start: 2 outliers final: 1 residues processed: 840 average time/residue: 0.1916 time to fit residues: 267.1769 Evaluate side-chains 708 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 707 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 8 optimal weight: 0.0770 chunk 146 optimal weight: 50.0000 chunk 252 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 399 optimal weight: 30.0000 chunk 455 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 277 optimal weight: 20.0000 chunk 170 optimal weight: 40.0000 chunk 421 optimal weight: 8.9990 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 HIS A 792 HIS ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1098 GLN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1269 HIS C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 HIS ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 335 ASN ** k 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN ** m 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.128472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092381 restraints weight = 144714.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094689 restraints weight = 89165.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.096490 restraints weight = 62337.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097485 restraints weight = 48350.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.098361 restraints weight = 40974.941| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38078 Z= 0.164 Angle : 0.779 16.699 52019 Z= 0.393 Chirality : 0.044 0.266 6157 Planarity : 0.005 0.084 6855 Dihedral : 5.067 37.197 5553 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.54 % Favored : 89.92 % Rotamer: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.04 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.13), residues: 4277 helix: 0.04 (0.14), residues: 1382 sheet: -1.15 (0.23), residues: 495 loop : -1.70 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 282 TYR 0.023 0.002 TYR C 258 PHE 0.018 0.002 PHE A 96 TRP 0.017 0.002 TRP O 276 HIS 0.007 0.001 HIS C 685 Details of bonding type rmsd covalent geometry : bond 0.00348 (38076) covalent geometry : angle 0.77912 (52015) SS BOND : bond 0.01909 ( 2) SS BOND : angle 2.02152 ( 4) hydrogen bonds : bond 0.03375 ( 1681) hydrogen bonds : angle 4.77982 ( 4725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 857 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9222 (tp30) cc_final: 0.8980 (tp30) REVERT: A 102 VAL cc_start: 0.9165 (t) cc_final: 0.8963 (t) REVERT: A 109 PHE cc_start: 0.8539 (m-10) cc_final: 0.8117 (m-10) REVERT: A 115 MET cc_start: 0.9077 (ptm) cc_final: 0.8173 (ptm) REVERT: A 134 LYS cc_start: 0.9075 (mppt) cc_final: 0.8791 (mppt) REVERT: A 138 LYS cc_start: 0.7908 (tppp) cc_final: 0.7074 (tppp) REVERT: A 166 ASP cc_start: 0.9007 (t0) cc_final: 0.8714 (t0) REVERT: A 196 LEU cc_start: 0.9305 (mt) cc_final: 0.9087 (mt) REVERT: A 200 LEU cc_start: 0.9695 (tp) cc_final: 0.9435 (tp) REVERT: A 236 ARG cc_start: 0.9251 (ttp-110) cc_final: 0.8954 (ttp80) REVERT: A 248 HIS cc_start: 0.9553 (m90) cc_final: 0.9337 (m90) REVERT: A 259 LEU cc_start: 0.9788 (mm) cc_final: 0.9543 (mm) REVERT: A 295 LEU cc_start: 0.9735 (mm) cc_final: 0.9478 (mm) REVERT: A 296 LYS cc_start: 0.9392 (tppp) cc_final: 0.9029 (tppt) REVERT: A 298 GLN cc_start: 0.9095 (pp30) cc_final: 0.8726 (pp30) REVERT: A 421 MET cc_start: 0.8397 (tpp) cc_final: 0.8156 (tpp) REVERT: A 431 MET cc_start: 0.8109 (tpt) cc_final: 0.7455 (tpp) REVERT: A 507 TYR cc_start: 0.7820 (t80) cc_final: 0.7603 (t80) REVERT: A 560 ASN cc_start: 0.9272 (t0) cc_final: 0.8968 (t0) REVERT: A 631 LYS cc_start: 0.9432 (mmpt) cc_final: 0.9011 (mmmt) REVERT: A 645 MET cc_start: 0.9306 (mtt) cc_final: 0.9069 (mtp) REVERT: A 680 PHE cc_start: 0.8880 (m-80) cc_final: 0.8617 (m-80) REVERT: A 737 GLU cc_start: 0.9039 (tp30) cc_final: 0.8763 (tp30) REVERT: A 749 ILE cc_start: 0.9553 (pt) cc_final: 0.9285 (mp) REVERT: A 797 ARG cc_start: 0.8600 (mpt90) cc_final: 0.8202 (mmt180) REVERT: A 832 TYR cc_start: 0.9101 (t80) cc_final: 0.8461 (t80) REVERT: A 872 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8073 (pm20) REVERT: A 945 MET cc_start: 0.9109 (ttt) cc_final: 0.8908 (ttm) REVERT: A 949 ASP cc_start: 0.9150 (t0) cc_final: 0.8664 (t0) REVERT: A 959 MET cc_start: 0.8463 (mmp) cc_final: 0.7778 (mmt) REVERT: A 983 PHE cc_start: 0.8966 (m-80) cc_final: 0.8616 (m-80) REVERT: A 1004 LYS cc_start: 0.9341 (mptt) cc_final: 0.9138 (mmtm) REVERT: A 1005 MET cc_start: 0.7694 (ppp) cc_final: 0.6367 (ppp) REVERT: A 1055 LEU cc_start: 0.9620 (tp) cc_final: 0.9167 (tp) REVERT: A 1059 LEU cc_start: 0.9385 (mt) cc_final: 0.9099 (mt) REVERT: A 1083 LEU cc_start: 0.9698 (tt) cc_final: 0.9259 (tt) REVERT: A 1086 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 1147 ASN cc_start: 0.9525 (t0) cc_final: 0.9115 (t0) REVERT: A 1160 ASP cc_start: 0.8846 (p0) cc_final: 0.7975 (p0) REVERT: A 1176 LEU cc_start: 0.9329 (pp) cc_final: 0.8842 (mp) REVERT: A 1245 MET cc_start: 0.9636 (tpt) cc_final: 0.9210 (tpp) REVERT: A 1276 TYR cc_start: 0.8372 (m-10) cc_final: 0.8107 (m-10) REVERT: A 1281 ASN cc_start: 0.9326 (p0) cc_final: 0.9058 (p0) REVERT: A 1313 MET cc_start: 0.9263 (mtm) cc_final: 0.8760 (mtt) REVERT: A 1344 CYS cc_start: 0.8428 (p) cc_final: 0.7950 (p) REVERT: A 1351 TYR cc_start: 0.9092 (m-80) cc_final: 0.8795 (m-80) REVERT: A 1354 LEU cc_start: 0.9569 (tp) cc_final: 0.9292 (tt) REVERT: A 1361 MET cc_start: 0.9517 (ttt) cc_final: 0.8785 (tpp) REVERT: A 1373 ASP cc_start: 0.8271 (t0) cc_final: 0.7431 (t0) REVERT: A 1377 LEU cc_start: 0.9150 (tp) cc_final: 0.8911 (mt) REVERT: C 85 LEU cc_start: 0.9325 (mt) cc_final: 0.8856 (mt) REVERT: C 197 LEU cc_start: 0.9787 (tt) cc_final: 0.9532 (tt) REVERT: C 201 LEU cc_start: 0.9579 (mm) cc_final: 0.9329 (mm) REVERT: C 242 MET cc_start: 0.8724 (tpt) cc_final: 0.8139 (tpp) REVERT: C 243 PHE cc_start: 0.9236 (m-80) cc_final: 0.8631 (m-10) REVERT: C 245 MET cc_start: 0.9395 (mmp) cc_final: 0.9102 (mmm) REVERT: C 281 ARG cc_start: 0.8531 (mpt180) cc_final: 0.8070 (mpt180) REVERT: C 291 THR cc_start: 0.9120 (t) cc_final: 0.8732 (m) REVERT: C 383 ASP cc_start: 0.8541 (p0) cc_final: 0.8107 (p0) REVERT: C 395 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8911 (tm-30) REVERT: C 416 ASP cc_start: 0.8519 (m-30) cc_final: 0.8157 (m-30) REVERT: C 429 ASN cc_start: 0.9359 (m-40) cc_final: 0.8855 (t0) REVERT: C 461 ASN cc_start: 0.9801 (t0) cc_final: 0.8776 (t0) REVERT: C 463 ASP cc_start: 0.9186 (m-30) cc_final: 0.8866 (m-30) REVERT: C 468 GLN cc_start: 0.9275 (tp40) cc_final: 0.8869 (tp40) REVERT: C 530 MET cc_start: 0.9129 (tpt) cc_final: 0.8745 (tpt) REVERT: C 534 HIS cc_start: 0.8927 (t70) cc_final: 0.8431 (t-90) REVERT: C 565 PHE cc_start: 0.9100 (m-10) cc_final: 0.8608 (m-10) REVERT: C 608 ARG cc_start: 0.9131 (mtp85) cc_final: 0.8765 (mtp85) REVERT: C 685 HIS cc_start: 0.8965 (m-70) cc_final: 0.8571 (m170) REVERT: C 689 TYR cc_start: 0.8954 (m-80) cc_final: 0.8208 (m-80) REVERT: C 718 ARG cc_start: 0.9549 (tmt-80) cc_final: 0.9243 (tpt170) REVERT: C 719 GLN cc_start: 0.9522 (tp-100) cc_final: 0.9285 (tp-100) REVERT: C 722 THR cc_start: 0.9195 (m) cc_final: 0.7980 (m) REVERT: C 764 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: C 959 MET cc_start: 0.8669 (ttt) cc_final: 0.8422 (mmm) REVERT: C 983 PHE cc_start: 0.9199 (m-80) cc_final: 0.8713 (m-80) REVERT: C 1005 MET cc_start: 0.9287 (ttt) cc_final: 0.8464 (tpp) REVERT: C 1131 THR cc_start: 0.9022 (p) cc_final: 0.8203 (p) REVERT: C 1140 ASP cc_start: 0.9523 (p0) cc_final: 0.8900 (t70) REVERT: C 1157 MET cc_start: 0.9588 (mmm) cc_final: 0.9365 (mmm) REVERT: C 1188 LEU cc_start: 0.9459 (mp) cc_final: 0.9193 (mp) REVERT: C 1223 ASN cc_start: 0.9444 (t0) cc_final: 0.9200 (t0) REVERT: C 1231 MET cc_start: 0.8876 (ppp) cc_final: 0.8665 (ppp) REVERT: C 1258 ARG cc_start: 0.8582 (ptt-90) cc_final: 0.8097 (ptt-90) REVERT: C 1275 LEU cc_start: 0.9368 (tp) cc_final: 0.8844 (tp) REVERT: C 1276 TYR cc_start: 0.9000 (m-10) cc_final: 0.8502 (m-10) REVERT: C 1295 PHE cc_start: 0.8702 (m-80) cc_final: 0.8323 (m-80) REVERT: C 1321 GLN cc_start: 0.8119 (tm130) cc_final: 0.7909 (tm-30) REVERT: F 46 ILE cc_start: 0.9454 (pt) cc_final: 0.9109 (pt) REVERT: F 115 LEU cc_start: 0.9216 (mm) cc_final: 0.8887 (mm) REVERT: F 139 LEU cc_start: 0.9325 (tp) cc_final: 0.8993 (tp) REVERT: F 141 ILE cc_start: 0.9143 (mm) cc_final: 0.8928 (mm) REVERT: F 200 ILE cc_start: 0.9497 (pt) cc_final: 0.9231 (tt) REVERT: F 208 MET cc_start: 0.8954 (pmm) cc_final: 0.8684 (pmm) REVERT: F 290 ARG cc_start: 0.8538 (mpp-170) cc_final: 0.8328 (mpp-170) REVERT: O 7 GLU cc_start: 0.8870 (pm20) cc_final: 0.8408 (tm-30) REVERT: O 67 TYR cc_start: 0.9328 (m-80) cc_final: 0.9102 (m-10) REVERT: O 69 MET cc_start: 0.8559 (mmt) cc_final: 0.8022 (mmm) REVERT: O 137 PHE cc_start: 0.8556 (m-80) cc_final: 0.7863 (m-80) REVERT: O 184 TYR cc_start: 0.8606 (m-80) cc_final: 0.7992 (m-80) REVERT: O 313 ILE cc_start: 0.9492 (tp) cc_final: 0.9241 (tp) REVERT: O 314 GLN cc_start: 0.9104 (pm20) cc_final: 0.8827 (pm20) REVERT: X 268 LYS cc_start: 0.8883 (pttm) cc_final: 0.8411 (pptt) REVERT: X 336 GLU cc_start: 0.8580 (tt0) cc_final: 0.7834 (tp30) REVERT: X 422 TYR cc_start: 0.7743 (p90) cc_final: 0.6410 (p90) REVERT: X 457 TRP cc_start: 0.7443 (m-90) cc_final: 0.6860 (m-90) REVERT: k 28 ILE cc_start: 0.5824 (mp) cc_final: 0.5284 (mp) REVERT: k 483 HIS cc_start: 0.8563 (t-90) cc_final: 0.8303 (t-90) REVERT: k 527 PHE cc_start: 0.9260 (t80) cc_final: 0.8864 (t80) REVERT: k 592 TYR cc_start: 0.9509 (m-10) cc_final: 0.9081 (m-80) REVERT: k 649 LEU cc_start: 0.9356 (mm) cc_final: 0.9131 (mm) REVERT: l 26 PHE cc_start: 0.4905 (t80) cc_final: 0.4126 (t80) outliers start: 2 outliers final: 0 residues processed: 859 average time/residue: 0.2325 time to fit residues: 329.7354 Evaluate side-chains 721 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 720 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 291 optimal weight: 0.0370 chunk 136 optimal weight: 70.0000 chunk 31 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 387 optimal weight: 60.0000 chunk 52 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 326 optimal weight: 50.0000 chunk 301 optimal weight: 70.0000 chunk 376 optimal weight: 60.0000 chunk 349 optimal weight: 10.0000 overall best weight: 8.8070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1081 GLN ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 HIS ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 65 HIS k 389 HIS ** k 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN ** m 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.127431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091448 restraints weight = 146542.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.093815 restraints weight = 89357.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095226 restraints weight = 63569.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096519 restraints weight = 50796.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097392 restraints weight = 42470.093| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.004 0.060 38078 Z= 0.192 Angle : 0.795 16.583 52019 Z= 0.401 Chirality : 0.044 0.278 6157 Planarity : 0.005 0.081 6855 Dihedral : 5.104 36.908 5553 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.22 % Favored : 89.24 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.13), residues: 4277 helix: 0.01 (0.14), residues: 1372 sheet: -1.30 (0.23), residues: 503 loop : -1.68 (0.13), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG k 509 TYR 0.026 0.002 TYR C 402 PHE 0.022 0.002 PHE C1246 TRP 0.019 0.002 TRP O 276 HIS 0.010 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00403 (38076) covalent geometry : angle 0.79481 (52015) SS BOND : bond 0.00609 ( 2) SS BOND : angle 1.89495 ( 4) hydrogen bonds : bond 0.03435 ( 1681) hydrogen bonds : angle 4.77920 ( 4725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 845 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8670 (m-10) cc_final: 0.8147 (m-10) REVERT: A 115 MET cc_start: 0.9136 (ptm) cc_final: 0.8402 (ptm) REVERT: A 138 LYS cc_start: 0.7625 (tppp) cc_final: 0.7195 (tppp) REVERT: A 166 ASP cc_start: 0.9046 (t0) cc_final: 0.8658 (t0) REVERT: A 196 LEU cc_start: 0.9340 (mt) cc_final: 0.9088 (mt) REVERT: A 200 LEU cc_start: 0.9696 (tp) cc_final: 0.9441 (tp) REVERT: A 236 ARG cc_start: 0.9266 (ttp-110) cc_final: 0.8987 (ttp80) REVERT: A 295 LEU cc_start: 0.9684 (mm) cc_final: 0.9362 (mm) REVERT: A 298 GLN cc_start: 0.9107 (pp30) cc_final: 0.8745 (pp30) REVERT: A 299 LEU cc_start: 0.9595 (mt) cc_final: 0.9199 (mt) REVERT: A 421 MET cc_start: 0.8415 (tpp) cc_final: 0.8124 (tpp) REVERT: A 431 MET cc_start: 0.8127 (tpt) cc_final: 0.7442 (tpp) REVERT: A 493 LEU cc_start: 0.9776 (mm) cc_final: 0.9565 (mm) REVERT: A 507 TYR cc_start: 0.7848 (t80) cc_final: 0.7589 (t80) REVERT: A 560 ASN cc_start: 0.9254 (t0) cc_final: 0.8957 (t0) REVERT: A 573 ASP cc_start: 0.9017 (t0) cc_final: 0.8786 (t0) REVERT: A 631 LYS cc_start: 0.9418 (mmpt) cc_final: 0.9026 (mmmt) REVERT: A 737 GLU cc_start: 0.9078 (tp30) cc_final: 0.8778 (tp30) REVERT: A 797 ARG cc_start: 0.8607 (mpt90) cc_final: 0.8282 (mmt180) REVERT: A 824 GLU cc_start: 0.9060 (pm20) cc_final: 0.8638 (pp20) REVERT: A 832 TYR cc_start: 0.9088 (t80) cc_final: 0.8589 (t80) REVERT: A 872 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8044 (pm20) REVERT: A 949 ASP cc_start: 0.9117 (t0) cc_final: 0.8610 (t0) REVERT: A 983 PHE cc_start: 0.8916 (m-80) cc_final: 0.8546 (m-80) REVERT: A 1004 LYS cc_start: 0.9383 (mptt) cc_final: 0.9178 (mmtm) REVERT: A 1005 MET cc_start: 0.7752 (ppp) cc_final: 0.7334 (ppp) REVERT: A 1055 LEU cc_start: 0.9607 (tp) cc_final: 0.9405 (tp) REVERT: A 1079 THR cc_start: 0.8668 (t) cc_final: 0.8248 (t) REVERT: A 1083 LEU cc_start: 0.9679 (tt) cc_final: 0.9225 (tt) REVERT: A 1086 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7638 (mt-10) REVERT: A 1097 ILE cc_start: 0.9362 (tp) cc_final: 0.8909 (tp) REVERT: A 1147 ASN cc_start: 0.9505 (t0) cc_final: 0.9275 (t0) REVERT: A 1160 ASP cc_start: 0.8825 (p0) cc_final: 0.8023 (p0) REVERT: A 1245 MET cc_start: 0.9615 (tpt) cc_final: 0.9199 (tpp) REVERT: A 1281 ASN cc_start: 0.9322 (p0) cc_final: 0.9069 (p0) REVERT: A 1313 MET cc_start: 0.9280 (mtm) cc_final: 0.8806 (mtt) REVERT: A 1344 CYS cc_start: 0.8513 (p) cc_final: 0.8105 (p) REVERT: A 1351 TYR cc_start: 0.9116 (m-80) cc_final: 0.8849 (m-80) REVERT: C 197 LEU cc_start: 0.9785 (tt) cc_final: 0.9482 (tt) REVERT: C 201 LEU cc_start: 0.9375 (mm) cc_final: 0.9092 (mm) REVERT: C 242 MET cc_start: 0.8755 (tpt) cc_final: 0.8292 (tpp) REVERT: C 243 PHE cc_start: 0.9247 (m-80) cc_final: 0.8602 (m-10) REVERT: C 245 MET cc_start: 0.9454 (mmp) cc_final: 0.9125 (mmm) REVERT: C 291 THR cc_start: 0.9101 (t) cc_final: 0.8780 (m) REVERT: C 416 ASP cc_start: 0.8514 (m-30) cc_final: 0.8178 (m-30) REVERT: C 423 MET cc_start: 0.8888 (tpt) cc_final: 0.8240 (tpt) REVERT: C 429 ASN cc_start: 0.9323 (m-40) cc_final: 0.8852 (t0) REVERT: C 461 ASN cc_start: 0.9811 (t0) cc_final: 0.9284 (t0) REVERT: C 463 ASP cc_start: 0.9202 (m-30) cc_final: 0.8893 (m-30) REVERT: C 468 GLN cc_start: 0.9349 (tp40) cc_final: 0.9012 (tp40) REVERT: C 525 GLU cc_start: 0.9198 (mp0) cc_final: 0.8972 (mp0) REVERT: C 531 MET cc_start: 0.7733 (mpp) cc_final: 0.7528 (mpp) REVERT: C 534 HIS cc_start: 0.8939 (t70) cc_final: 0.8386 (t-90) REVERT: C 608 ARG cc_start: 0.9137 (mtp85) cc_final: 0.8837 (mtp85) REVERT: C 685 HIS cc_start: 0.9059 (m-70) cc_final: 0.8383 (m-70) REVERT: C 689 TYR cc_start: 0.8940 (m-80) cc_final: 0.8098 (m-80) REVERT: C 718 ARG cc_start: 0.9547 (tmt-80) cc_final: 0.9241 (tpt170) REVERT: C 719 GLN cc_start: 0.9506 (tp-100) cc_final: 0.9258 (tp-100) REVERT: C 722 THR cc_start: 0.9141 (m) cc_final: 0.7820 (m) REVERT: C 917 MET cc_start: 0.9540 (tpp) cc_final: 0.9127 (tpt) REVERT: C 983 PHE cc_start: 0.9187 (m-80) cc_final: 0.8601 (m-80) REVERT: C 1005 MET cc_start: 0.9360 (ttt) cc_final: 0.8392 (tpp) REVERT: C 1131 THR cc_start: 0.8955 (p) cc_final: 0.8066 (p) REVERT: C 1134 LEU cc_start: 0.9241 (tp) cc_final: 0.8944 (tp) REVERT: C 1157 MET cc_start: 0.9585 (mmm) cc_final: 0.9379 (mmm) REVERT: C 1188 LEU cc_start: 0.9407 (mp) cc_final: 0.9204 (mp) REVERT: C 1223 ASN cc_start: 0.9457 (t0) cc_final: 0.9217 (t0) REVERT: C 1275 LEU cc_start: 0.9383 (tp) cc_final: 0.8871 (tp) REVERT: C 1276 TYR cc_start: 0.8961 (m-10) cc_final: 0.8462 (m-10) REVERT: C 1295 PHE cc_start: 0.8695 (m-80) cc_final: 0.8324 (m-80) REVERT: F 46 ILE cc_start: 0.9448 (pt) cc_final: 0.9085 (pt) REVERT: F 115 LEU cc_start: 0.9207 (mm) cc_final: 0.8930 (mm) REVERT: F 139 LEU cc_start: 0.9319 (tp) cc_final: 0.9014 (tp) REVERT: F 141 ILE cc_start: 0.9187 (mm) cc_final: 0.8919 (mm) REVERT: F 200 ILE cc_start: 0.9510 (pt) cc_final: 0.9249 (tt) REVERT: F 208 MET cc_start: 0.8811 (pmm) cc_final: 0.8568 (pmm) REVERT: O 7 GLU cc_start: 0.8866 (pm20) cc_final: 0.8417 (tm-30) REVERT: O 67 TYR cc_start: 0.9309 (m-80) cc_final: 0.9059 (m-10) REVERT: O 69 MET cc_start: 0.8623 (mmt) cc_final: 0.8404 (mmt) REVERT: O 137 PHE cc_start: 0.8619 (m-80) cc_final: 0.7981 (m-80) REVERT: O 184 TYR cc_start: 0.8707 (m-80) cc_final: 0.8079 (m-80) REVERT: O 313 ILE cc_start: 0.9474 (tp) cc_final: 0.9225 (tp) REVERT: O 314 GLN cc_start: 0.9085 (pm20) cc_final: 0.8838 (pm20) REVERT: X 336 GLU cc_start: 0.8713 (tt0) cc_final: 0.7849 (tp30) REVERT: X 422 TYR cc_start: 0.8072 (p90) cc_final: 0.6626 (p90) REVERT: X 457 TRP cc_start: 0.7379 (m-90) cc_final: 0.6805 (m-90) REVERT: k 28 ILE cc_start: 0.5764 (mp) cc_final: 0.5125 (mp) REVERT: k 483 HIS cc_start: 0.8568 (t-90) cc_final: 0.8334 (t-90) REVERT: k 527 PHE cc_start: 0.9270 (t80) cc_final: 0.8883 (t80) REVERT: k 592 TYR cc_start: 0.9499 (m-10) cc_final: 0.9105 (m-80) REVERT: k 649 LEU cc_start: 0.9383 (mm) cc_final: 0.9165 (mm) REVERT: l 26 PHE cc_start: 0.4772 (t80) cc_final: 0.3966 (t80) outliers start: 0 outliers final: 0 residues processed: 845 average time/residue: 0.1964 time to fit residues: 275.1914 Evaluate side-chains 724 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 379 optimal weight: 50.0000 chunk 446 optimal weight: 50.0000 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 414 optimal weight: 5.9990 chunk 204 optimal weight: 6.9990 chunk 230 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 chunk 114 optimal weight: 40.0000 chunk 499 optimal weight: 40.0000 chunk 319 optimal weight: 50.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 267 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 HIS ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN ** k 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN m 25 ASN o3133 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.128503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092384 restraints weight = 149567.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094704 restraints weight = 91534.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096154 restraints weight = 63880.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.097492 restraints weight = 50534.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.098307 restraints weight = 41946.019| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 : 0.003 0.059 38078 Z= 0.154 Angle : 0.783 16.291 52019 Z= 0.392 Chirality : 0.044 0.281 6157 Planarity : 0.005 0.077 6855 Dihedral : 5.016 35.865 5553 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.40 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.13), residues: 4277 helix: 0.08 (0.14), residues: 1382 sheet: -1.12 (0.23), residues: 482 loop : -1.68 (0.13), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 290 TYR 0.023 0.002 TYR A 409 PHE 0.028 0.002 PHE C1246 TRP 0.026 0.002 TRP k 376 HIS 0.010 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00330 (38076) covalent geometry : angle 0.78303 (52015) SS BOND : bond 0.00427 ( 2) SS BOND : angle 1.49982 ( 4) hydrogen bonds : bond 0.03264 ( 1681) hydrogen bonds : angle 4.68708 ( 4725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 872 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9204 (tp30) cc_final: 0.9003 (tp30) REVERT: A 109 PHE cc_start: 0.8572 (m-10) cc_final: 0.8232 (m-10) REVERT: A 115 MET cc_start: 0.9163 (ptm) cc_final: 0.8479 (ptm) REVERT: A 134 LYS cc_start: 0.9108 (mppt) cc_final: 0.8827 (mppt) REVERT: A 138 LYS cc_start: 0.7701 (tppp) cc_final: 0.7137 (tppp) REVERT: A 166 ASP cc_start: 0.9004 (t0) cc_final: 0.8603 (t0) REVERT: A 196 LEU cc_start: 0.9307 (mt) cc_final: 0.9088 (mt) REVERT: A 200 LEU cc_start: 0.9699 (tp) cc_final: 0.9432 (tp) REVERT: A 236 ARG cc_start: 0.9238 (ttp-110) cc_final: 0.8964 (ttp80) REVERT: A 259 LEU cc_start: 0.9731 (mm) cc_final: 0.9471 (mm) REVERT: A 298 GLN cc_start: 0.9098 (pp30) cc_final: 0.8594 (pp30) REVERT: A 299 LEU cc_start: 0.9625 (mt) cc_final: 0.9157 (mt) REVERT: A 300 LEU cc_start: 0.9548 (mm) cc_final: 0.9220 (mm) REVERT: A 421 MET cc_start: 0.8355 (tpp) cc_final: 0.8077 (tpp) REVERT: A 431 MET cc_start: 0.8095 (tpt) cc_final: 0.7438 (tpp) REVERT: A 493 LEU cc_start: 0.9836 (mm) cc_final: 0.9604 (mm) REVERT: A 560 ASN cc_start: 0.9284 (t0) cc_final: 0.8986 (t0) REVERT: A 573 ASP cc_start: 0.9059 (t0) cc_final: 0.8821 (t0) REVERT: A 631 LYS cc_start: 0.9408 (mmpt) cc_final: 0.9034 (mmmt) REVERT: A 660 LEU cc_start: 0.9615 (tp) cc_final: 0.9228 (tp) REVERT: A 680 PHE cc_start: 0.8162 (m-80) cc_final: 0.7914 (m-80) REVERT: A 688 MET cc_start: 0.8844 (ptp) cc_final: 0.8421 (pmm) REVERT: A 737 GLU cc_start: 0.8997 (tp30) cc_final: 0.8641 (tp30) REVERT: A 763 ASP cc_start: 0.9003 (p0) cc_final: 0.8789 (p0) REVERT: A 789 MET cc_start: 0.8599 (mmm) cc_final: 0.8208 (mmp) REVERT: A 797 ARG cc_start: 0.8504 (mpt90) cc_final: 0.8208 (mmt180) REVERT: A 832 TYR cc_start: 0.9094 (t80) cc_final: 0.8627 (t80) REVERT: A 872 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8048 (pm20) REVERT: A 917 MET cc_start: 0.9396 (mpp) cc_final: 0.9170 (mpp) REVERT: A 949 ASP cc_start: 0.9017 (t0) cc_final: 0.8569 (t0) REVERT: A 983 PHE cc_start: 0.8914 (m-80) cc_final: 0.8480 (m-80) REVERT: A 1005 MET cc_start: 0.7694 (ppp) cc_final: 0.7245 (ppp) REVERT: A 1055 LEU cc_start: 0.9622 (tp) cc_final: 0.9178 (tp) REVERT: A 1059 LEU cc_start: 0.9394 (mt) cc_final: 0.9089 (mt) REVERT: A 1083 LEU cc_start: 0.9705 (tt) cc_final: 0.9245 (tt) REVERT: A 1086 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7320 (mt-10) REVERT: A 1147 ASN cc_start: 0.9486 (t0) cc_final: 0.9227 (t0) REVERT: A 1160 ASP cc_start: 0.8798 (p0) cc_final: 0.8015 (p0) REVERT: A 1245 MET cc_start: 0.9580 (tpt) cc_final: 0.9110 (tpp) REVERT: A 1276 TYR cc_start: 0.8333 (m-10) cc_final: 0.8125 (m-10) REVERT: A 1281 ASN cc_start: 0.9235 (p0) cc_final: 0.8913 (p0) REVERT: A 1313 MET cc_start: 0.9256 (mtm) cc_final: 0.8780 (mtt) REVERT: A 1344 CYS cc_start: 0.8304 (p) cc_final: 0.7890 (p) REVERT: A 1351 TYR cc_start: 0.9089 (m-80) cc_final: 0.8698 (m-80) REVERT: A 1373 ASP cc_start: 0.8309 (t0) cc_final: 0.7924 (t0) REVERT: C 85 LEU cc_start: 0.9251 (mt) cc_final: 0.9018 (mt) REVERT: C 197 LEU cc_start: 0.9760 (tt) cc_final: 0.9494 (tt) REVERT: C 201 LEU cc_start: 0.9377 (mm) cc_final: 0.9076 (mm) REVERT: C 242 MET cc_start: 0.8764 (tpt) cc_final: 0.8148 (tpp) REVERT: C 243 PHE cc_start: 0.9219 (m-80) cc_final: 0.8591 (m-10) REVERT: C 245 MET cc_start: 0.9447 (mmp) cc_final: 0.9124 (mmm) REVERT: C 253 ARG cc_start: 0.9520 (tpp-160) cc_final: 0.9247 (tpp-160) REVERT: C 281 ARG cc_start: 0.8526 (mpt180) cc_final: 0.8313 (mpt180) REVERT: C 291 THR cc_start: 0.9018 (t) cc_final: 0.8635 (m) REVERT: C 326 ASN cc_start: 0.9521 (m-40) cc_final: 0.9174 (m-40) REVERT: C 341 ASP cc_start: 0.9244 (p0) cc_final: 0.8786 (p0) REVERT: C 383 ASP cc_start: 0.8095 (p0) cc_final: 0.7743 (p0) REVERT: C 395 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8661 (tm-30) REVERT: C 416 ASP cc_start: 0.8484 (m-30) cc_final: 0.8147 (m-30) REVERT: C 423 MET cc_start: 0.8913 (tpt) cc_final: 0.8276 (tpt) REVERT: C 429 ASN cc_start: 0.9320 (m-40) cc_final: 0.8840 (t0) REVERT: C 461 ASN cc_start: 0.9808 (t0) cc_final: 0.9278 (t0) REVERT: C 463 ASP cc_start: 0.9214 (m-30) cc_final: 0.8914 (m-30) REVERT: C 468 GLN cc_start: 0.9325 (tp40) cc_final: 0.8997 (tp40) REVERT: C 525 GLU cc_start: 0.9246 (mp0) cc_final: 0.8990 (pm20) REVERT: C 534 HIS cc_start: 0.8899 (t70) cc_final: 0.8321 (t-90) REVERT: C 608 ARG cc_start: 0.9149 (mtp85) cc_final: 0.8821 (mtp85) REVERT: C 628 LYS cc_start: 0.9703 (ptpp) cc_final: 0.9438 (ptpp) REVERT: C 685 HIS cc_start: 0.8861 (m90) cc_final: 0.8418 (m-70) REVERT: C 689 TYR cc_start: 0.8918 (m-80) cc_final: 0.8108 (m-80) REVERT: C 718 ARG cc_start: 0.9536 (tmt-80) cc_final: 0.9237 (tpt170) REVERT: C 719 GLN cc_start: 0.9480 (tp-100) cc_final: 0.9213 (tp-100) REVERT: C 722 THR cc_start: 0.9138 (m) cc_final: 0.7825 (m) REVERT: C 917 MET cc_start: 0.9543 (tpp) cc_final: 0.9200 (tpp) REVERT: C 983 PHE cc_start: 0.9218 (m-80) cc_final: 0.8763 (m-80) REVERT: C 1005 MET cc_start: 0.9358 (ttt) cc_final: 0.8634 (tpp) REVERT: C 1131 THR cc_start: 0.8967 (p) cc_final: 0.8115 (p) REVERT: C 1134 LEU cc_start: 0.9202 (tp) cc_final: 0.8898 (tp) REVERT: C 1157 MET cc_start: 0.9543 (mmm) cc_final: 0.9324 (mmm) REVERT: C 1188 LEU cc_start: 0.9485 (mp) cc_final: 0.9235 (mp) REVERT: C 1231 MET cc_start: 0.8802 (ppp) cc_final: 0.8467 (ppp) REVERT: C 1258 ARG cc_start: 0.8638 (ptt-90) cc_final: 0.8118 (ptt-90) REVERT: C 1264 TRP cc_start: 0.9203 (m-10) cc_final: 0.8733 (m-10) REVERT: C 1275 LEU cc_start: 0.9368 (tp) cc_final: 0.8865 (tp) REVERT: C 1276 TYR cc_start: 0.9006 (m-10) cc_final: 0.8451 (m-10) REVERT: C 1295 PHE cc_start: 0.8649 (m-80) cc_final: 0.8332 (m-80) REVERT: F 115 LEU cc_start: 0.9241 (mm) cc_final: 0.8948 (mm) REVERT: F 139 LEU cc_start: 0.9295 (tp) cc_final: 0.8993 (tp) REVERT: F 200 ILE cc_start: 0.9488 (pt) cc_final: 0.9217 (tt) REVERT: O 7 GLU cc_start: 0.8856 (pm20) cc_final: 0.8418 (tm-30) REVERT: O 34 PHE cc_start: 0.9041 (m-80) cc_final: 0.8553 (m-80) REVERT: O 67 TYR cc_start: 0.9309 (m-80) cc_final: 0.9050 (m-10) REVERT: O 124 ASP cc_start: 0.8825 (p0) cc_final: 0.8500 (p0) REVERT: O 184 TYR cc_start: 0.8642 (m-80) cc_final: 0.7977 (m-80) REVERT: O 313 ILE cc_start: 0.9474 (tp) cc_final: 0.9167 (tp) REVERT: O 314 GLN cc_start: 0.9072 (pm20) cc_final: 0.8823 (pm20) REVERT: X 336 GLU cc_start: 0.8651 (tt0) cc_final: 0.7849 (tp30) REVERT: X 422 TYR cc_start: 0.8060 (p90) cc_final: 0.6524 (p90) REVERT: X 457 TRP cc_start: 0.7337 (m-90) cc_final: 0.6799 (m-90) REVERT: k 28 ILE cc_start: 0.5916 (mp) cc_final: 0.5331 (mp) REVERT: k 483 HIS cc_start: 0.8523 (t-90) cc_final: 0.8251 (t-90) REVERT: k 527 PHE cc_start: 0.9303 (t80) cc_final: 0.8889 (t80) REVERT: k 592 TYR cc_start: 0.9427 (m-10) cc_final: 0.8993 (m-80) REVERT: k 610 MET cc_start: 0.4018 (pmm) cc_final: 0.3702 (pmm) REVERT: k 649 LEU cc_start: 0.9380 (mm) cc_final: 0.9173 (mm) REVERT: l 26 PHE cc_start: 0.5003 (t80) cc_final: 0.4066 (t80) outliers start: 0 outliers final: 0 residues processed: 872 average time/residue: 0.1990 time to fit residues: 287.8841 Evaluate side-chains 719 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 719 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 8 optimal weight: 0.0770 chunk 423 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 0.0000 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 0.0170 chunk 51 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 359 optimal weight: 50.0000 chunk 77 optimal weight: 0.5980 chunk 175 optimal weight: 40.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 506 GLN ** k 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.131105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094723 restraints weight = 148194.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097299 restraints weight = 88483.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099112 restraints weight = 62056.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100080 restraints weight = 48217.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.100941 restraints weight = 41008.406| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 38078 Z= 0.139 Angle : 0.783 16.307 52019 Z= 0.390 Chirality : 0.044 0.298 6157 Planarity : 0.005 0.081 6855 Dihedral : 4.898 35.238 5553 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.31 % Favored : 90.16 % Rotamer: Outliers : 0.03 % Allowed : 1.29 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.06 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.13), residues: 4277 helix: 0.10 (0.14), residues: 1387 sheet: -0.96 (0.24), residues: 456 loop : -1.65 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 290 TYR 0.025 0.002 TYR k 391 PHE 0.032 0.002 PHE O 137 TRP 0.031 0.002 TRP k 376 HIS 0.011 0.001 HIS A1057 Details of bonding type rmsd covalent geometry : bond 0.00295 (38076) covalent geometry : angle 0.78260 (52015) SS BOND : bond 0.00228 ( 2) SS BOND : angle 1.05925 ( 4) hydrogen bonds : bond 0.03143 ( 1681) hydrogen bonds : angle 4.55946 ( 4725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 888 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 PHE cc_start: 0.8921 (t80) cc_final: 0.8469 (t80) REVERT: A 98 GLU cc_start: 0.9238 (tp30) cc_final: 0.9032 (tp30) REVERT: A 109 PHE cc_start: 0.8391 (m-10) cc_final: 0.7943 (m-10) REVERT: A 138 LYS cc_start: 0.7658 (tppp) cc_final: 0.7226 (tppp) REVERT: A 166 ASP cc_start: 0.9063 (t0) cc_final: 0.8561 (t0) REVERT: A 196 LEU cc_start: 0.9243 (mt) cc_final: 0.9029 (mt) REVERT: A 200 LEU cc_start: 0.9717 (tp) cc_final: 0.9460 (tp) REVERT: A 236 ARG cc_start: 0.9211 (ttp-110) cc_final: 0.8925 (ttp80) REVERT: A 259 LEU cc_start: 0.9749 (mm) cc_final: 0.9489 (mm) REVERT: A 295 LEU cc_start: 0.9511 (mm) cc_final: 0.9283 (mm) REVERT: A 298 GLN cc_start: 0.9135 (pp30) cc_final: 0.8351 (pp30) REVERT: A 299 LEU cc_start: 0.9602 (mt) cc_final: 0.9045 (mt) REVERT: A 300 LEU cc_start: 0.9540 (mm) cc_final: 0.9202 (mm) REVERT: A 395 GLU cc_start: 0.7375 (mp0) cc_final: 0.7098 (mp0) REVERT: A 399 ARG cc_start: 0.8922 (mmt90) cc_final: 0.8144 (mmm-85) REVERT: A 421 MET cc_start: 0.8200 (tpp) cc_final: 0.7974 (tpp) REVERT: A 431 MET cc_start: 0.8047 (tpt) cc_final: 0.7415 (tpp) REVERT: A 459 PHE cc_start: 0.8847 (p90) cc_final: 0.8213 (p90) REVERT: A 473 ASP cc_start: 0.8813 (m-30) cc_final: 0.8593 (m-30) REVERT: A 560 ASN cc_start: 0.9290 (t0) cc_final: 0.8946 (t0) REVERT: A 619 ARG cc_start: 0.8180 (mpt-90) cc_final: 0.7860 (mtt-85) REVERT: A 631 LYS cc_start: 0.9369 (mmpt) cc_final: 0.9025 (mmmt) REVERT: A 737 GLU cc_start: 0.8961 (tp30) cc_final: 0.8554 (tp30) REVERT: A 789 MET cc_start: 0.8595 (mmm) cc_final: 0.8248 (mmp) REVERT: A 797 ARG cc_start: 0.8397 (mpt90) cc_final: 0.8157 (mmt180) REVERT: A 832 TYR cc_start: 0.9073 (t80) cc_final: 0.8574 (t80) REVERT: A 872 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8050 (pm20) REVERT: A 949 ASP cc_start: 0.8915 (t0) cc_final: 0.8476 (t0) REVERT: A 983 PHE cc_start: 0.8911 (m-80) cc_final: 0.8287 (m-80) REVERT: A 1005 MET cc_start: 0.7606 (ppp) cc_final: 0.6461 (ppp) REVERT: A 1083 LEU cc_start: 0.9692 (tt) cc_final: 0.9259 (tt) REVERT: A 1086 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7112 (mt-10) REVERT: A 1097 ILE cc_start: 0.9384 (tp) cc_final: 0.8813 (tp) REVERT: A 1147 ASN cc_start: 0.9477 (t0) cc_final: 0.9120 (t0) REVERT: A 1152 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7199 (ptt180) REVERT: A 1160 ASP cc_start: 0.8589 (p0) cc_final: 0.8102 (p0) REVERT: A 1245 MET cc_start: 0.9488 (tpt) cc_final: 0.9071 (tpp) REVERT: A 1276 TYR cc_start: 0.8183 (m-10) cc_final: 0.7891 (m-10) REVERT: A 1313 MET cc_start: 0.9272 (mtm) cc_final: 0.8748 (mtt) REVERT: A 1332 ARG cc_start: 0.8738 (ttp80) cc_final: 0.8391 (ttp80) REVERT: A 1344 CYS cc_start: 0.8305 (p) cc_final: 0.7879 (p) REVERT: A 1351 TYR cc_start: 0.9065 (m-80) cc_final: 0.8840 (m-80) REVERT: A 1361 MET cc_start: 0.9468 (ttm) cc_final: 0.9081 (tpp) REVERT: A 1373 ASP cc_start: 0.8413 (t0) cc_final: 0.7223 (t0) REVERT: C 135 ARG cc_start: 0.9408 (tpp80) cc_final: 0.9138 (tpp80) REVERT: C 177 MET cc_start: 0.9128 (mpp) cc_final: 0.8837 (mpp) REVERT: C 242 MET cc_start: 0.8646 (tpt) cc_final: 0.8263 (tpp) REVERT: C 243 PHE cc_start: 0.9185 (m-80) cc_final: 0.8606 (m-10) REVERT: C 245 MET cc_start: 0.9378 (mmp) cc_final: 0.9173 (mmm) REVERT: C 261 ASP cc_start: 0.9314 (t70) cc_final: 0.8996 (t70) REVERT: C 281 ARG cc_start: 0.8503 (mpt180) cc_final: 0.8201 (mpt180) REVERT: C 291 THR cc_start: 0.8849 (t) cc_final: 0.8477 (m) REVERT: C 326 ASN cc_start: 0.9476 (m-40) cc_final: 0.9137 (m-40) REVERT: C 341 ASP cc_start: 0.9027 (p0) cc_final: 0.8707 (p0) REVERT: C 395 GLU cc_start: 0.9295 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 416 ASP cc_start: 0.8500 (m-30) cc_final: 0.8152 (m-30) REVERT: C 423 MET cc_start: 0.8788 (tpt) cc_final: 0.8171 (tpt) REVERT: C 427 GLN cc_start: 0.9390 (mp10) cc_final: 0.8938 (pt0) REVERT: C 429 ASN cc_start: 0.9360 (m-40) cc_final: 0.8980 (t0) REVERT: C 461 ASN cc_start: 0.9815 (t0) cc_final: 0.9311 (t0) REVERT: C 463 ASP cc_start: 0.9276 (m-30) cc_final: 0.8999 (m-30) REVERT: C 468 GLN cc_start: 0.9307 (tp40) cc_final: 0.9013 (tp40) REVERT: C 525 GLU cc_start: 0.9247 (mp0) cc_final: 0.8935 (mp0) REVERT: C 534 HIS cc_start: 0.8786 (t70) cc_final: 0.8231 (t-90) REVERT: C 563 PHE cc_start: 0.8913 (m-80) cc_final: 0.8674 (m-80) REVERT: C 565 PHE cc_start: 0.9084 (m-10) cc_final: 0.8662 (m-10) REVERT: C 608 ARG cc_start: 0.9123 (mtp85) cc_final: 0.8737 (mtp85) REVERT: C 628 LYS cc_start: 0.9694 (ptpp) cc_final: 0.9318 (tppt) REVERT: C 685 HIS cc_start: 0.8855 (m90) cc_final: 0.8350 (m-70) REVERT: C 689 TYR cc_start: 0.8857 (m-80) cc_final: 0.8082 (m-80) REVERT: C 718 ARG cc_start: 0.9505 (tmt-80) cc_final: 0.9137 (tpt170) REVERT: C 719 GLN cc_start: 0.9424 (tp-100) cc_final: 0.9114 (tp-100) REVERT: C 917 MET cc_start: 0.9534 (tpp) cc_final: 0.9229 (tpp) REVERT: C 983 PHE cc_start: 0.9190 (m-80) cc_final: 0.8740 (m-80) REVERT: C 1005 MET cc_start: 0.9349 (ttt) cc_final: 0.8426 (tpp) REVERT: C 1035 ASP cc_start: 0.8377 (t0) cc_final: 0.8065 (t0) REVERT: C 1084 TYR cc_start: 0.8858 (t80) cc_final: 0.8617 (t80) REVERT: C 1126 THR cc_start: 0.8752 (p) cc_final: 0.8482 (t) REVERT: C 1131 THR cc_start: 0.8920 (p) cc_final: 0.8178 (p) REVERT: C 1134 LEU cc_start: 0.9099 (tp) cc_final: 0.8861 (tp) REVERT: C 1188 LEU cc_start: 0.9456 (mp) cc_final: 0.9202 (mp) REVERT: C 1223 ASN cc_start: 0.9272 (t0) cc_final: 0.9071 (t0) REVERT: C 1258 ARG cc_start: 0.8561 (ptt-90) cc_final: 0.8000 (ptt-90) REVERT: C 1264 TRP cc_start: 0.9252 (m-10) cc_final: 0.8868 (m-10) REVERT: C 1276 TYR cc_start: 0.8914 (m-10) cc_final: 0.8620 (m-10) REVERT: C 1295 PHE cc_start: 0.8666 (m-80) cc_final: 0.8348 (m-80) REVERT: C 1300 GLU cc_start: 0.8242 (pp20) cc_final: 0.7769 (tm-30) REVERT: C 1377 LEU cc_start: 0.8800 (tp) cc_final: 0.8591 (tp) REVERT: F 63 LEU cc_start: 0.9194 (mt) cc_final: 0.8926 (mt) REVERT: F 115 LEU cc_start: 0.9198 (mm) cc_final: 0.8828 (mm) REVERT: F 139 LEU cc_start: 0.9237 (tp) cc_final: 0.8965 (tp) REVERT: F 148 GLU cc_start: 0.9010 (pp20) cc_final: 0.8660 (pm20) REVERT: F 200 ILE cc_start: 0.9462 (pt) cc_final: 0.9180 (tt) REVERT: O 6 PHE cc_start: 0.8643 (t80) cc_final: 0.8266 (t80) REVERT: O 7 GLU cc_start: 0.8866 (pm20) cc_final: 0.8428 (tm-30) REVERT: O 34 PHE cc_start: 0.8976 (m-80) cc_final: 0.8483 (m-80) REVERT: O 67 TYR cc_start: 0.9389 (m-80) cc_final: 0.9143 (m-10) REVERT: O 69 MET cc_start: 0.8354 (mmt) cc_final: 0.7955 (mmm) REVERT: O 113 ILE cc_start: 0.9318 (mm) cc_final: 0.8902 (tp) REVERT: O 137 PHE cc_start: 0.8573 (m-80) cc_final: 0.7515 (m-80) REVERT: O 184 TYR cc_start: 0.8663 (m-80) cc_final: 0.7958 (m-80) REVERT: O 290 ARG cc_start: 0.8429 (pmt170) cc_final: 0.8091 (pmt170) REVERT: O 313 ILE cc_start: 0.9517 (tp) cc_final: 0.9185 (tp) REVERT: O 314 GLN cc_start: 0.9140 (pm20) cc_final: 0.8646 (pm20) REVERT: X 336 GLU cc_start: 0.8554 (tt0) cc_final: 0.7787 (tp30) REVERT: X 337 GLN cc_start: 0.8082 (pm20) cc_final: 0.7742 (pm20) REVERT: X 422 TYR cc_start: 0.7795 (p90) cc_final: 0.6022 (p90) REVERT: X 457 TRP cc_start: 0.7534 (m-90) cc_final: 0.7021 (m-90) REVERT: k 483 HIS cc_start: 0.8513 (t-90) cc_final: 0.8233 (t-90) REVERT: k 527 PHE cc_start: 0.9272 (t80) cc_final: 0.8880 (t80) REVERT: k 592 TYR cc_start: 0.9417 (m-10) cc_final: 0.8992 (m-80) REVERT: l 26 PHE cc_start: 0.4474 (t80) cc_final: 0.3757 (t80) outliers start: 1 outliers final: 0 residues processed: 888 average time/residue: 0.1969 time to fit residues: 289.5669 Evaluate side-chains 756 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 756 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 242 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 436 optimal weight: 40.0000 chunk 204 optimal weight: 40.0000 chunk 341 optimal weight: 2.9990 chunk 314 optimal weight: 40.0000 chunk 480 optimal weight: 30.0000 chunk 307 optimal weight: 50.0000 chunk 380 optimal weight: 60.0000 chunk 365 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1321 GLN ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN F 314 GLN O 192 HIS ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN ** k 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 GLN l 90 ASN n3123 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.129252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.092755 restraints weight = 150357.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094933 restraints weight = 90541.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.097069 restraints weight = 64016.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.098142 restraints weight = 50184.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098980 restraints weight = 42599.237| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38078 Z= 0.156 Angle : 0.792 16.193 52019 Z= 0.396 Chirality : 0.044 0.301 6157 Planarity : 0.005 0.076 6855 Dihedral : 4.849 34.901 5553 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.35 % Favored : 90.11 % Rotamer: Outliers : 0.03 % Allowed : 0.86 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.13), residues: 4277 helix: 0.11 (0.14), residues: 1376 sheet: -0.94 (0.24), residues: 466 loop : -1.62 (0.13), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 797 TYR 0.047 0.002 TYR A 852 PHE 0.025 0.002 PHE O 137 TRP 0.068 0.003 TRP k 365 HIS 0.009 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00335 (38076) covalent geometry : angle 0.79199 (52015) SS BOND : bond 0.00479 ( 2) SS BOND : angle 1.02472 ( 4) hydrogen bonds : bond 0.03176 ( 1681) hydrogen bonds : angle 4.56612 ( 4725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 857 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8514 (m-10) cc_final: 0.7990 (m-10) REVERT: A 138 LYS cc_start: 0.7771 (tppp) cc_final: 0.7272 (tppp) REVERT: A 166 ASP cc_start: 0.9053 (t0) cc_final: 0.8728 (t0) REVERT: A 196 LEU cc_start: 0.9138 (mt) cc_final: 0.8927 (mt) REVERT: A 200 LEU cc_start: 0.9720 (tp) cc_final: 0.9484 (tp) REVERT: A 233 ASP cc_start: 0.9356 (t70) cc_final: 0.9110 (t0) REVERT: A 236 ARG cc_start: 0.9231 (ttp-110) cc_final: 0.8506 (mtm110) REVERT: A 242 MET cc_start: 0.8219 (ppp) cc_final: 0.7674 (ppp) REVERT: A 299 LEU cc_start: 0.9502 (mt) cc_final: 0.9284 (mt) REVERT: A 399 ARG cc_start: 0.8920 (mmt90) cc_final: 0.8245 (mmp80) REVERT: A 431 MET cc_start: 0.8088 (tpt) cc_final: 0.7441 (tpp) REVERT: A 459 PHE cc_start: 0.8870 (p90) cc_final: 0.8245 (p90) REVERT: A 560 ASN cc_start: 0.9254 (t0) cc_final: 0.8887 (t0) REVERT: A 573 ASP cc_start: 0.8909 (t0) cc_final: 0.8641 (t0) REVERT: A 631 LYS cc_start: 0.9400 (mmpt) cc_final: 0.9030 (mmmt) REVERT: A 688 MET cc_start: 0.8785 (ptp) cc_final: 0.8300 (pmm) REVERT: A 737 GLU cc_start: 0.9016 (tp30) cc_final: 0.8651 (tp30) REVERT: A 797 ARG cc_start: 0.8440 (mpt90) cc_final: 0.8136 (mmt180) REVERT: A 832 TYR cc_start: 0.9143 (t80) cc_final: 0.8737 (t80) REVERT: A 872 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8060 (pm20) REVERT: A 917 MET cc_start: 0.9396 (mpp) cc_final: 0.9132 (mpp) REVERT: A 923 ARG cc_start: 0.7899 (ppt170) cc_final: 0.7375 (ppt170) REVERT: A 949 ASP cc_start: 0.8930 (t0) cc_final: 0.8478 (t0) REVERT: A 983 PHE cc_start: 0.8993 (m-80) cc_final: 0.8466 (m-80) REVERT: A 1005 MET cc_start: 0.7477 (ppp) cc_final: 0.7078 (ppp) REVERT: A 1055 LEU cc_start: 0.9604 (tp) cc_final: 0.9159 (tp) REVERT: A 1059 LEU cc_start: 0.9386 (mt) cc_final: 0.9130 (mt) REVERT: A 1086 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 1147 ASN cc_start: 0.9469 (t0) cc_final: 0.9215 (t0) REVERT: A 1152 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7249 (ptt180) REVERT: A 1176 LEU cc_start: 0.9259 (pp) cc_final: 0.9019 (mp) REVERT: A 1216 GLN cc_start: 0.9639 (mm-40) cc_final: 0.9148 (mm-40) REVERT: A 1245 MET cc_start: 0.9545 (tpt) cc_final: 0.9150 (tpp) REVERT: A 1276 TYR cc_start: 0.8245 (m-10) cc_final: 0.7967 (m-10) REVERT: A 1281 ASN cc_start: 0.9579 (t0) cc_final: 0.9052 (p0) REVERT: A 1313 MET cc_start: 0.9262 (mtm) cc_final: 0.8793 (mtt) REVERT: A 1332 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8361 (ttp80) REVERT: A 1351 TYR cc_start: 0.9089 (m-80) cc_final: 0.8885 (m-80) REVERT: C 242 MET cc_start: 0.8701 (tpt) cc_final: 0.8315 (tpp) REVERT: C 243 PHE cc_start: 0.9184 (m-80) cc_final: 0.8591 (m-10) REVERT: C 245 MET cc_start: 0.9414 (mmp) cc_final: 0.9138 (mmm) REVERT: C 261 ASP cc_start: 0.9332 (t70) cc_final: 0.9041 (t70) REVERT: C 281 ARG cc_start: 0.8519 (mpt180) cc_final: 0.8248 (mpt180) REVERT: C 291 THR cc_start: 0.8912 (t) cc_final: 0.8563 (m) REVERT: C 326 ASN cc_start: 0.9479 (m-40) cc_final: 0.9178 (m-40) REVERT: C 341 ASP cc_start: 0.9007 (p0) cc_final: 0.8713 (p0) REVERT: C 416 ASP cc_start: 0.8532 (m-30) cc_final: 0.8169 (m-30) REVERT: C 429 ASN cc_start: 0.9334 (m-40) cc_final: 0.8862 (t0) REVERT: C 461 ASN cc_start: 0.9810 (t0) cc_final: 0.9325 (t0) REVERT: C 463 ASP cc_start: 0.9298 (m-30) cc_final: 0.9023 (m-30) REVERT: C 468 GLN cc_start: 0.9294 (tp40) cc_final: 0.9057 (tp40) REVERT: C 525 GLU cc_start: 0.9259 (mp0) cc_final: 0.8990 (mp0) REVERT: C 534 HIS cc_start: 0.8783 (t70) cc_final: 0.8233 (t-90) REVERT: C 563 PHE cc_start: 0.8945 (m-80) cc_final: 0.8708 (m-80) REVERT: C 608 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8754 (mtp85) REVERT: C 628 LYS cc_start: 0.9707 (ptpp) cc_final: 0.9445 (ptpp) REVERT: C 644 TYR cc_start: 0.9010 (m-80) cc_final: 0.8806 (m-80) REVERT: C 685 HIS cc_start: 0.8881 (m90) cc_final: 0.8296 (m-70) REVERT: C 689 TYR cc_start: 0.8841 (m-80) cc_final: 0.8133 (m-80) REVERT: C 718 ARG cc_start: 0.9506 (tmt-80) cc_final: 0.9203 (tpt170) REVERT: C 719 GLN cc_start: 0.9466 (tp-100) cc_final: 0.9183 (tp-100) REVERT: C 722 THR cc_start: 0.9075 (m) cc_final: 0.7718 (m) REVERT: C 763 ASP cc_start: 0.9410 (t70) cc_final: 0.9077 (t0) REVERT: C 917 MET cc_start: 0.9539 (tpp) cc_final: 0.9195 (tpp) REVERT: C 983 PHE cc_start: 0.9187 (m-80) cc_final: 0.8746 (m-80) REVERT: C 1005 MET cc_start: 0.9379 (ttt) cc_final: 0.8440 (tpp) REVERT: C 1035 ASP cc_start: 0.8314 (t0) cc_final: 0.8041 (t0) REVERT: C 1084 TYR cc_start: 0.8980 (t80) cc_final: 0.8648 (t80) REVERT: C 1131 THR cc_start: 0.8958 (p) cc_final: 0.8169 (p) REVERT: C 1134 LEU cc_start: 0.9114 (tp) cc_final: 0.8823 (tp) REVERT: C 1144 THR cc_start: 0.8802 (m) cc_final: 0.8541 (m) REVERT: C 1188 LEU cc_start: 0.9490 (mp) cc_final: 0.9223 (mp) REVERT: C 1231 MET cc_start: 0.8798 (ppp) cc_final: 0.8509 (ppp) REVERT: C 1245 MET cc_start: 0.9384 (tmm) cc_final: 0.9091 (tmm) REVERT: C 1264 TRP cc_start: 0.9183 (m-10) cc_final: 0.8801 (m-10) REVERT: C 1295 PHE cc_start: 0.8650 (m-80) cc_final: 0.8315 (m-80) REVERT: C 1300 GLU cc_start: 0.8428 (pp20) cc_final: 0.7934 (tm-30) REVERT: F 115 LEU cc_start: 0.9181 (mm) cc_final: 0.8863 (mm) REVERT: F 139 LEU cc_start: 0.9237 (tp) cc_final: 0.8957 (tp) REVERT: F 200 ILE cc_start: 0.9490 (pt) cc_final: 0.9189 (tt) REVERT: O 6 PHE cc_start: 0.8565 (t80) cc_final: 0.8164 (t80) REVERT: O 7 GLU cc_start: 0.8880 (pm20) cc_final: 0.8416 (tm-30) REVERT: O 34 PHE cc_start: 0.8908 (m-80) cc_final: 0.8427 (m-80) REVERT: O 67 TYR cc_start: 0.9292 (m-80) cc_final: 0.9024 (m-10) REVERT: O 69 MET cc_start: 0.8750 (mmt) cc_final: 0.8313 (mmm) REVERT: O 113 ILE cc_start: 0.9429 (mm) cc_final: 0.8968 (tp) REVERT: O 137 PHE cc_start: 0.8654 (m-80) cc_final: 0.7665 (m-80) REVERT: O 184 TYR cc_start: 0.8686 (m-80) cc_final: 0.7964 (m-80) REVERT: O 313 ILE cc_start: 0.9522 (tp) cc_final: 0.9181 (tp) REVERT: O 314 GLN cc_start: 0.9110 (pm20) cc_final: 0.8811 (pm20) REVERT: X 336 GLU cc_start: 0.8659 (tt0) cc_final: 0.8004 (tp30) REVERT: X 337 GLN cc_start: 0.8160 (pm20) cc_final: 0.7281 (pm20) REVERT: X 422 TYR cc_start: 0.7908 (p90) cc_final: 0.6207 (p90) REVERT: X 457 TRP cc_start: 0.7582 (m-90) cc_final: 0.7052 (m-90) REVERT: k 483 HIS cc_start: 0.8552 (t-90) cc_final: 0.8284 (t-90) REVERT: k 527 PHE cc_start: 0.9278 (t80) cc_final: 0.8890 (t80) REVERT: k 592 TYR cc_start: 0.9424 (m-10) cc_final: 0.8986 (m-80) REVERT: k 610 MET cc_start: 0.3987 (pmm) cc_final: 0.3422 (pmm) REVERT: l 26 PHE cc_start: 0.5258 (t80) cc_final: 0.4290 (t80) outliers start: 1 outliers final: 0 residues processed: 857 average time/residue: 0.1999 time to fit residues: 283.3370 Evaluate side-chains 724 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 724 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 65 optimal weight: 0.8980 chunk 369 optimal weight: 60.0000 chunk 350 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 472 optimal weight: 20.0000 chunk 249 optimal weight: 0.0470 chunk 421 optimal weight: 20.0000 chunk 135 optimal weight: 60.0000 chunk 478 optimal weight: 20.0000 chunk 331 optimal weight: 50.0000 chunk 108 optimal weight: 20.0000 overall best weight: 12.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 86 HIS O 192 HIS ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 390 HIS ** k 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 506 GLN l 90 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.125742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090671 restraints weight = 147627.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092429 restraints weight = 94894.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093802 restraints weight = 67555.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095031 restraints weight = 53516.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.095781 restraints weight = 45848.426| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 38078 Z= 0.243 Angle : 0.871 16.295 52019 Z= 0.440 Chirality : 0.047 0.357 6157 Planarity : 0.006 0.124 6855 Dihedral : 5.236 35.981 5553 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.45 % Favored : 89.01 % Rotamer: Outliers : 0.03 % Allowed : 0.55 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.13), residues: 4277 helix: -0.14 (0.14), residues: 1381 sheet: -1.15 (0.22), residues: 514 loop : -1.68 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 379 TYR 0.040 0.003 TYR A 409 PHE 0.031 0.003 PHE A 244 TRP 0.077 0.003 TRP k 365 HIS 0.013 0.002 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00505 (38076) covalent geometry : angle 0.87082 (52015) SS BOND : bond 0.00761 ( 2) SS BOND : angle 1.85989 ( 4) hydrogen bonds : bond 0.03613 ( 1681) hydrogen bonds : angle 4.88092 ( 4725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8554 Ramachandran restraints generated. 4277 Oldfield, 0 Emsley, 4277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 813 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8760 (m-10) cc_final: 0.8398 (m-10) REVERT: A 134 LYS cc_start: 0.9052 (mppt) cc_final: 0.8660 (mppt) REVERT: A 138 LYS cc_start: 0.7852 (tppp) cc_final: 0.7508 (tppp) REVERT: A 166 ASP cc_start: 0.9303 (t0) cc_final: 0.8954 (t0) REVERT: A 200 LEU cc_start: 0.9703 (tp) cc_final: 0.9471 (tp) REVERT: A 259 LEU cc_start: 0.9719 (mm) cc_final: 0.9506 (mm) REVERT: A 394 LEU cc_start: 0.9527 (tt) cc_final: 0.9070 (tt) REVERT: A 399 ARG cc_start: 0.9001 (mmt90) cc_final: 0.8261 (mmm-85) REVERT: A 421 MET cc_start: 0.8892 (tpp) cc_final: 0.8644 (tpp) REVERT: A 473 ASP cc_start: 0.8721 (m-30) cc_final: 0.8489 (m-30) REVERT: A 475 MET cc_start: 0.8727 (ppp) cc_final: 0.8407 (ppp) REVERT: A 498 LEU cc_start: 0.9052 (mt) cc_final: 0.8690 (tp) REVERT: A 547 PHE cc_start: 0.9352 (t80) cc_final: 0.9057 (t80) REVERT: A 560 ASN cc_start: 0.9235 (t0) cc_final: 0.8903 (t0) REVERT: A 573 ASP cc_start: 0.8944 (t0) cc_final: 0.8683 (t0) REVERT: A 631 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9067 (mmmt) REVERT: A 688 MET cc_start: 0.8893 (ptp) cc_final: 0.8382 (pmm) REVERT: A 737 GLU cc_start: 0.9194 (tp30) cc_final: 0.8814 (tp30) REVERT: A 797 ARG cc_start: 0.8706 (mpt90) cc_final: 0.8291 (mmt180) REVERT: A 832 TYR cc_start: 0.9115 (t80) cc_final: 0.8556 (t80) REVERT: A 848 MET cc_start: 0.5077 (mtm) cc_final: 0.3852 (mpp) REVERT: A 872 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8005 (pm20) REVERT: A 917 MET cc_start: 0.9435 (mpp) cc_final: 0.9216 (mpp) REVERT: A 923 ARG cc_start: 0.8128 (ppt170) cc_final: 0.7590 (ppt170) REVERT: A 945 MET cc_start: 0.9162 (ttt) cc_final: 0.8775 (ttm) REVERT: A 949 ASP cc_start: 0.8965 (t0) cc_final: 0.8503 (t0) REVERT: A 983 PHE cc_start: 0.8951 (m-80) cc_final: 0.8498 (m-80) REVERT: A 1005 MET cc_start: 0.7526 (ppp) cc_final: 0.7162 (ppp) REVERT: A 1086 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 1125 TYR cc_start: 0.8333 (m-80) cc_final: 0.8086 (m-80) REVERT: A 1152 ARG cc_start: 0.8265 (ptm160) cc_final: 0.7449 (ptt180) REVERT: A 1160 ASP cc_start: 0.8693 (p0) cc_final: 0.8224 (p0) REVERT: A 1216 GLN cc_start: 0.9674 (mm-40) cc_final: 0.9398 (mm-40) REVERT: A 1245 MET cc_start: 0.9600 (tpt) cc_final: 0.9083 (tpp) REVERT: A 1256 THR cc_start: 0.8685 (p) cc_final: 0.7807 (t) REVERT: A 1281 ASN cc_start: 0.9598 (t0) cc_final: 0.9021 (p0) REVERT: A 1313 MET cc_start: 0.9226 (mtm) cc_final: 0.8859 (mtp) REVERT: A 1347 PHE cc_start: 0.9218 (m-80) cc_final: 0.8989 (m-80) REVERT: C 242 MET cc_start: 0.8784 (tpt) cc_final: 0.8346 (tpp) REVERT: C 243 PHE cc_start: 0.9241 (m-80) cc_final: 0.8532 (m-10) REVERT: C 245 MET cc_start: 0.9543 (mmp) cc_final: 0.9200 (mmm) REVERT: C 326 ASN cc_start: 0.9539 (m-40) cc_final: 0.9212 (m-40) REVERT: C 341 ASP cc_start: 0.9122 (p0) cc_final: 0.8846 (p0) REVERT: C 416 ASP cc_start: 0.8403 (m-30) cc_final: 0.7981 (m-30) REVERT: C 427 GLN cc_start: 0.9411 (mp10) cc_final: 0.8868 (pt0) REVERT: C 429 ASN cc_start: 0.9371 (m-40) cc_final: 0.8968 (t0) REVERT: C 461 ASN cc_start: 0.9811 (t0) cc_final: 0.9461 (t0) REVERT: C 463 ASP cc_start: 0.9327 (m-30) cc_final: 0.9045 (m-30) REVERT: C 468 GLN cc_start: 0.9296 (tp40) cc_final: 0.9050 (tp40) REVERT: C 525 GLU cc_start: 0.9153 (mp0) cc_final: 0.8899 (mp0) REVERT: C 534 HIS cc_start: 0.8800 (t70) cc_final: 0.8223 (t-90) REVERT: C 563 PHE cc_start: 0.8982 (m-80) cc_final: 0.8664 (m-80) REVERT: C 685 HIS cc_start: 0.8973 (m90) cc_final: 0.8244 (m-70) REVERT: C 689 TYR cc_start: 0.8849 (m-80) cc_final: 0.8182 (m-80) REVERT: C 718 ARG cc_start: 0.9545 (tmt-80) cc_final: 0.9216 (tpt170) REVERT: C 719 GLN cc_start: 0.9492 (tp-100) cc_final: 0.9230 (tp-100) REVERT: C 722 THR cc_start: 0.9159 (m) cc_final: 0.7788 (m) REVERT: C 737 GLU cc_start: 0.9208 (pp20) cc_final: 0.9002 (pp20) REVERT: C 983 PHE cc_start: 0.9210 (m-80) cc_final: 0.8740 (m-80) REVERT: C 1005 MET cc_start: 0.9307 (ttt) cc_final: 0.8684 (tpp) REVERT: C 1035 ASP cc_start: 0.8219 (t0) cc_final: 0.7828 (t0) REVERT: C 1131 THR cc_start: 0.8943 (p) cc_final: 0.8253 (p) REVERT: C 1134 LEU cc_start: 0.9191 (tp) cc_final: 0.8799 (tp) REVERT: C 1231 MET cc_start: 0.8862 (ppp) cc_final: 0.8544 (ppp) REVERT: C 1245 MET cc_start: 0.9447 (tmm) cc_final: 0.9097 (tmm) REVERT: C 1275 LEU cc_start: 0.9507 (tp) cc_final: 0.9067 (tp) REVERT: C 1276 TYR cc_start: 0.9023 (m-10) cc_final: 0.8536 (m-10) REVERT: C 1295 PHE cc_start: 0.8761 (m-80) cc_final: 0.8323 (m-80) REVERT: C 1300 GLU cc_start: 0.8561 (pp20) cc_final: 0.8076 (pp20) REVERT: F 115 LEU cc_start: 0.9167 (mm) cc_final: 0.8798 (mm) REVERT: F 139 LEU cc_start: 0.9318 (tp) cc_final: 0.8992 (tp) REVERT: F 141 ILE cc_start: 0.9127 (mm) cc_final: 0.8663 (mm) REVERT: F 154 VAL cc_start: 0.8799 (p) cc_final: 0.8554 (m) REVERT: F 200 ILE cc_start: 0.9561 (pt) cc_final: 0.9257 (tt) REVERT: F 201 ARG cc_start: 0.8759 (tmm160) cc_final: 0.8353 (tmm-80) REVERT: F 203 LEU cc_start: 0.9719 (tp) cc_final: 0.9456 (tp) REVERT: O 7 GLU cc_start: 0.8877 (pm20) cc_final: 0.8457 (mp0) REVERT: O 34 PHE cc_start: 0.9020 (m-80) cc_final: 0.8568 (m-80) REVERT: O 69 MET cc_start: 0.8902 (mmt) cc_final: 0.8249 (mmm) REVERT: O 137 PHE cc_start: 0.8700 (m-80) cc_final: 0.7629 (m-80) REVERT: O 179 TYR cc_start: 0.7938 (t80) cc_final: 0.7710 (t80) REVERT: O 184 TYR cc_start: 0.8624 (m-80) cc_final: 0.8005 (m-80) REVERT: X 336 GLU cc_start: 0.8932 (tt0) cc_final: 0.8118 (tp30) REVERT: X 457 TRP cc_start: 0.7473 (m-90) cc_final: 0.6911 (m-90) REVERT: k 28 ILE cc_start: 0.5486 (mp) cc_final: 0.4687 (mp) REVERT: k 398 VAL cc_start: 0.3709 (t) cc_final: 0.3439 (t) REVERT: k 483 HIS cc_start: 0.8640 (t-90) cc_final: 0.8438 (t70) REVERT: k 527 PHE cc_start: 0.9293 (t80) cc_final: 0.8896 (t80) REVERT: k 592 TYR cc_start: 0.9349 (m-10) cc_final: 0.8880 (m-80) REVERT: k 610 MET cc_start: 0.3266 (pmm) cc_final: 0.2229 (pmm) REVERT: l 26 PHE cc_start: 0.5190 (t80) cc_final: 0.4488 (t80) REVERT: m 37 MET cc_start: 0.7251 (pmm) cc_final: 0.7045 (pmm) REVERT: o 3104 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7779 (mmp80) outliers start: 1 outliers final: 0 residues processed: 813 average time/residue: 0.1981 time to fit residues: 267.4919 Evaluate side-chains 684 residues out of total 3625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 342 optimal weight: 5.9990 chunk 352 optimal weight: 8.9990 chunk 493 optimal weight: 50.0000 chunk 315 optimal weight: 50.0000 chunk 409 optimal weight: 0.5980 chunk 203 optimal weight: 10.0000 chunk 327 optimal weight: 40.0000 chunk 246 optimal weight: 8.9990 chunk 428 optimal weight: 9.9990 chunk 472 optimal weight: 40.0000 chunk 273 optimal weight: 0.0050 overall best weight: 4.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 HIS ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 GLN ** X 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN k 506 GLN l 90 ASN n3123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.127529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.091625 restraints weight = 150031.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.094166 restraints weight = 90221.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095834 restraints weight = 63350.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096755 restraints weight = 49354.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.097550 restraints weight = 42277.884| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 38078 Z= 0.154 Angle : 0.821 16.187 52019 Z= 0.409 Chirality : 0.045 0.299 6157 Planarity : 0.005 0.122 6855 Dihedral : 5.079 35.534 5553 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.42 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.13), residues: 4277 helix: -0.02 (0.14), residues: 1384 sheet: -1.31 (0.22), residues: 516 loop : -1.63 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG k 507 TYR 0.031 0.002 TYR A 852 PHE 0.027 0.002 PHE C 657 TRP 0.079 0.003 TRP k 365 HIS 0.009 0.001 HIS A 792 Details of bonding type rmsd covalent geometry : bond 0.00334 (38076) covalent geometry : angle 0.82053 (52015) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.17967 ( 4) hydrogen bonds : bond 0.03285 ( 1681) hydrogen bonds : angle 4.68867 ( 4725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7524.01 seconds wall clock time: 130 minutes 4.43 seconds (7804.43 seconds total)