Starting phenix.real_space_refine on Tue Apr 7 08:41:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d3e_30555/04_2026/7d3e_30555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d3e_30555/04_2026/7d3e_30555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d3e_30555/04_2026/7d3e_30555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d3e_30555/04_2026/7d3e_30555.map" model { file = "/net/cci-nas-00/data/ceres_data/7d3e_30555/04_2026/7d3e_30555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d3e_30555/04_2026/7d3e_30555.cif" } resolution = 2.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 10 5.49 5 S 88 5.16 5 Na 4 4.78 5 C 16754 2.51 5 N 4448 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 142 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1380, 10545 Classifications: {'peptide': 1380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 2, 'PTRANS': 76, 'TRANS': 1301} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 829 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 26, 'TRP:plan': 3, 'GLN:plan1': 16, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 10, 'ASN:plan1': 7, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 402 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2085 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 257} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1380, 10545 Classifications: {'peptide': 1380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 2, 'PTRANS': 76, 'TRANS': 1301} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 829 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ARG:plan': 18, 'GLU:plan': 26, 'TRP:plan': 3, 'GLN:plan1': 16, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 10, 'ASN:plan1': 7, 'PHE:plan': 7} Unresolved non-hydrogen planarities: 402 Chain: "D" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2085 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 257} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 231 Unusual residues: {' NA': 2, 'FAD': 1, 'HEM': 2, 'NAG': 3, 'NDP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 231 Unusual residues: {' NA': 2, 'FAD': 1, 'HEM': 2, 'NAG': 3, 'NDP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.38, per 1000 atoms: 0.21 Number of scatterers: 26012 At special positions: 0 Unit cell: (149.435, 130.625, 169.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 88 16.00 P 10 15.00 Na 4 11.00 O 4704 8.00 N 4448 7.00 C 16754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A1165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C1165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 579 " distance=2.03 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 234 " 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=4, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN E 5 " - " MAN E 6 " " MAN E 8 " - " MAN E 9 " " MAN F 4 " - " MAN F 5 " " MAN F 5 " - " MAN F 6 " " MAN F 8 " - " MAN F 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " MAN E 7 " - " MAN E 10 " " BMA F 3 " - " MAN F 4 " " MAN F 7 " - " MAN F 10 " ALPHA1-6 " BMA E 3 " - " MAN E 7 " " MAN E 7 " - " MAN E 8 " " BMA F 3 " - " MAN F 7 " " MAN F 7 " - " MAN F 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1605 " - " ASN A 94 " " NAG A1606 " - " ASN A 534 " " NAG A1607 " - " ASN A 342 " " NAG B 501 " - " ASN B 84 " " NAG B 502 " - " ASN B 121 " " NAG C1605 " - " ASN C 94 " " NAG C1606 " - " ASN C 534 " " NAG C1607 " - " ASN C 342 " " NAG D 501 " - " ASN D 84 " " NAG D 502 " - " ASN D 121 " " NAG E 1 " - " ASN B 109 " " NAG F 1 " - " ASN D 109 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 20 sheets defined 54.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.658A pdb=" N ARG A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.635A pdb=" N GLY A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 267 Processing helix chain 'A' and resid 271 through 294 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.614A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 454 through 460 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.556A pdb=" N SER A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 511 Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.519A pdb=" N GLY A 522 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 536 through 546 Processing helix chain 'A' and resid 548 through 552 Processing helix chain 'A' and resid 591 through 619 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 718 through 736 removed outlier: 3.670A pdb=" N SER A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 772 removed outlier: 3.731A pdb=" N THR A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 792 through 800 Processing helix chain 'A' and resid 803 through 811 Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 837 through 848 Processing helix chain 'A' and resid 854 through 864 Processing helix chain 'A' and resid 873 through 887 removed outlier: 4.324A pdb=" N ILE A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 904 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 1027 through 1041 Processing helix chain 'A' and resid 1041 through 1069 Processing helix chain 'A' and resid 1074 through 1078 removed outlier: 3.592A pdb=" N THR A1078 " --> pdb=" O ILE A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1100 Processing helix chain 'A' and resid 1101 through 1104 Processing helix chain 'A' and resid 1105 through 1113 Processing helix chain 'A' and resid 1115 through 1120 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1125 through 1158 removed outlier: 4.083A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1167 Processing helix chain 'A' and resid 1181 through 1188 Processing helix chain 'A' and resid 1189 through 1209 Processing helix chain 'A' and resid 1210 through 1217 Processing helix chain 'A' and resid 1218 through 1226 Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.710A pdb=" N GLY A1239 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1270 removed outlier: 4.828A pdb=" N VAL A1255 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Proline residue: A1256 - end of helix Processing helix chain 'A' and resid 1312 through 1314 No H-bonds generated for 'chain 'A' and resid 1312 through 1314' Processing helix chain 'A' and resid 1340 through 1352 removed outlier: 4.193A pdb=" N ALA A1352 " --> pdb=" O GLU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1375 through 1380 Processing helix chain 'A' and resid 1390 through 1393 removed outlier: 3.583A pdb=" N THR A1393 " --> pdb=" O ILE A1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1390 through 1393' Processing helix chain 'A' and resid 1394 through 1409 Processing helix chain 'A' and resid 1429 through 1443 removed outlier: 3.842A pdb=" N ALA A1433 " --> pdb=" O PHE A1429 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1461 removed outlier: 3.544A pdb=" N PHE A1461 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1474 Processing helix chain 'A' and resid 1497 through 1509 Processing helix chain 'A' and resid 1522 through 1539 removed outlier: 3.939A pdb=" N GLN A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 42 Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 50 through 73 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 168 through 200 removed outlier: 3.856A pdb=" N GLN B 172 " --> pdb=" O GLY B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 230 removed outlier: 3.654A pdb=" N GLY B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 275 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.658A pdb=" N ARG C 84 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 111 Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 227 through 231 removed outlier: 4.636A pdb=" N GLY C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 267 Processing helix chain 'C' and resid 271 through 294 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.614A pdb=" N VAL C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 401 through 406 Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 434 through 442 Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 454 through 460 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.557A pdb=" N SER C 489 " --> pdb=" O GLY C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 518 through 522 removed outlier: 3.520A pdb=" N GLY C 522 " --> pdb=" O THR C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 536 through 546 Processing helix chain 'C' and resid 548 through 552 Processing helix chain 'C' and resid 591 through 619 Proline residue: C 606 - end of helix Processing helix chain 'C' and resid 718 through 736 removed outlier: 3.670A pdb=" N SER C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 772 removed outlier: 3.725A pdb=" N THR C 766 " --> pdb=" O HIS C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 Processing helix chain 'C' and resid 792 through 800 Processing helix chain 'C' and resid 803 through 811 Processing helix chain 'C' and resid 817 through 827 Processing helix chain 'C' and resid 837 through 848 Processing helix chain 'C' and resid 854 through 864 Processing helix chain 'C' and resid 873 through 887 removed outlier: 4.324A pdb=" N ILE C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 904 Processing helix chain 'C' and resid 918 through 925 Processing helix chain 'C' and resid 1027 through 1041 Processing helix chain 'C' and resid 1041 through 1069 Processing helix chain 'C' and resid 1074 through 1078 removed outlier: 3.594A pdb=" N THR C1078 " --> pdb=" O ILE C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1100 Processing helix chain 'C' and resid 1101 through 1104 Processing helix chain 'C' and resid 1105 through 1113 Processing helix chain 'C' and resid 1115 through 1120 Processing helix chain 'C' and resid 1122 through 1124 No H-bonds generated for 'chain 'C' and resid 1122 through 1124' Processing helix chain 'C' and resid 1125 through 1158 removed outlier: 4.064A pdb=" N VAL C1139 " --> pdb=" O SER C1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1167 Processing helix chain 'C' and resid 1181 through 1188 Processing helix chain 'C' and resid 1189 through 1209 Processing helix chain 'C' and resid 1210 through 1217 Processing helix chain 'C' and resid 1218 through 1226 removed outlier: 3.524A pdb=" N TRP C1222 " --> pdb=" O PHE C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1227 through 1239 removed outlier: 3.664A pdb=" N GLY C1239 " --> pdb=" O LEU C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1248 through 1270 removed outlier: 4.828A pdb=" N VAL C1255 " --> pdb=" O ILE C1251 " (cutoff:3.500A) Proline residue: C1256 - end of helix Processing helix chain 'C' and resid 1312 through 1314 No H-bonds generated for 'chain 'C' and resid 1312 through 1314' Processing helix chain 'C' and resid 1340 through 1352 removed outlier: 4.193A pdb=" N ALA C1352 " --> pdb=" O GLU C1348 " (cutoff:3.500A) Processing helix chain 'C' and resid 1375 through 1380 Processing helix chain 'C' and resid 1390 through 1393 removed outlier: 3.583A pdb=" N THR C1393 " --> pdb=" O ILE C1390 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1390 through 1393' Processing helix chain 'C' and resid 1394 through 1409 Processing helix chain 'C' and resid 1429 through 1443 removed outlier: 3.842A pdb=" N ALA C1433 " --> pdb=" O PHE C1429 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C1434 " --> pdb=" O GLU C1430 " (cutoff:3.500A) Processing helix chain 'C' and resid 1457 through 1461 removed outlier: 3.540A pdb=" N PHE C1461 " --> pdb=" O ALA C1458 " (cutoff:3.500A) Processing helix chain 'C' and resid 1462 through 1474 Processing helix chain 'C' and resid 1497 through 1509 Processing helix chain 'C' and resid 1522 through 1539 removed outlier: 3.940A pdb=" N GLN C1539 " --> pdb=" O LEU C1535 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 42 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 50 through 73 Processing helix chain 'D' and resid 137 through 149 Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 168 through 200 removed outlier: 3.856A pdb=" N GLN D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 230 removed outlier: 3.654A pdb=" N GLY D 206 " --> pdb=" O VAL D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 275 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AA2, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 409 Processing sheet with id=AA5, first strand: chain 'A' and resid 677 through 682 removed outlier: 5.781A pdb=" N VAL A 677 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP A 672 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 690 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 801 through 802 Processing sheet with id=AA7, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 5.197A pdb=" N SER A1276 " --> pdb=" O GLN A1293 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG A1291 " --> pdb=" O VAL A1278 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A1280 " --> pdb=" O HIS A1289 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS A1289 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A1282 " --> pdb=" O VAL A1287 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL A1287 " --> pdb=" O LEU A1282 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1490 through 1493 removed outlier: 9.693A pdb=" N ILE A1490 " --> pdb=" O VAL A1448 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A1450 " --> pdb=" O ILE A1490 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N HIS A1492 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE A1452 " --> pdb=" O HIS A1492 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL A1382 " --> pdb=" O LYS A1514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 122 through 131 removed outlier: 8.217A pdb=" N GLU B 122 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 124 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N SER B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N VAL B 117 " --> pdb=" O TRP B 94 " (cutoff:3.500A) removed outlier: 12.622A pdb=" N TRP B 94 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 238 removed outlier: 4.567A pdb=" N LEU B 236 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 126 Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AB4, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB5, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AB6, first strand: chain 'C' and resid 677 through 682 removed outlier: 5.784A pdb=" N VAL C 677 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP C 672 " --> pdb=" O VAL C 677 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 690 " --> pdb=" O LYS C 705 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 801 through 802 Processing sheet with id=AB8, first strand: chain 'C' and resid 1319 through 1322 removed outlier: 5.197A pdb=" N SER C1276 " --> pdb=" O GLN C1293 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG C1291 " --> pdb=" O VAL C1278 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C1280 " --> pdb=" O HIS C1289 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS C1289 " --> pdb=" O ALA C1280 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C1282 " --> pdb=" O VAL C1287 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL C1287 " --> pdb=" O LEU C1282 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1490 through 1493 removed outlier: 9.691A pdb=" N ILE C1490 " --> pdb=" O VAL C1448 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL C1450 " --> pdb=" O ILE C1490 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N HIS C1492 " --> pdb=" O VAL C1450 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C1452 " --> pdb=" O HIS C1492 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL C1382 " --> pdb=" O LYS C1514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 122 through 131 removed outlier: 8.216A pdb=" N GLU D 122 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE D 124 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER D 96 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 11.456A pdb=" N VAL D 117 " --> pdb=" O TRP D 94 " (cutoff:3.500A) removed outlier: 12.620A pdb=" N TRP D 94 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 236 through 238 removed outlier: 4.567A pdb=" N LEU D 236 " --> pdb=" O LEU D 243 " (cutoff:3.500A) 1433 hydrogen bonds defined for protein. 4119 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: 5.58 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10993 1.39 - 1.56: 15585 1.56 - 1.73: 20 1.73 - 1.90: 132 1.90 - 2.07: 16 Bond restraints: 26746 Sorted by residual: bond pdb=" O2B NDP C1603 " pdb=" P2B NDP C1603 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.45e+01 bond pdb=" O2B NDP A1603 " pdb=" P2B NDP A1603 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.43e+01 bond pdb=" O5D NDP C1603 " pdb=" PN NDP C1603 " ideal model delta sigma weight residual 1.757 1.608 0.149 3.50e-02 8.16e+02 1.81e+01 bond pdb=" O5D NDP A1603 " pdb=" PN NDP A1603 " ideal model delta sigma weight residual 1.757 1.608 0.149 3.50e-02 8.16e+02 1.81e+01 bond pdb=" C4A FAD C1604 " pdb=" C5A FAD C1604 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 26741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 36236 3.07 - 6.14: 277 6.14 - 9.21: 41 9.21 - 12.28: 0 12.28 - 15.35: 6 Bond angle restraints: 36560 Sorted by residual: angle pdb=" C5B NDP A1603 " pdb=" O5B NDP A1603 " pdb=" PA NDP A1603 " ideal model delta sigma weight residual 103.84 119.19 -15.35 1.91e+00 2.73e-01 6.42e+01 angle pdb=" C5B NDP C1603 " pdb=" O5B NDP C1603 " pdb=" PA NDP C1603 " ideal model delta sigma weight residual 103.84 119.12 -15.28 1.91e+00 2.73e-01 6.37e+01 angle pdb=" PA NDP A1603 " pdb=" O3 NDP A1603 " pdb=" PN NDP A1603 " ideal model delta sigma weight residual 107.74 120.32 -12.58 1.95e+00 2.62e-01 4.14e+01 angle pdb=" PA NDP C1603 " pdb=" O3 NDP C1603 " pdb=" PN NDP C1603 " ideal model delta sigma weight residual 107.74 120.26 -12.52 1.95e+00 2.62e-01 4.11e+01 angle pdb=" C5D NDP A1603 " pdb=" O5D NDP A1603 " pdb=" PN NDP A1603 " ideal model delta sigma weight residual 104.93 119.56 -14.63 2.66e+00 1.41e-01 3.03e+01 ... (remaining 36555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.55: 15163 22.55 - 45.10: 549 45.10 - 67.66: 71 67.66 - 90.21: 57 90.21 - 112.76: 26 Dihedral angle restraints: 15866 sinusoidal: 6304 harmonic: 9562 Sorted by residual: dihedral pdb=" CA HIS A1018 " pdb=" C HIS A1018 " pdb=" N ARG A1019 " pdb=" CA ARG A1019 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS C1018 " pdb=" C HIS C1018 " pdb=" N ARG C1019 " pdb=" CA ARG C1019 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C5B NDP A1603 " pdb=" O5B NDP A1603 " pdb=" PA NDP A1603 " pdb=" O3 NDP A1603 " ideal model delta sinusoidal sigma weight residual 175.04 62.28 112.76 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 15863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3562 0.060 - 0.120: 530 0.120 - 0.181: 31 0.181 - 0.241: 5 0.241 - 0.301: 2 Chirality restraints: 4130 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 109 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4127 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1361 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A1362 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1362 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1362 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C1361 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO C1362 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C1362 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1362 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 55 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 56 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.024 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 283 2.58 - 3.16: 21909 3.16 - 3.74: 43525 3.74 - 4.32: 59416 4.32 - 4.90: 97209 Nonbonded interactions: 222342 Sorted by model distance: nonbonded pdb=" NE2 HIS A1225 " pdb="FE HEM A1601 " model vdw 2.000 3.080 nonbonded pdb=" NE2 HIS A1144 " pdb="FE HEM A1602 " model vdw 2.000 3.080 nonbonded pdb=" OH TYR D 87 " pdb=" OH TYR D 126 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR B 87 " pdb=" OH TYR B 126 " model vdw 2.219 3.040 nonbonded pdb=" OG SER C1482 " pdb=" OG1 THR C1485 " model vdw 2.226 3.040 ... (remaining 222337 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.290 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.342 26788 Z= 0.205 Angle : 0.685 15.348 36666 Z= 0.335 Chirality : 0.042 0.301 4130 Planarity : 0.004 0.053 4604 Dihedral : 13.631 112.760 9666 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.44 % Allowed : 2.51 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.86 (0.15), residues: 3256 helix: 1.33 (0.13), residues: 1596 sheet: -0.76 (0.26), residues: 352 loop : 0.17 (0.19), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1080 TYR 0.010 0.001 TYR C 435 PHE 0.021 0.001 PHE C 329 TRP 0.009 0.001 TRP C 252 HIS 0.004 0.001 HIS C1130 Details of bonding type rmsd covalent geometry : bond 0.00479 (26746) covalent geometry : angle 0.67833 (36560) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.44486 ( 16) hydrogen bonds : bond 0.12492 ( 1433) hydrogen bonds : angle 6.06262 ( 4119) Misc. bond : bond 0.26004 ( 4) link_ALPHA1-2 : bond 0.00182 ( 6) link_ALPHA1-2 : angle 2.08699 ( 18) link_ALPHA1-3 : bond 0.00272 ( 4) link_ALPHA1-3 : angle 1.86303 ( 12) link_ALPHA1-6 : bond 0.00366 ( 4) link_ALPHA1-6 : angle 1.75823 ( 12) link_BETA1-4 : bond 0.00457 ( 4) link_BETA1-4 : angle 2.54242 ( 12) link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 2.05954 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 632 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9200 (mmm) cc_final: 0.8882 (mmm) REVERT: A 154 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8753 (mt-10) REVERT: A 164 ASP cc_start: 0.8737 (m-30) cc_final: 0.8407 (m-30) REVERT: A 210 GLN cc_start: 0.8094 (mp10) cc_final: 0.7881 (pm20) REVERT: A 225 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8001 (tt0) REVERT: A 242 GLU cc_start: 0.9105 (pt0) cc_final: 0.8901 (pt0) REVERT: A 466 GLU cc_start: 0.9107 (mp0) cc_final: 0.8895 (mp0) REVERT: A 503 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 569 ARG cc_start: 0.8494 (ptp90) cc_final: 0.8173 (ptp90) REVERT: A 806 GLU cc_start: 0.9102 (tp30) cc_final: 0.8531 (tp30) REVERT: A 809 GLU cc_start: 0.8894 (tp30) cc_final: 0.8488 (tp30) REVERT: A 817 ASP cc_start: 0.8832 (t0) cc_final: 0.8261 (t0) REVERT: A 1025 SER cc_start: 0.9170 (m) cc_final: 0.8871 (t) REVERT: A 1029 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8358 (tm-30) REVERT: A 1032 GLN cc_start: 0.9336 (tp-100) cc_final: 0.9123 (tm-30) REVERT: A 1033 GLN cc_start: 0.9051 (mm110) cc_final: 0.8408 (mm-40) REVERT: A 1042 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8152 (ttm170) REVERT: A 1061 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 1119 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8309 (tpt-90) REVERT: A 1211 HIS cc_start: 0.7686 (t70) cc_final: 0.7252 (t-90) REVERT: A 1215 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7519 (mtp85) REVERT: A 1372 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 1441 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8600 (tm-30) REVERT: A 1474 HIS cc_start: 0.9053 (m90) cc_final: 0.8739 (m-70) REVERT: A 1499 GLU cc_start: 0.8585 (pp20) cc_final: 0.8049 (tm-30) REVERT: A 1530 GLU cc_start: 0.8389 (tt0) cc_final: 0.8142 (tt0) REVERT: A 1535 LEU cc_start: 0.9427 (tt) cc_final: 0.9172 (tt) REVERT: A 1548 TYR cc_start: 0.7386 (m-80) cc_final: 0.6772 (m-10) REVERT: B 37 THR cc_start: 0.8866 (m) cc_final: 0.8489 (t) REVERT: B 80 GLN cc_start: 0.9183 (tt0) cc_final: 0.8976 (tt0) REVERT: B 129 GLU cc_start: 0.9001 (tt0) cc_final: 0.8797 (tt0) REVERT: B 226 MET cc_start: 0.8702 (mmt) cc_final: 0.8485 (mmp) REVERT: B 260 LEU cc_start: 0.8801 (tt) cc_final: 0.8471 (tm) REVERT: C 40 MET cc_start: 0.9195 (mmm) cc_final: 0.8916 (mmm) REVERT: C 43 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8675 (mmm160) REVERT: C 154 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8735 (mt-10) REVERT: C 164 ASP cc_start: 0.8707 (m-30) cc_final: 0.8383 (m-30) REVERT: C 210 GLN cc_start: 0.8116 (mp10) cc_final: 0.7884 (pm20) REVERT: C 225 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7977 (tt0) REVERT: C 466 GLU cc_start: 0.9110 (mp0) cc_final: 0.8745 (mp0) REVERT: C 503 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 569 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8299 (ptp90) REVERT: C 806 GLU cc_start: 0.9108 (tp30) cc_final: 0.8542 (tp30) REVERT: C 809 GLU cc_start: 0.8890 (tp30) cc_final: 0.8464 (tp30) REVERT: C 817 ASP cc_start: 0.8811 (t0) cc_final: 0.8271 (t0) REVERT: C 1025 SER cc_start: 0.9181 (m) cc_final: 0.8877 (t) REVERT: C 1029 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8328 (tm-30) REVERT: C 1033 GLN cc_start: 0.9045 (mm110) cc_final: 0.8281 (mm-40) REVERT: C 1042 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8153 (ttm170) REVERT: C 1119 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8306 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7738 (t70) cc_final: 0.7301 (t-90) REVERT: C 1215 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7571 (mtp85) REVERT: C 1237 ILE cc_start: 0.9140 (mt) cc_final: 0.8805 (mp) REVERT: C 1372 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 1374 HIS cc_start: 0.7792 (m170) cc_final: 0.7045 (m170) REVERT: C 1427 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8805 (ptm160) REVERT: C 1441 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8662 (tm-30) REVERT: C 1459 GLU cc_start: 0.9223 (mp0) cc_final: 0.8819 (pt0) REVERT: C 1474 HIS cc_start: 0.9090 (m90) cc_final: 0.8784 (m-70) REVERT: C 1481 ARG cc_start: 0.8890 (mpt-90) cc_final: 0.8595 (mpt-90) REVERT: C 1499 GLU cc_start: 0.8598 (pp20) cc_final: 0.8048 (tm-30) REVERT: C 1535 LEU cc_start: 0.9451 (tt) cc_final: 0.9182 (tt) REVERT: C 1548 TYR cc_start: 0.7373 (m-80) cc_final: 0.6798 (m-10) REVERT: D 37 THR cc_start: 0.8890 (m) cc_final: 0.8551 (t) REVERT: D 80 GLN cc_start: 0.9193 (tt0) cc_final: 0.8977 (tt0) REVERT: D 129 GLU cc_start: 0.8999 (tt0) cc_final: 0.8792 (tt0) REVERT: D 226 MET cc_start: 0.8705 (mmt) cc_final: 0.8467 (mmp) REVERT: D 260 LEU cc_start: 0.8764 (tt) cc_final: 0.8447 (tm) outliers start: 11 outliers final: 2 residues processed: 636 average time/residue: 0.6143 time to fit residues: 451.6429 Evaluate side-chains 486 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 484 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain C residue 1255 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN A1245 GLN A1543 HIS C1032 GLN C1040 ASN ** C1245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1543 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.081233 restraints weight = 44642.676| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.14 r_work: 0.2830 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.558 26788 Z= 0.348 Angle : 0.728 16.417 36666 Z= 0.347 Chirality : 0.047 0.204 4130 Planarity : 0.005 0.055 4604 Dihedral : 11.382 114.949 4318 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.19 % Allowed : 11.04 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.97 (0.15), residues: 3256 helix: 1.57 (0.13), residues: 1572 sheet: -0.76 (0.26), residues: 340 loop : 0.02 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 804 TYR 0.017 0.002 TYR A 310 PHE 0.030 0.002 PHE A 299 TRP 0.018 0.002 TRP A1222 HIS 0.009 0.001 HIS C1144 Details of bonding type rmsd covalent geometry : bond 0.00822 (26746) covalent geometry : angle 0.71846 (36560) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.83858 ( 16) hydrogen bonds : bond 0.05108 ( 1433) hydrogen bonds : angle 5.18300 ( 4119) Misc. bond : bond 0.43605 ( 4) link_ALPHA1-2 : bond 0.00663 ( 6) link_ALPHA1-2 : angle 2.64709 ( 18) link_ALPHA1-3 : bond 0.00644 ( 4) link_ALPHA1-3 : angle 1.81774 ( 12) link_ALPHA1-6 : bond 0.00970 ( 4) link_ALPHA1-6 : angle 2.49878 ( 12) link_BETA1-4 : bond 0.00785 ( 4) link_BETA1-4 : angle 3.37581 ( 12) link_NAG-ASN : bond 0.00958 ( 12) link_NAG-ASN : angle 2.21421 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 515 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8834 (mt-10) REVERT: A 164 ASP cc_start: 0.8825 (m-30) cc_final: 0.8498 (m-30) REVERT: A 225 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8457 (tt0) REVERT: A 229 ARG cc_start: 0.8260 (tmm160) cc_final: 0.7905 (tmm160) REVERT: A 527 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8939 (ttmm) REVERT: A 586 ASP cc_start: 0.9024 (t70) cc_final: 0.8710 (t0) REVERT: A 806 GLU cc_start: 0.8943 (tp30) cc_final: 0.8428 (tp30) REVERT: A 809 GLU cc_start: 0.8730 (tp30) cc_final: 0.8256 (tp30) REVERT: A 817 ASP cc_start: 0.8849 (t0) cc_final: 0.8347 (t0) REVERT: A 862 MET cc_start: 0.9250 (tmm) cc_final: 0.9034 (tmm) REVERT: A 1025 SER cc_start: 0.9090 (m) cc_final: 0.8814 (t) REVERT: A 1029 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 1042 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8268 (ttm170) REVERT: A 1211 HIS cc_start: 0.7778 (t70) cc_final: 0.7402 (t-90) REVERT: A 1293 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: A 1372 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7461 (tm-30) REVERT: A 1374 HIS cc_start: 0.7888 (m170) cc_final: 0.7136 (m170) REVERT: A 1432 LEU cc_start: 0.9394 (tm) cc_final: 0.9127 (tp) REVERT: A 1441 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 1459 GLU cc_start: 0.9102 (mp0) cc_final: 0.8782 (pt0) REVERT: A 1474 HIS cc_start: 0.8881 (m90) cc_final: 0.8517 (m-70) REVERT: A 1499 GLU cc_start: 0.8515 (pp20) cc_final: 0.8152 (tm-30) REVERT: A 1503 ASN cc_start: 0.8756 (t0) cc_final: 0.8550 (t0) REVERT: B 29 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6972 (mpp) REVERT: B 171 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8445 (ttt90) REVERT: B 260 LEU cc_start: 0.9005 (tt) cc_final: 0.8656 (tm) REVERT: C 154 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8837 (mt-10) REVERT: C 164 ASP cc_start: 0.8795 (m-30) cc_final: 0.8471 (m-30) REVERT: C 225 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8431 (tt0) REVERT: C 229 ARG cc_start: 0.8276 (tmm160) cc_final: 0.7957 (tmm160) REVERT: C 527 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8955 (ttmm) REVERT: C 586 ASP cc_start: 0.9041 (t70) cc_final: 0.8710 (t0) REVERT: C 806 GLU cc_start: 0.8963 (tp30) cc_final: 0.8449 (tp30) REVERT: C 809 GLU cc_start: 0.8733 (tp30) cc_final: 0.8217 (tp30) REVERT: C 817 ASP cc_start: 0.8779 (t0) cc_final: 0.8280 (t0) REVERT: C 1025 SER cc_start: 0.9124 (m) cc_final: 0.8843 (t) REVERT: C 1029 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8417 (tm-30) REVERT: C 1032 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 1033 GLN cc_start: 0.8927 (mm110) cc_final: 0.8364 (mm-40) REVERT: C 1042 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8367 (ttm170) REVERT: C 1119 ARG cc_start: 0.8591 (mmm-85) cc_final: 0.8198 (tpt170) REVERT: C 1177 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: C 1211 HIS cc_start: 0.7870 (t70) cc_final: 0.7432 (t-90) REVERT: C 1215 ARG cc_start: 0.7906 (mtm180) cc_final: 0.7664 (mtp85) REVERT: C 1372 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 1374 HIS cc_start: 0.7931 (m170) cc_final: 0.7301 (m170) REVERT: C 1432 LEU cc_start: 0.9398 (tm) cc_final: 0.9122 (tp) REVERT: C 1459 GLU cc_start: 0.9076 (mp0) cc_final: 0.8797 (pt0) REVERT: C 1474 HIS cc_start: 0.8846 (m90) cc_final: 0.8554 (m-70) REVERT: C 1499 GLU cc_start: 0.8528 (pp20) cc_final: 0.8119 (tm-30) REVERT: C 1503 ASN cc_start: 0.8773 (t0) cc_final: 0.8573 (t0) REVERT: C 1548 TYR cc_start: 0.7811 (m-80) cc_final: 0.7327 (m-10) REVERT: D 50 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6713 (mtt180) REVERT: D 171 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8458 (ttt90) REVERT: D 260 LEU cc_start: 0.9017 (tt) cc_final: 0.8680 (tm) outliers start: 80 outliers final: 29 residues processed: 544 average time/residue: 0.6120 time to fit residues: 385.5873 Evaluate side-chains 519 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 482 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1177 GLU Chi-restraints excluded: chain C residue 1207 VAL Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1402 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 143 optimal weight: 9.9990 chunk 297 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 63 optimal weight: 50.0000 chunk 171 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1028 HIS A1118 ASN A1211 HIS A1245 GLN A1509 HIS A1543 HIS C 376 GLN C1118 ASN C1245 GLN C1509 HIS C1543 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.118690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085000 restraints weight = 44274.620| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.14 r_work: 0.2885 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.423 26788 Z= 0.144 Angle : 0.603 10.884 36666 Z= 0.290 Chirality : 0.041 0.209 4130 Planarity : 0.004 0.042 4604 Dihedral : 10.766 113.873 4318 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.51 % Allowed : 13.04 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.10 (0.15), residues: 3256 helix: 1.70 (0.13), residues: 1582 sheet: -0.79 (0.26), residues: 364 loop : 0.10 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 804 TYR 0.015 0.001 TYR C1099 PHE 0.015 0.001 PHE C 253 TRP 0.021 0.001 TRP C1342 HIS 0.006 0.001 HIS A1211 Details of bonding type rmsd covalent geometry : bond 0.00333 (26746) covalent geometry : angle 0.59576 (36560) SS BOND : bond 0.00089 ( 8) SS BOND : angle 0.44801 ( 16) hydrogen bonds : bond 0.04208 ( 1433) hydrogen bonds : angle 4.91150 ( 4119) Misc. bond : bond 0.30575 ( 4) link_ALPHA1-2 : bond 0.00161 ( 6) link_ALPHA1-2 : angle 1.85303 ( 18) link_ALPHA1-3 : bond 0.00641 ( 4) link_ALPHA1-3 : angle 1.32340 ( 12) link_ALPHA1-6 : bond 0.00329 ( 4) link_ALPHA1-6 : angle 1.95016 ( 12) link_BETA1-4 : bond 0.00651 ( 4) link_BETA1-4 : angle 3.18353 ( 12) link_NAG-ASN : bond 0.00376 ( 12) link_NAG-ASN : angle 1.58380 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 526 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8845 (mt-10) REVERT: A 164 ASP cc_start: 0.8722 (m-30) cc_final: 0.8486 (m-30) REVERT: A 586 ASP cc_start: 0.9018 (t70) cc_final: 0.8728 (t0) REVERT: A 604 CYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 804 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8311 (ttm110) REVERT: A 806 GLU cc_start: 0.8915 (tp30) cc_final: 0.8672 (tp30) REVERT: A 809 GLU cc_start: 0.8690 (tp30) cc_final: 0.8178 (tp30) REVERT: A 817 ASP cc_start: 0.8811 (t0) cc_final: 0.8356 (t0) REVERT: A 1025 SER cc_start: 0.9064 (m) cc_final: 0.8831 (p) REVERT: A 1029 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 1032 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8313 (tm-30) REVERT: A 1033 GLN cc_start: 0.8880 (mm110) cc_final: 0.8189 (mm110) REVERT: A 1042 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8292 (ttm170) REVERT: A 1061 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8405 (tm-30) REVERT: A 1293 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: A 1372 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 1374 HIS cc_start: 0.7828 (m170) cc_final: 0.7220 (m170) REVERT: A 1432 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (tp) REVERT: A 1459 GLU cc_start: 0.9067 (mp0) cc_final: 0.8774 (pt0) REVERT: A 1474 HIS cc_start: 0.8792 (m90) cc_final: 0.8519 (m-70) REVERT: A 1507 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8533 (mm-30) REVERT: A 1513 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8515 (mmm-85) REVERT: A 1548 TYR cc_start: 0.7665 (m-80) cc_final: 0.7155 (m-10) REVERT: B 50 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6623 (mtt180) REVERT: B 260 LEU cc_start: 0.8984 (tt) cc_final: 0.8632 (tm) REVERT: C 154 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8842 (mt-10) REVERT: C 164 ASP cc_start: 0.8711 (m-30) cc_final: 0.8446 (m-30) REVERT: C 208 ASP cc_start: 0.8328 (m-30) cc_final: 0.8127 (m-30) REVERT: C 586 ASP cc_start: 0.9063 (t70) cc_final: 0.8748 (t0) REVERT: C 604 CYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8335 (p) REVERT: C 806 GLU cc_start: 0.8918 (tp30) cc_final: 0.8681 (tp30) REVERT: C 809 GLU cc_start: 0.8722 (tp30) cc_final: 0.8217 (tp30) REVERT: C 813 LEU cc_start: 0.9297 (mt) cc_final: 0.9059 (mt) REVERT: C 817 ASP cc_start: 0.8767 (t0) cc_final: 0.8242 (t0) REVERT: C 1025 SER cc_start: 0.9108 (m) cc_final: 0.8855 (p) REVERT: C 1029 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8297 (tm-30) REVERT: C 1032 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8428 (tm-30) REVERT: C 1033 GLN cc_start: 0.8919 (mm110) cc_final: 0.8349 (mm-40) REVERT: C 1042 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8290 (ttm170) REVERT: C 1061 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8356 (tm-30) REVERT: C 1119 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8212 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7812 (t70) cc_final: 0.7402 (t-90) REVERT: C 1215 ARG cc_start: 0.7869 (mtm180) cc_final: 0.7661 (mtp85) REVERT: C 1345 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8315 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8582 (pp20) cc_final: 0.8051 (pp20) REVERT: C 1372 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7412 (tm-30) REVERT: C 1374 HIS cc_start: 0.7688 (m170) cc_final: 0.7060 (m170) REVERT: C 1432 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8982 (tp) REVERT: C 1459 GLU cc_start: 0.9077 (mp0) cc_final: 0.8820 (pt0) REVERT: C 1474 HIS cc_start: 0.8804 (m90) cc_final: 0.8519 (m-70) REVERT: C 1481 ARG cc_start: 0.8642 (mpp80) cc_final: 0.8326 (mpt-90) REVERT: C 1499 GLU cc_start: 0.8433 (pp20) cc_final: 0.8051 (tm-30) REVERT: C 1507 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8550 (mm-30) REVERT: C 1513 ARG cc_start: 0.8745 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: C 1548 TYR cc_start: 0.7664 (m-80) cc_final: 0.7269 (m-10) REVERT: D 50 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: D 260 LEU cc_start: 0.9000 (tt) cc_final: 0.8658 (tm) outliers start: 88 outliers final: 32 residues processed: 559 average time/residue: 0.5796 time to fit residues: 378.4207 Evaluate side-chains 534 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 495 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 863 TYR Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1432 LEU Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 209 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 5 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 263 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A1118 ASN A1245 GLN A1528 ASN A1543 HIS C 225 GLN C1118 ASN C1245 GLN C1528 ASN C1543 HIS D 102 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085370 restraints weight = 44173.864| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.11 r_work: 0.2891 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.391 26788 Z= 0.154 Angle : 0.607 10.232 36666 Z= 0.290 Chirality : 0.042 0.262 4130 Planarity : 0.004 0.043 4604 Dihedral : 10.252 111.605 4318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.95 % Allowed : 13.60 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.21 (0.15), residues: 3256 helix: 1.81 (0.13), residues: 1592 sheet: -0.76 (0.26), residues: 364 loop : 0.12 (0.19), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 171 TYR 0.011 0.001 TYR C 435 PHE 0.026 0.002 PHE A 767 TRP 0.025 0.001 TRP C1342 HIS 0.005 0.001 HIS C1144 Details of bonding type rmsd covalent geometry : bond 0.00365 (26746) covalent geometry : angle 0.59820 (36560) SS BOND : bond 0.00092 ( 8) SS BOND : angle 0.49369 ( 16) hydrogen bonds : bond 0.04052 ( 1433) hydrogen bonds : angle 4.77812 ( 4119) Misc. bond : bond 0.29084 ( 4) link_ALPHA1-2 : bond 0.00097 ( 6) link_ALPHA1-2 : angle 2.00370 ( 18) link_ALPHA1-3 : bond 0.00718 ( 4) link_ALPHA1-3 : angle 1.42953 ( 12) link_ALPHA1-6 : bond 0.00330 ( 4) link_ALPHA1-6 : angle 2.10479 ( 12) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 3.60954 ( 12) link_NAG-ASN : bond 0.00844 ( 12) link_NAG-ASN : angle 1.84433 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 512 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8837 (mt-10) REVERT: A 461 ASN cc_start: 0.8977 (p0) cc_final: 0.8489 (p0) REVERT: A 527 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8921 (ttmm) REVERT: A 586 ASP cc_start: 0.9027 (t70) cc_final: 0.8724 (t0) REVERT: A 804 ARG cc_start: 0.8601 (ttm110) cc_final: 0.8296 (ttt90) REVERT: A 806 GLU cc_start: 0.8933 (tp30) cc_final: 0.8654 (tp30) REVERT: A 809 GLU cc_start: 0.8675 (tp30) cc_final: 0.8154 (tp30) REVERT: A 813 LEU cc_start: 0.9307 (mt) cc_final: 0.9073 (mt) REVERT: A 814 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8460 (mmmm) REVERT: A 817 ASP cc_start: 0.8834 (t0) cc_final: 0.8350 (t0) REVERT: A 1025 SER cc_start: 0.9084 (m) cc_final: 0.8850 (p) REVERT: A 1029 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8390 (tm-30) REVERT: A 1032 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8448 (tm-30) REVERT: A 1033 GLN cc_start: 0.8885 (mm110) cc_final: 0.8298 (mm-40) REVERT: A 1042 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8275 (ttm170) REVERT: A 1061 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 1372 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 1374 HIS cc_start: 0.7785 (m170) cc_final: 0.7123 (m170) REVERT: A 1432 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9130 (tp) REVERT: A 1459 GLU cc_start: 0.9045 (mp0) cc_final: 0.8789 (pt0) REVERT: A 1474 HIS cc_start: 0.8808 (m90) cc_final: 0.8524 (m-70) REVERT: A 1507 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8529 (mm-30) REVERT: A 1541 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8513 (ttp-110) REVERT: A 1548 TYR cc_start: 0.7725 (m-80) cc_final: 0.7283 (m-10) REVERT: B 33 THR cc_start: 0.9038 (m) cc_final: 0.8819 (p) REVERT: B 50 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6536 (mtt180) REVERT: B 51 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 260 LEU cc_start: 0.8998 (tt) cc_final: 0.8644 (tm) REVERT: C 154 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8832 (mt-10) REVERT: C 208 ASP cc_start: 0.8315 (m-30) cc_final: 0.8113 (m-30) REVERT: C 527 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8937 (ttmm) REVERT: C 586 ASP cc_start: 0.9042 (t70) cc_final: 0.8711 (t0) REVERT: C 806 GLU cc_start: 0.8917 (tp30) cc_final: 0.8663 (tp30) REVERT: C 809 GLU cc_start: 0.8713 (tp30) cc_final: 0.8207 (tp30) REVERT: C 813 LEU cc_start: 0.9306 (mt) cc_final: 0.9070 (mt) REVERT: C 814 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8395 (mmmm) REVERT: C 817 ASP cc_start: 0.8849 (t0) cc_final: 0.8329 (t0) REVERT: C 836 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8662 (t) REVERT: C 1025 SER cc_start: 0.9087 (m) cc_final: 0.8849 (p) REVERT: C 1029 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8420 (tm-30) REVERT: C 1032 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8494 (tm-30) REVERT: C 1033 GLN cc_start: 0.8934 (mm110) cc_final: 0.8438 (mm-40) REVERT: C 1042 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8249 (ttm170) REVERT: C 1061 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8409 (tm-30) REVERT: C 1119 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8174 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7828 (t70) cc_final: 0.7390 (t-90) REVERT: C 1215 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7495 (mtm180) REVERT: C 1345 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8456 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8602 (pp20) cc_final: 0.8208 (pp20) REVERT: C 1372 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7420 (tm-30) REVERT: C 1374 HIS cc_start: 0.7749 (m170) cc_final: 0.7283 (m170) REVERT: C 1459 GLU cc_start: 0.9053 (mp0) cc_final: 0.8800 (pt0) REVERT: C 1474 HIS cc_start: 0.8824 (m90) cc_final: 0.8533 (m-70) REVERT: C 1481 ARG cc_start: 0.8657 (mpp80) cc_final: 0.8264 (mpt-90) REVERT: C 1507 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 1513 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8528 (mmm-85) REVERT: C 1539 GLN cc_start: 0.8708 (pm20) cc_final: 0.8471 (pm20) REVERT: C 1541 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8402 (ttp-110) REVERT: C 1548 TYR cc_start: 0.7681 (m-80) cc_final: 0.7353 (m-10) REVERT: D 50 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6820 (mtt180) REVERT: D 51 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7867 (tp) REVERT: D 53 TRP cc_start: 0.7118 (t-100) cc_final: 0.6656 (t-100) REVERT: D 260 LEU cc_start: 0.9021 (tt) cc_final: 0.8673 (tm) outliers start: 99 outliers final: 36 residues processed: 550 average time/residue: 0.5881 time to fit residues: 378.1286 Evaluate side-chains 543 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 495 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1351 SER Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1541 ARG Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 863 TYR Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1541 ARG Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 310 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 50.0000 chunk 99 optimal weight: 0.9980 chunk 226 optimal weight: 50.0000 chunk 312 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 62 optimal weight: 50.0000 chunk 301 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1211 HIS A1528 ASN A1543 HIS C1245 GLN C1528 ASN C1543 HIS D 102 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.082439 restraints weight = 44259.044| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.12 r_work: 0.2838 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.436 26788 Z= 0.266 Angle : 0.680 14.016 36666 Z= 0.324 Chirality : 0.045 0.294 4130 Planarity : 0.004 0.045 4604 Dihedral : 10.413 113.394 4318 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.94 % Allowed : 13.92 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.13 (0.15), residues: 3256 helix: 1.78 (0.13), residues: 1584 sheet: -0.75 (0.27), residues: 352 loop : 0.01 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 164 TYR 0.016 0.002 TYR A1099 PHE 0.023 0.002 PHE C 101 TRP 0.028 0.002 TRP C1342 HIS 0.007 0.001 HIS C1144 Details of bonding type rmsd covalent geometry : bond 0.00631 (26746) covalent geometry : angle 0.66859 (36560) SS BOND : bond 0.00150 ( 8) SS BOND : angle 0.66014 ( 16) hydrogen bonds : bond 0.04463 ( 1433) hydrogen bonds : angle 4.83748 ( 4119) Misc. bond : bond 0.36257 ( 4) link_ALPHA1-2 : bond 0.00515 ( 6) link_ALPHA1-2 : angle 2.42496 ( 18) link_ALPHA1-3 : bond 0.00793 ( 4) link_ALPHA1-3 : angle 1.62882 ( 12) link_ALPHA1-6 : bond 0.00783 ( 4) link_ALPHA1-6 : angle 2.28723 ( 12) link_BETA1-4 : bond 0.00464 ( 4) link_BETA1-4 : angle 3.73126 ( 12) link_NAG-ASN : bond 0.01341 ( 12) link_NAG-ASN : angle 2.60700 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 503 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8864 (mt-10) REVERT: A 208 ASP cc_start: 0.8334 (m-30) cc_final: 0.8103 (m-30) REVERT: A 272 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8172 (t0) REVERT: A 329 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8516 (p90) REVERT: A 461 ASN cc_start: 0.8972 (p0) cc_final: 0.8514 (p0) REVERT: A 527 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8934 (ttmm) REVERT: A 586 ASP cc_start: 0.9014 (t70) cc_final: 0.8719 (t0) REVERT: A 804 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8418 (ttm110) REVERT: A 806 GLU cc_start: 0.8993 (tp30) cc_final: 0.8474 (tp30) REVERT: A 809 GLU cc_start: 0.8782 (tp30) cc_final: 0.8278 (tp30) REVERT: A 813 LEU cc_start: 0.9373 (mt) cc_final: 0.9172 (mt) REVERT: A 814 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8476 (mmmm) REVERT: A 817 ASP cc_start: 0.8869 (t0) cc_final: 0.8368 (t0) REVERT: A 1025 SER cc_start: 0.9079 (m) cc_final: 0.8854 (p) REVERT: A 1029 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8469 (tm-30) REVERT: A 1032 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8491 (tm-30) REVERT: A 1033 GLN cc_start: 0.8927 (mm110) cc_final: 0.8386 (mm-40) REVERT: A 1061 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8460 (tm-30) REVERT: A 1329 GLU cc_start: 0.8616 (tp30) cc_final: 0.8401 (tm-30) REVERT: A 1372 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 1374 HIS cc_start: 0.7819 (m170) cc_final: 0.7033 (m170) REVERT: A 1432 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9154 (tp) REVERT: A 1459 GLU cc_start: 0.9050 (mp0) cc_final: 0.8783 (pt0) REVERT: A 1474 HIS cc_start: 0.8893 (m90) cc_final: 0.8555 (m-70) REVERT: A 1541 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8137 (ttp-110) REVERT: B 50 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6645 (mtt180) REVERT: B 51 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7860 (tp) REVERT: B 260 LEU cc_start: 0.8999 (tt) cc_final: 0.8628 (tm) REVERT: C 154 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8859 (mt-10) REVERT: C 272 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8172 (t0) REVERT: C 329 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8596 (p90) REVERT: C 461 ASN cc_start: 0.9015 (p0) cc_final: 0.8556 (p0) REVERT: C 527 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8970 (ttmm) REVERT: C 586 ASP cc_start: 0.9042 (t70) cc_final: 0.8720 (t0) REVERT: C 806 GLU cc_start: 0.8965 (tp30) cc_final: 0.8765 (tp30) REVERT: C 809 GLU cc_start: 0.8738 (tp30) cc_final: 0.8257 (tp30) REVERT: C 813 LEU cc_start: 0.9365 (mt) cc_final: 0.9126 (mt) REVERT: C 817 ASP cc_start: 0.8829 (t0) cc_final: 0.8276 (t0) REVERT: C 836 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8612 (t) REVERT: C 1025 SER cc_start: 0.9104 (m) cc_final: 0.8862 (p) REVERT: C 1029 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8452 (tm-30) REVERT: C 1032 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8516 (tm-30) REVERT: C 1033 GLN cc_start: 0.8965 (mm110) cc_final: 0.8467 (mm-40) REVERT: C 1042 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8307 (ttm170) REVERT: C 1061 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8472 (tm-30) REVERT: C 1119 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8084 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7813 (t70) cc_final: 0.7186 (t-90) REVERT: C 1215 ARG cc_start: 0.7859 (mtm180) cc_final: 0.7413 (mtm180) REVERT: C 1345 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8458 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8630 (pp20) cc_final: 0.8193 (pp20) REVERT: C 1372 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7408 (tm-30) REVERT: C 1374 HIS cc_start: 0.7747 (m170) cc_final: 0.7041 (m170) REVERT: C 1459 GLU cc_start: 0.9072 (mp0) cc_final: 0.8808 (pt0) REVERT: C 1474 HIS cc_start: 0.8878 (m90) cc_final: 0.8588 (m-70) REVERT: C 1481 ARG cc_start: 0.8655 (mpp80) cc_final: 0.8449 (mpp80) REVERT: C 1541 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8126 (ttp-110) REVERT: C 1548 TYR cc_start: 0.7743 (m-80) cc_final: 0.7329 (m-10) REVERT: D 50 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.6877 (mtt180) REVERT: D 51 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7936 (tm) REVERT: D 260 LEU cc_start: 0.9014 (tt) cc_final: 0.8648 (tm) outliers start: 124 outliers final: 50 residues processed: 555 average time/residue: 0.5943 time to fit residues: 384.3755 Evaluate side-chains 546 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 481 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1401 ASP Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1541 ARG Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 863 TYR Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1541 ARG Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 137 optimal weight: 9.9990 chunk 267 optimal weight: 0.0050 chunk 233 optimal weight: 0.0670 chunk 238 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 272 optimal weight: 0.9990 chunk 201 optimal weight: 0.9990 chunk 292 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 overall best weight: 1.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 GLN A1528 ASN C1528 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087560 restraints weight = 43965.251| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.06 r_work: 0.2935 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.338 26788 Z= 0.131 Angle : 0.620 9.137 36666 Z= 0.294 Chirality : 0.042 0.246 4130 Planarity : 0.004 0.043 4604 Dihedral : 9.953 113.831 4318 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.15 % Allowed : 15.99 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.23 (0.15), residues: 3256 helix: 1.87 (0.13), residues: 1588 sheet: -0.75 (0.26), residues: 364 loop : 0.06 (0.19), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 164 TYR 0.012 0.001 TYR C 435 PHE 0.029 0.001 PHE A 767 TRP 0.035 0.001 TRP C1342 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00303 (26746) covalent geometry : angle 0.60704 (36560) SS BOND : bond 0.00081 ( 8) SS BOND : angle 0.44407 ( 16) hydrogen bonds : bond 0.03831 ( 1433) hydrogen bonds : angle 4.67769 ( 4119) Misc. bond : bond 0.26786 ( 4) link_ALPHA1-2 : bond 0.00199 ( 6) link_ALPHA1-2 : angle 1.78768 ( 18) link_ALPHA1-3 : bond 0.00915 ( 4) link_ALPHA1-3 : angle 1.27816 ( 12) link_ALPHA1-6 : bond 0.00269 ( 4) link_ALPHA1-6 : angle 1.92680 ( 12) link_BETA1-4 : bond 0.00470 ( 4) link_BETA1-4 : angle 3.79820 ( 12) link_NAG-ASN : bond 0.01282 ( 12) link_NAG-ASN : angle 2.89716 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 530 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8821 (mt-10) REVERT: A 208 ASP cc_start: 0.8314 (m-30) cc_final: 0.8087 (m-30) REVERT: A 329 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8616 (p90) REVERT: A 461 ASN cc_start: 0.8914 (p0) cc_final: 0.8477 (p0) REVERT: A 546 ASN cc_start: 0.8801 (t0) cc_final: 0.8271 (t0) REVERT: A 586 ASP cc_start: 0.9045 (t70) cc_final: 0.8777 (t0) REVERT: A 806 GLU cc_start: 0.8903 (tp30) cc_final: 0.8694 (tp30) REVERT: A 809 GLU cc_start: 0.8632 (tp30) cc_final: 0.8081 (tp30) REVERT: A 814 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8446 (mmmm) REVERT: A 817 ASP cc_start: 0.8897 (t0) cc_final: 0.8402 (t0) REVERT: A 1029 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 1032 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 1033 GLN cc_start: 0.8889 (mm110) cc_final: 0.8264 (mm-40) REVERT: A 1042 ARG cc_start: 0.8590 (ttp80) cc_final: 0.8259 (ttm170) REVERT: A 1061 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 1205 MET cc_start: 0.8374 (ttm) cc_final: 0.8120 (ttm) REVERT: A 1459 GLU cc_start: 0.9003 (mp0) cc_final: 0.8770 (pt0) REVERT: A 1474 HIS cc_start: 0.8775 (m90) cc_final: 0.8508 (m-70) REVERT: A 1541 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8488 (ttp-110) REVERT: A 1548 TYR cc_start: 0.7594 (m-10) cc_final: 0.7093 (m-10) REVERT: B 50 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6638 (mtt180) REVERT: B 51 LEU cc_start: 0.8045 (mm) cc_final: 0.7810 (tp) REVERT: B 53 TRP cc_start: 0.7515 (t-100) cc_final: 0.7206 (t-100) REVERT: B 129 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: B 260 LEU cc_start: 0.9018 (tt) cc_final: 0.8667 (tm) REVERT: C 154 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8813 (mt-10) REVERT: C 329 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8606 (p90) REVERT: C 429 ASP cc_start: 0.9272 (t0) cc_final: 0.8983 (t0) REVERT: C 461 ASN cc_start: 0.8945 (p0) cc_final: 0.8470 (p0) REVERT: C 546 ASN cc_start: 0.8851 (t0) cc_final: 0.8351 (t0) REVERT: C 586 ASP cc_start: 0.9056 (t70) cc_final: 0.8782 (t0) REVERT: C 806 GLU cc_start: 0.8870 (tp30) cc_final: 0.8625 (tp30) REVERT: C 809 GLU cc_start: 0.8660 (tp30) cc_final: 0.8171 (tp30) REVERT: C 817 ASP cc_start: 0.8918 (t0) cc_final: 0.8327 (t0) REVERT: C 1029 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8349 (tm-30) REVERT: C 1032 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8382 (tm-30) REVERT: C 1033 GLN cc_start: 0.8923 (mm110) cc_final: 0.8331 (mm-40) REVERT: C 1042 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8249 (ttm170) REVERT: C 1061 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8397 (tm-30) REVERT: C 1119 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8132 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7852 (t70) cc_final: 0.7387 (t-90) REVERT: C 1215 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7458 (mtm180) REVERT: C 1345 ARG cc_start: 0.8932 (mmm-85) cc_final: 0.8371 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8586 (pp20) cc_final: 0.8242 (pp20) REVERT: C 1459 GLU cc_start: 0.9034 (mp0) cc_final: 0.8793 (pt0) REVERT: C 1474 HIS cc_start: 0.8765 (m90) cc_final: 0.8539 (m-70) REVERT: C 1499 GLU cc_start: 0.8527 (pp20) cc_final: 0.8094 (tm-30) REVERT: C 1530 GLU cc_start: 0.8318 (tt0) cc_final: 0.7955 (tt0) REVERT: D 129 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8870 (tt0) REVERT: D 260 LEU cc_start: 0.9020 (tt) cc_final: 0.8677 (tm) outliers start: 79 outliers final: 36 residues processed: 562 average time/residue: 0.5452 time to fit residues: 359.6288 Evaluate side-chains 539 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 496 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1541 ARG Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 101 optimal weight: 0.0470 chunk 246 optimal weight: 20.0000 chunk 271 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 overall best weight: 2.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN C1245 GLN C1528 ASN D 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.087661 restraints weight = 43920.757| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.04 r_work: 0.2923 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.333 26788 Z= 0.159 Angle : 0.645 10.385 36666 Z= 0.306 Chirality : 0.043 0.303 4130 Planarity : 0.004 0.077 4604 Dihedral : 9.812 112.271 4318 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.15 % Allowed : 17.22 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.27 (0.15), residues: 3256 helix: 1.86 (0.13), residues: 1606 sheet: -0.70 (0.26), residues: 364 loop : 0.12 (0.19), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 164 TYR 0.012 0.001 TYR A1066 PHE 0.026 0.002 PHE C1116 TRP 0.036 0.001 TRP C1342 HIS 0.006 0.001 HIS C1374 Details of bonding type rmsd covalent geometry : bond 0.00378 (26746) covalent geometry : angle 0.63230 (36560) SS BOND : bond 0.00100 ( 8) SS BOND : angle 0.48965 ( 16) hydrogen bonds : bond 0.03924 ( 1433) hydrogen bonds : angle 4.62899 ( 4119) Misc. bond : bond 0.27601 ( 4) link_ALPHA1-2 : bond 0.00115 ( 6) link_ALPHA1-2 : angle 1.98609 ( 18) link_ALPHA1-3 : bond 0.00880 ( 4) link_ALPHA1-3 : angle 1.38821 ( 12) link_ALPHA1-6 : bond 0.00474 ( 4) link_ALPHA1-6 : angle 2.03983 ( 12) link_BETA1-4 : bond 0.00647 ( 4) link_BETA1-4 : angle 3.73038 ( 12) link_NAG-ASN : bond 0.01511 ( 12) link_NAG-ASN : angle 2.97930 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 514 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8851 (mt-10) REVERT: A 208 ASP cc_start: 0.8304 (m-30) cc_final: 0.8045 (m-30) REVERT: A 272 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8163 (t0) REVERT: A 328 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8671 (mm-40) REVERT: A 329 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8574 (p90) REVERT: A 461 ASN cc_start: 0.8909 (p0) cc_final: 0.8440 (p0) REVERT: A 527 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8947 (ttmm) REVERT: A 546 ASN cc_start: 0.8795 (t0) cc_final: 0.8264 (t0) REVERT: A 586 ASP cc_start: 0.9050 (t70) cc_final: 0.8771 (t0) REVERT: A 806 GLU cc_start: 0.8938 (tp30) cc_final: 0.8437 (tp30) REVERT: A 809 GLU cc_start: 0.8663 (tp30) cc_final: 0.8139 (tp30) REVERT: A 814 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8629 (tppp) REVERT: A 817 ASP cc_start: 0.8802 (t0) cc_final: 0.8440 (t0) REVERT: A 1029 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8467 (tm-30) REVERT: A 1032 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 1033 GLN cc_start: 0.8904 (mm110) cc_final: 0.8348 (mm-40) REVERT: A 1042 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8278 (ttm170) REVERT: A 1061 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 1205 MET cc_start: 0.8393 (ttm) cc_final: 0.8111 (ttm) REVERT: A 1296 GLN cc_start: 0.8235 (pm20) cc_final: 0.7896 (pp30) REVERT: A 1329 GLU cc_start: 0.8526 (tp30) cc_final: 0.8111 (tm-30) REVERT: A 1345 ARG cc_start: 0.8905 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: A 1459 GLU cc_start: 0.9033 (mp0) cc_final: 0.8800 (pt0) REVERT: A 1474 HIS cc_start: 0.8773 (m90) cc_final: 0.8524 (m-70) REVERT: A 1548 TYR cc_start: 0.7501 (m-10) cc_final: 0.7187 (m-10) REVERT: B 50 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6675 (mtt180) REVERT: B 51 LEU cc_start: 0.8063 (mm) cc_final: 0.7813 (tp) REVERT: B 260 LEU cc_start: 0.9018 (tt) cc_final: 0.8663 (tm) REVERT: C 154 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8841 (mt-10) REVERT: C 272 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8106 (t0) REVERT: C 329 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8622 (p90) REVERT: C 461 ASN cc_start: 0.8955 (p0) cc_final: 0.8526 (p0) REVERT: C 491 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8396 (ttp-110) REVERT: C 527 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8972 (ttmm) REVERT: C 546 ASN cc_start: 0.8797 (t0) cc_final: 0.8290 (t0) REVERT: C 586 ASP cc_start: 0.9058 (t70) cc_final: 0.8766 (t0) REVERT: C 806 GLU cc_start: 0.8894 (tp30) cc_final: 0.8368 (tp30) REVERT: C 809 GLU cc_start: 0.8707 (tp30) cc_final: 0.8216 (tp30) REVERT: C 817 ASP cc_start: 0.8836 (t0) cc_final: 0.8503 (t0) REVERT: C 836 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8622 (t) REVERT: C 837 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8603 (t80) REVERT: C 1029 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 1032 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8443 (tm-30) REVERT: C 1033 GLN cc_start: 0.8938 (mm110) cc_final: 0.8421 (mm-40) REVERT: C 1042 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8245 (ttm170) REVERT: C 1061 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 1119 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8227 (tpt170) REVERT: C 1211 HIS cc_start: 0.7882 (t70) cc_final: 0.7407 (t-90) REVERT: C 1215 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7487 (mtm180) REVERT: C 1345 ARG cc_start: 0.8951 (mmm-85) cc_final: 0.8366 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8572 (pp20) cc_final: 0.8196 (pp20) REVERT: C 1459 GLU cc_start: 0.9048 (mp0) cc_final: 0.8812 (pt0) REVERT: C 1474 HIS cc_start: 0.8740 (m90) cc_final: 0.8522 (m-70) REVERT: C 1481 ARG cc_start: 0.8530 (mpp80) cc_final: 0.8189 (mpt-90) REVERT: C 1499 GLU cc_start: 0.8570 (pp20) cc_final: 0.8169 (tm-30) REVERT: C 1530 GLU cc_start: 0.8408 (tt0) cc_final: 0.7855 (tt0) REVERT: C 1548 TYR cc_start: 0.7513 (m-10) cc_final: 0.6870 (m-10) REVERT: D 50 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6805 (mtt180) REVERT: D 260 LEU cc_start: 0.9000 (tt) cc_final: 0.8654 (tm) outliers start: 79 outliers final: 37 residues processed: 552 average time/residue: 0.5767 time to fit residues: 371.7754 Evaluate side-chains 542 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 493 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 823 MET Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 301 optimal weight: 6.9990 chunk 249 optimal weight: 0.0010 chunk 231 optimal weight: 50.0000 chunk 247 optimal weight: 30.0000 chunk 290 optimal weight: 10.0000 chunk 55 optimal weight: 0.0060 chunk 152 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 overall best weight: 4.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A1211 HIS C1118 ASN C1245 GLN C1528 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.085249 restraints weight = 44216.583| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.05 r_work: 0.2889 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.369 26788 Z= 0.225 Angle : 0.686 12.924 36666 Z= 0.326 Chirality : 0.044 0.302 4130 Planarity : 0.005 0.086 4604 Dihedral : 10.006 113.355 4318 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.87 % Allowed : 18.02 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.18 (0.15), residues: 3256 helix: 1.81 (0.13), residues: 1604 sheet: -0.72 (0.25), residues: 364 loop : 0.03 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 459 TYR 0.012 0.002 TYR C1064 PHE 0.031 0.002 PHE A 767 TRP 0.040 0.001 TRP C1342 HIS 0.006 0.001 HIS C1144 Details of bonding type rmsd covalent geometry : bond 0.00538 (26746) covalent geometry : angle 0.67298 (36560) SS BOND : bond 0.00139 ( 8) SS BOND : angle 0.58577 ( 16) hydrogen bonds : bond 0.04194 ( 1433) hydrogen bonds : angle 4.68251 ( 4119) Misc. bond : bond 0.32141 ( 4) link_ALPHA1-2 : bond 0.00363 ( 6) link_ALPHA1-2 : angle 2.22102 ( 18) link_ALPHA1-3 : bond 0.00872 ( 4) link_ALPHA1-3 : angle 1.50925 ( 12) link_ALPHA1-6 : bond 0.00574 ( 4) link_ALPHA1-6 : angle 2.16884 ( 12) link_BETA1-4 : bond 0.00672 ( 4) link_BETA1-4 : angle 3.76182 ( 12) link_NAG-ASN : bond 0.01525 ( 12) link_NAG-ASN : angle 3.16825 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 497 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8867 (mt-10) REVERT: A 272 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8203 (t0) REVERT: A 328 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8730 (mm-40) REVERT: A 329 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8615 (p90) REVERT: A 461 ASN cc_start: 0.8917 (p0) cc_final: 0.8481 (p0) REVERT: A 527 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8963 (ttmm) REVERT: A 546 ASN cc_start: 0.8807 (t0) cc_final: 0.8283 (t0) REVERT: A 586 ASP cc_start: 0.9053 (t70) cc_final: 0.8788 (t0) REVERT: A 806 GLU cc_start: 0.8974 (tp30) cc_final: 0.8419 (tp30) REVERT: A 809 GLU cc_start: 0.8724 (tp30) cc_final: 0.8228 (tp30) REVERT: A 817 ASP cc_start: 0.8695 (t0) cc_final: 0.8490 (t0) REVERT: A 1029 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8489 (tm-30) REVERT: A 1032 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 1033 GLN cc_start: 0.8930 (mm110) cc_final: 0.8364 (mm-40) REVERT: A 1061 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8514 (tm-30) REVERT: A 1205 MET cc_start: 0.8441 (ttm) cc_final: 0.8169 (ttm) REVERT: A 1296 GLN cc_start: 0.8232 (pm20) cc_final: 0.7940 (pp30) REVERT: A 1459 GLU cc_start: 0.9040 (mp0) cc_final: 0.8802 (pt0) REVERT: A 1474 HIS cc_start: 0.8848 (m90) cc_final: 0.8580 (m-70) REVERT: A 1548 TYR cc_start: 0.7580 (m-10) cc_final: 0.7215 (m-10) REVERT: B 50 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6756 (mtt180) REVERT: B 51 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 260 LEU cc_start: 0.9019 (tt) cc_final: 0.8651 (tm) REVERT: C 154 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8859 (mt-10) REVERT: C 208 ASP cc_start: 0.8270 (m-30) cc_final: 0.8034 (m-30) REVERT: C 272 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8165 (t0) REVERT: C 329 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8679 (p90) REVERT: C 461 ASN cc_start: 0.8960 (p0) cc_final: 0.8529 (p0) REVERT: C 527 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8990 (ttmm) REVERT: C 546 ASN cc_start: 0.8842 (t0) cc_final: 0.8331 (t0) REVERT: C 586 ASP cc_start: 0.9057 (t70) cc_final: 0.8752 (t0) REVERT: C 806 GLU cc_start: 0.8953 (tp30) cc_final: 0.8418 (tp30) REVERT: C 809 GLU cc_start: 0.8746 (tp30) cc_final: 0.8278 (tp30) REVERT: C 817 ASP cc_start: 0.8738 (t0) cc_final: 0.8499 (t0) REVERT: C 836 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8575 (t) REVERT: C 837 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8404 (t80) REVERT: C 1029 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 1032 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8439 (tm-30) REVERT: C 1033 GLN cc_start: 0.8963 (mm110) cc_final: 0.8364 (mm-40) REVERT: C 1061 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8506 (tm-30) REVERT: C 1119 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8150 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7848 (t70) cc_final: 0.7290 (t-90) REVERT: C 1215 ARG cc_start: 0.7868 (mtm180) cc_final: 0.7459 (mtm180) REVERT: C 1345 ARG cc_start: 0.8972 (mmm-85) cc_final: 0.8352 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8583 (pp20) cc_final: 0.8083 (pp20) REVERT: C 1459 GLU cc_start: 0.9064 (mp0) cc_final: 0.8828 (pt0) REVERT: C 1474 HIS cc_start: 0.8812 (m90) cc_final: 0.8579 (m-70) REVERT: C 1481 ARG cc_start: 0.8567 (mpp80) cc_final: 0.8218 (mpt-90) REVERT: C 1499 GLU cc_start: 0.8583 (pp20) cc_final: 0.8101 (tm-30) REVERT: C 1530 GLU cc_start: 0.8428 (tt0) cc_final: 0.7962 (tt0) REVERT: C 1548 TYR cc_start: 0.7552 (m-10) cc_final: 0.7134 (m-10) REVERT: D 50 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6712 (mtt180) REVERT: D 260 LEU cc_start: 0.9001 (tt) cc_final: 0.8645 (tm) outliers start: 72 outliers final: 37 residues processed: 535 average time/residue: 0.5813 time to fit residues: 363.0212 Evaluate side-chains 532 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 483 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 328 GLN Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 274 optimal weight: 0.7980 chunk 60 optimal weight: 50.0000 chunk 297 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 179 optimal weight: 0.4980 chunk 279 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 HIS A1245 GLN C1528 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.087394 restraints weight = 44110.658| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.05 r_work: 0.2931 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.320 26788 Z= 0.147 Angle : 0.664 10.639 36666 Z= 0.314 Chirality : 0.043 0.249 4130 Planarity : 0.004 0.078 4604 Dihedral : 9.751 113.810 4318 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 18.66 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.24 (0.15), residues: 3256 helix: 1.86 (0.13), residues: 1602 sheet: -0.70 (0.25), residues: 362 loop : 0.08 (0.19), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 459 TYR 0.012 0.001 TYR C1052 PHE 0.018 0.001 PHE A1413 TRP 0.045 0.001 TRP C1342 HIS 0.006 0.001 HIS C1374 Details of bonding type rmsd covalent geometry : bond 0.00347 (26746) covalent geometry : angle 0.65183 (36560) SS BOND : bond 0.00101 ( 8) SS BOND : angle 0.47015 ( 16) hydrogen bonds : bond 0.03841 ( 1433) hydrogen bonds : angle 4.60422 ( 4119) Misc. bond : bond 0.27171 ( 4) link_ALPHA1-2 : bond 0.00116 ( 6) link_ALPHA1-2 : angle 1.83414 ( 18) link_ALPHA1-3 : bond 0.00975 ( 4) link_ALPHA1-3 : angle 1.32737 ( 12) link_ALPHA1-6 : bond 0.00359 ( 4) link_ALPHA1-6 : angle 1.98182 ( 12) link_BETA1-4 : bond 0.00648 ( 4) link_BETA1-4 : angle 3.75245 ( 12) link_NAG-ASN : bond 0.01489 ( 12) link_NAG-ASN : angle 3.01863 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 512 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8847 (mt-10) REVERT: A 208 ASP cc_start: 0.8248 (m-30) cc_final: 0.7872 (t70) REVERT: A 272 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8134 (t0) REVERT: A 329 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8625 (p90) REVERT: A 461 ASN cc_start: 0.8894 (p0) cc_final: 0.8459 (p0) REVERT: A 527 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8931 (ttmm) REVERT: A 546 ASN cc_start: 0.8754 (t0) cc_final: 0.8228 (t0) REVERT: A 586 ASP cc_start: 0.9064 (t70) cc_final: 0.8805 (t0) REVERT: A 806 GLU cc_start: 0.8938 (tp30) cc_final: 0.8386 (tp30) REVERT: A 809 GLU cc_start: 0.8677 (tp30) cc_final: 0.8164 (tp30) REVERT: A 1029 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1032 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 1033 GLN cc_start: 0.8900 (mm110) cc_final: 0.8266 (mm-40) REVERT: A 1061 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8470 (tm-30) REVERT: A 1205 MET cc_start: 0.8360 (ttm) cc_final: 0.8074 (ttm) REVERT: A 1296 GLN cc_start: 0.8160 (pm20) cc_final: 0.7739 (pp30) REVERT: A 1329 GLU cc_start: 0.8521 (tp30) cc_final: 0.8102 (tm-30) REVERT: A 1459 GLU cc_start: 0.9023 (mp0) cc_final: 0.8802 (pt0) REVERT: A 1474 HIS cc_start: 0.8793 (m90) cc_final: 0.8550 (m-70) REVERT: A 1548 TYR cc_start: 0.7408 (m-10) cc_final: 0.7169 (m-10) REVERT: B 50 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6844 (mtt180) REVERT: B 51 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7808 (tp) REVERT: B 260 LEU cc_start: 0.9019 (tt) cc_final: 0.8656 (tm) REVERT: C 154 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8821 (mt-10) REVERT: C 208 ASP cc_start: 0.8259 (m-30) cc_final: 0.8029 (m-30) REVERT: C 272 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8112 (t0) REVERT: C 329 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8603 (p90) REVERT: C 461 ASN cc_start: 0.8918 (p0) cc_final: 0.8515 (p0) REVERT: C 491 ARG cc_start: 0.8696 (ttp-110) cc_final: 0.8481 (ttp-110) REVERT: C 527 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8964 (ttmm) REVERT: C 546 ASN cc_start: 0.8792 (t0) cc_final: 0.8279 (t0) REVERT: C 586 ASP cc_start: 0.9034 (t70) cc_final: 0.8741 (t0) REVERT: C 806 GLU cc_start: 0.8932 (tp30) cc_final: 0.8373 (tp30) REVERT: C 809 GLU cc_start: 0.8699 (tp30) cc_final: 0.8201 (tp30) REVERT: C 836 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8501 (t) REVERT: C 837 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8339 (t80) REVERT: C 1029 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 1032 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 1033 GLN cc_start: 0.8949 (mm110) cc_final: 0.8353 (mm-40) REVERT: C 1042 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8275 (ttm170) REVERT: C 1060 LEU cc_start: 0.9275 (mt) cc_final: 0.9064 (mt) REVERT: C 1061 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8670 (tm-30) REVERT: C 1119 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8187 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7862 (t70) cc_final: 0.7377 (t-90) REVERT: C 1215 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7459 (mtm180) REVERT: C 1245 GLN cc_start: 0.8555 (mt0) cc_final: 0.8260 (mt0) REVERT: C 1315 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.6846 (m) REVERT: C 1345 ARG cc_start: 0.8972 (mmm-85) cc_final: 0.8423 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8586 (pp20) cc_final: 0.8239 (pp20) REVERT: C 1459 GLU cc_start: 0.9037 (mp0) cc_final: 0.8810 (pt0) REVERT: C 1499 GLU cc_start: 0.8508 (pp20) cc_final: 0.8021 (tm-30) REVERT: C 1530 GLU cc_start: 0.8405 (tt0) cc_final: 0.7826 (tt0) REVERT: C 1548 TYR cc_start: 0.7364 (m-10) cc_final: 0.6979 (m-10) REVERT: D 50 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6797 (mtt180) REVERT: D 260 LEU cc_start: 0.8988 (tt) cc_final: 0.8639 (tm) outliers start: 57 outliers final: 34 residues processed: 546 average time/residue: 0.5564 time to fit residues: 356.2999 Evaluate side-chains 528 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 482 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1315 THR Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 10 optimal weight: 0.7980 chunk 211 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 233 optimal weight: 0.2980 chunk 323 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 265 optimal weight: 2.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A1211 HIS B 102 GLN B 178 HIS ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1528 ASN D 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087191 restraints weight = 44249.672| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.06 r_work: 0.2923 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.326 26788 Z= 0.165 Angle : 0.677 11.497 36666 Z= 0.321 Chirality : 0.043 0.239 4130 Planarity : 0.004 0.083 4604 Dihedral : 9.690 112.912 4318 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 19.34 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.24 (0.15), residues: 3256 helix: 1.80 (0.13), residues: 1610 sheet: -0.68 (0.26), residues: 362 loop : 0.13 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 491 TYR 0.011 0.001 TYR A 435 PHE 0.032 0.002 PHE A 767 TRP 0.047 0.001 TRP C1342 HIS 0.005 0.001 HIS C1374 Details of bonding type rmsd covalent geometry : bond 0.00394 (26746) covalent geometry : angle 0.66473 (36560) SS BOND : bond 0.00110 ( 8) SS BOND : angle 0.49914 ( 16) hydrogen bonds : bond 0.03924 ( 1433) hydrogen bonds : angle 4.59218 ( 4119) Misc. bond : bond 0.27846 ( 4) link_ALPHA1-2 : bond 0.00095 ( 6) link_ALPHA1-2 : angle 1.97174 ( 18) link_ALPHA1-3 : bond 0.00948 ( 4) link_ALPHA1-3 : angle 1.38722 ( 12) link_ALPHA1-6 : bond 0.00352 ( 4) link_ALPHA1-6 : angle 2.07289 ( 12) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 3.74202 ( 12) link_NAG-ASN : bond 0.01460 ( 12) link_NAG-ASN : angle 3.04284 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 499 time to evaluate : 1.048 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: A 154 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8859 (mt-10) REVERT: A 208 ASP cc_start: 0.8256 (m-30) cc_final: 0.7882 (t70) REVERT: A 272 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8143 (t0) REVERT: A 329 PHE cc_start: 0.9269 (OUTLIER) cc_final: 0.8567 (p90) REVERT: A 461 ASN cc_start: 0.8888 (p0) cc_final: 0.8511 (p0) REVERT: A 527 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8950 (ttmm) REVERT: A 546 ASN cc_start: 0.8756 (t0) cc_final: 0.8232 (t0) REVERT: A 586 ASP cc_start: 0.9093 (t70) cc_final: 0.8804 (t0) REVERT: A 806 GLU cc_start: 0.9018 (tp30) cc_final: 0.8454 (tp30) REVERT: A 809 GLU cc_start: 0.8701 (tp30) cc_final: 0.8203 (tp30) REVERT: A 857 ARG cc_start: 0.7763 (ptp-170) cc_final: 0.6820 (ptp-170) REVERT: A 1029 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 1032 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 1033 GLN cc_start: 0.8910 (mm110) cc_final: 0.8350 (mm-40) REVERT: A 1061 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 1117 LEU cc_start: 0.9041 (mt) cc_final: 0.8828 (mm) REVERT: A 1205 MET cc_start: 0.8355 (ttm) cc_final: 0.8078 (ttm) REVERT: A 1459 GLU cc_start: 0.9013 (mp0) cc_final: 0.8804 (pt0) REVERT: A 1474 HIS cc_start: 0.8793 (m90) cc_final: 0.8583 (m-70) REVERT: B 50 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6737 (mtt180) REVERT: B 51 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7807 (tp) REVERT: B 260 LEU cc_start: 0.9011 (tt) cc_final: 0.8646 (tm) REVERT: C 154 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8842 (mt-10) REVERT: C 208 ASP cc_start: 0.8254 (m-30) cc_final: 0.8052 (m-30) REVERT: C 272 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8127 (t0) REVERT: C 329 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8604 (p90) REVERT: C 461 ASN cc_start: 0.8900 (p0) cc_final: 0.8484 (p0) REVERT: C 491 ARG cc_start: 0.8710 (ttp-110) cc_final: 0.8499 (ttp-110) REVERT: C 527 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8984 (ttmm) REVERT: C 546 ASN cc_start: 0.8795 (t0) cc_final: 0.8285 (t0) REVERT: C 586 ASP cc_start: 0.9058 (t70) cc_final: 0.8753 (t0) REVERT: C 804 ARG cc_start: 0.8376 (mtp-110) cc_final: 0.7930 (mtp180) REVERT: C 806 GLU cc_start: 0.9001 (tp30) cc_final: 0.8439 (tp30) REVERT: C 809 GLU cc_start: 0.8715 (tp30) cc_final: 0.8230 (tp30) REVERT: C 836 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8530 (t) REVERT: C 837 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8534 (t80) REVERT: C 1029 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8444 (tm-30) REVERT: C 1032 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 1033 GLN cc_start: 0.8956 (mm110) cc_final: 0.8364 (mm-40) REVERT: C 1060 LEU cc_start: 0.9271 (mt) cc_final: 0.9058 (mt) REVERT: C 1061 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 1119 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8156 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7869 (t70) cc_final: 0.7381 (t-90) REVERT: C 1215 ARG cc_start: 0.7867 (mtm180) cc_final: 0.7459 (mtm180) REVERT: C 1245 GLN cc_start: 0.8489 (mt0) cc_final: 0.8237 (mt0) REVERT: C 1345 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8427 (mmm-85) REVERT: C 1348 GLU cc_start: 0.8602 (pp20) cc_final: 0.8246 (pp20) REVERT: C 1459 GLU cc_start: 0.9046 (mp0) cc_final: 0.8816 (pt0) REVERT: C 1499 GLU cc_start: 0.8521 (pp20) cc_final: 0.8011 (tm-30) REVERT: D 50 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6706 (mtt180) REVERT: D 260 LEU cc_start: 0.8969 (tt) cc_final: 0.8620 (tm) outliers start: 52 outliers final: 35 residues processed: 529 average time/residue: 0.5751 time to fit residues: 355.7241 Evaluate side-chains 524 residues out of total 2868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 478 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1135 SER Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1515 ILE Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1135 SER Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1351 SER Chi-restraints excluded: chain C residue 1401 ASP Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 14 optimal weight: 4.9990 chunk 297 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 50.0000 chunk 93 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN A1211 HIS A1245 GLN C1528 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.084906 restraints weight = 43810.963| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.03 r_work: 0.2891 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.386 26788 Z= 0.236 Angle : 0.714 13.922 36666 Z= 0.340 Chirality : 0.045 0.226 4130 Planarity : 0.005 0.063 4604 Dihedral : 10.020 114.125 4318 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.39 % Allowed : 18.98 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.14 (0.15), residues: 3256 helix: 1.75 (0.13), residues: 1596 sheet: -0.64 (0.26), residues: 362 loop : 0.02 (0.19), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 133 TYR 0.015 0.002 TYR A1548 PHE 0.038 0.002 PHE A1370 TRP 0.048 0.002 TRP C1342 HIS 0.008 0.001 HIS C1444 Details of bonding type rmsd covalent geometry : bond 0.00563 (26746) covalent geometry : angle 0.70122 (36560) SS BOND : bond 0.00129 ( 8) SS BOND : angle 0.60897 ( 16) hydrogen bonds : bond 0.04241 ( 1433) hydrogen bonds : angle 4.67993 ( 4119) Misc. bond : bond 0.33393 ( 4) link_ALPHA1-2 : bond 0.00384 ( 6) link_ALPHA1-2 : angle 2.29933 ( 18) link_ALPHA1-3 : bond 0.00864 ( 4) link_ALPHA1-3 : angle 1.52902 ( 12) link_ALPHA1-6 : bond 0.00626 ( 4) link_ALPHA1-6 : angle 2.19215 ( 12) link_BETA1-4 : bond 0.00586 ( 4) link_BETA1-4 : angle 3.67687 ( 12) link_NAG-ASN : bond 0.01606 ( 12) link_NAG-ASN : angle 3.14840 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11058.12 seconds wall clock time: 188 minutes 16.40 seconds (11296.40 seconds total)