Starting phenix.real_space_refine on Mon Jul 6 08:33:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kd8_62265/07_2026/9kd8_62265.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kd8_62265/07_2026/9kd8_62265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kd8_62265/07_2026/9kd8_62265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kd8_62265/07_2026/9kd8_62265.map" model { file = "/net/cci-nas-00/data/ceres_data/9kd8_62265/07_2026/9kd8_62265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kd8_62265/07_2026/9kd8_62265.cif" } resolution = 2.46 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= 0.074 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 Zn 8 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 180 5.16 5 C 20656 2.51 5 N 5745 2.21 5 O 6403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 11153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1418, 11153 Classifications: {'peptide': 1418} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1351} Chain breaks: 4 Chain: "B" Number of atoms: 9378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9378 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 5 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 2, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 410 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 10} Chain: "T" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "M" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {'PXZ': 1} Classifications: {'peptide': 5, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'NMCIS': 1, 'NMTRANS': 1, 'PCIS': 1, 'TRANS': 1, None: 1} Not linked: pdbres="PXZ M 6 " pdbres="THR M 7 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PXZ:plan-1': 1, 'PXZ:plan-2': 1, 'SAR:plan-1': 1, 'MVA:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 61.904 85.990 118.312 1.00138.60 S ATOM 844 SG CYS A 110 59.973 89.163 117.678 1.00144.75 S ATOM 1149 SG CYS A 148 62.750 89.198 120.284 1.00144.25 S ATOM 1287 SG CYS A 167 59.568 87.262 120.946 1.00144.72 S ATOM 515 SG CYS A 67 48.665 77.077 73.322 1.00109.41 S ATOM 537 SG CYS A 70 49.651 80.266 71.464 1.00106.95 S ATOM 590 SG CYS A 77 52.361 77.822 72.658 1.00120.17 S ATOM 20037 SG CYS B1163 53.873 92.244 81.165 1.00103.66 S ATOM 20055 SG CYS B1166 54.828 89.981 83.778 1.00112.65 S ATOM 20180 SG CYS B1182 51.371 89.584 81.737 1.00103.29 S ATOM 20199 SG CYS B1185 51.929 92.068 84.598 1.00114.78 S ATOM 21178 SG CYS C 86 81.702 56.943 15.577 1.00128.16 S ATOM 21195 SG CYS C 88 79.450 55.386 18.298 1.00135.29 S ATOM 21228 SG CYS C 92 80.910 53.366 15.368 1.00117.18 S ATOM 21251 SG CYS C 95 83.080 54.613 18.305 1.00114.96 S ATOM 28918 SG CYS I 7 110.095 40.385 135.541 1.00122.66 S ATOM 28943 SG CYS I 10 106.359 40.241 134.755 1.00123.34 S ATOM 29109 SG CYS I 29 107.892 43.609 135.655 1.00154.46 S ATOM 29133 SG CYS I 32 107.584 40.859 138.242 1.00142.76 S ATOM 29460 SG CYS I 75 140.352 41.005 102.558 1.00 99.80 S ATOM 29482 SG CYS I 78 140.993 37.235 103.590 1.00112.48 S ATOM 29698 SG CYS I 103 138.176 38.298 100.992 1.00101.55 S ATOM 29718 SG CYS I 106 138.092 38.734 104.673 1.00103.18 S ATOM 29863 SG CYS J 7 107.167 49.448 37.723 1.00 85.35 S ATOM 29886 SG CYS J 10 108.484 50.656 34.352 1.00 81.84 S ATOM 30166 SG CYS J 45 110.706 50.697 37.475 1.00 95.52 S ATOM 30172 SG CYS J 46 109.736 47.499 35.527 1.00 89.99 S ATOM 31352 SG CYS L 31 72.771 25.756 51.331 1.00 99.20 S ATOM 31372 SG CYS L 34 72.966 21.893 50.322 1.00 89.43 S ATOM 31476 SG CYS L 48 69.661 23.898 50.575 1.00 89.71 S ATOM 31499 SG CYS L 51 71.770 22.751 53.519 1.00104.04 S Time building chain proxies: 6.06, per 1000 atoms: 0.18 Number of scatterers: 33056 At special positions: 0 Unit cell: (159.03, 149.73, 157.17, 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) Zn 8 29.99 S 180 16.00 P 63 15.00 Mg 1 11.99 O 6403 8.00 N 5745 7.00 C 20656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 TRANS " DVA M 2 " - " THR M 1 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 45 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DVA M 2 " pdb=" CB DVA M 8 " Number of C-beta restraints generated: 7498 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 52 sheets defined 39.0% alpha, 19.8% beta 24 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.989A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.686A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.728A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.187A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.632A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.827A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1125 removed outlier: 3.615A pdb=" N ALA A1125 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1145 Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.536A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1188 removed outlier: 4.143A pdb=" N GLN A1187 " --> pdb=" O SER A1184 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A1188 " --> pdb=" O PHE A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1184 through 1188' Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.551A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1270 removed outlier: 3.695A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 3.809A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1376 removed outlier: 4.090A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 removed outlier: 3.881A pdb=" N SER A1392 " --> pdb=" O PHE A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.629A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 3.657A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.646A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 79 through 82 Processing helix chain 'B' and resid 113 through 121 removed outlier: 5.541A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 359 removed outlier: 4.304A pdb=" N ILE B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 438 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 449 through 463 removed outlier: 4.268A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 592 through 606 Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 695 through 699 Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.612A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 784 through 788 removed outlier: 3.624A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.785A pdb=" N GLU B 810 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.642A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.814A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.634A pdb=" N CYS C 86 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.703A pdb=" N ASP C 117 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.846A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 267 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.503A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.523A pdb=" N ALA D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.746A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.742A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.545A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.542A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.894A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.065A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.833A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.499A pdb=" N LYS A 88 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N ILE A 235 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.595A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.642A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 6.101A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.443A pdb=" N LYS A 431 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 405 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU A 433 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.588A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 567 removed outlier: 6.195A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.491A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB4, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB5, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.692A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1281 through 1292 removed outlier: 3.870A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.850A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1441 through 1445 Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.044A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.044A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC5, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC6, first strand: chain 'B' and resid 223 through 227 removed outlier: 3.925A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.396A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.779A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.779A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD4, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.840A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AD9, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.569A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.412A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.920A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.286A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.286A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.485A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF1, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF2, first strand: chain 'G' and resid 106 through 111 removed outlier: 6.872A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF4, first strand: chain 'G' and resid 152 through 153 removed outlier: 3.612A pdb=" N SER G 156 " --> pdb=" O GLN G 153 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 14 through 17 Processing sheet with id=AF6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AF7, first strand: chain 'K' and resid 19 through 23 1447 hydrogen bonds defined for protein. 3966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 10.99 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5529 1.31 - 1.44: 8688 1.44 - 1.57: 19142 1.57 - 1.69: 124 1.69 - 1.82: 288 Bond restraints: 33771 Sorted by residual: bond pdb=" C12 PXZ M 6 " pdb=" C4 PXZ M 6 " ideal model delta sigma weight residual 1.354 1.542 -0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C1 PXZ M 6 " pdb=" C2 PXZ M 6 " ideal model delta sigma weight residual 1.372 1.519 -0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" C2 PXZ M 6 " pdb=" N2 PXZ M 6 " ideal model delta sigma weight residual 1.344 1.468 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C11 PXZ M 6 " pdb=" N10 PXZ M 6 " ideal model delta sigma weight residual 1.297 1.417 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C13 PXZ M 6 " pdb=" O5 PXZ M 6 " ideal model delta sigma weight residual 1.353 1.470 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 33766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 45527 2.49 - 4.98: 324 4.98 - 7.47: 18 7.47 - 9.96: 3 9.96 - 12.45: 1 Bond angle restraints: 45873 Sorted by residual: angle pdb=" C3' DT N 31 " pdb=" O3' DT N 31 " pdb=" P DG N 32 " ideal model delta sigma weight residual 120.20 107.75 12.45 1.50e+00 4.44e-01 6.89e+01 angle pdb=" C3' DT N 30 " pdb=" O3' DT N 30 " pdb=" P DT N 31 " ideal model delta sigma weight residual 120.20 110.31 9.89 1.50e+00 4.44e-01 4.35e+01 angle pdb=" O4' DC T 24 " pdb=" C4' DC T 24 " pdb=" C3' DC T 24 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" CA MVA M 11 " pdb=" C MVA M 11 " pdb=" O MVA M 11 " ideal model delta sigma weight residual 120.80 112.99 7.81 1.70e+00 3.46e-01 2.11e+01 angle pdb=" N3 DT T 15 " pdb=" C4 DT T 15 " pdb=" O4 DT T 15 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 45868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 20010 35.15 - 70.30: 501 70.30 - 105.45: 37 105.45 - 140.59: 0 140.59 - 175.74: 5 Dihedral angle restraints: 20553 sinusoidal: 8973 harmonic: 11580 Sorted by residual: dihedral pdb=" C SAR M 4 " pdb=" N SAR M 4 " pdb=" CA SAR M 4 " pdb=" CN SAR M 4 " ideal model delta sinusoidal sigma weight residual 80.20 -85.96 166.16 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C SAR M 10 " pdb=" N SAR M 10 " pdb=" CA SAR M 10 " pdb=" CN SAR M 10 " ideal model delta sinusoidal sigma weight residual 80.20 -81.60 161.80 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA GLN B 115 " pdb=" C GLN B 115 " pdb=" N GLU B 116 " pdb=" CA GLU B 116 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 20550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 5127 0.125 - 0.250: 30 0.250 - 0.374: 1 0.374 - 0.499: 2 0.499 - 0.624: 1 Chirality restraints: 5161 Sorted by residual: chirality pdb=" P DT N 30 " pdb=" OP1 DT N 30 " pdb=" OP2 DT N 30 " pdb=" O5' DT N 30 " both_signs ideal model delta sigma weight residual True 2.34 -2.96 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" P DT N 31 " pdb=" OP1 DT N 31 " pdb=" OP2 DT N 31 " pdb=" O5' DT N 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.80 -0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" P DG N 32 " pdb=" OP1 DG N 32 " pdb=" OP2 DG N 32 " pdb=" O5' DG N 32 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.42 2.00e-01 2.50e+01 4.35e+00 ... (remaining 5158 not shown) Planarity restraints: 5729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C0 PXZ M 6 " 0.021 2.00e-02 2.50e+03 2.75e-02 3.77e+01 pdb=" C0' PXZ M 6 " -0.009 2.00e-02 2.50e+03 pdb=" C1 PXZ M 6 " -0.002 2.00e-02 2.50e+03 pdb=" C11 PXZ M 6 " 0.029 2.00e-02 2.50e+03 pdb=" C12 PXZ M 6 " 0.025 2.00e-02 2.50e+03 pdb=" C13 PXZ M 6 " 0.021 2.00e-02 2.50e+03 pdb=" C14 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C15 PXZ M 6 " 0.010 2.00e-02 2.50e+03 pdb=" C16 PXZ M 6 " -0.012 2.00e-02 2.50e+03 pdb=" C2 PXZ M 6 " -0.018 2.00e-02 2.50e+03 pdb=" C3 PXZ M 6 " -0.017 2.00e-02 2.50e+03 pdb=" C4 PXZ M 6 " 0.014 2.00e-02 2.50e+03 pdb=" C6 PXZ M 6 " -0.009 2.00e-02 2.50e+03 pdb=" C7 PXZ M 6 " -0.029 2.00e-02 2.50e+03 pdb=" C8 PXZ M 6 " -0.042 2.00e-02 2.50e+03 pdb=" C9 PXZ M 6 " -0.020 2.00e-02 2.50e+03 pdb=" N10 PXZ M 6 " 0.053 2.00e-02 2.50e+03 pdb=" N2 PXZ M 6 " -0.037 2.00e-02 2.50e+03 pdb=" O3 PXZ M 6 " -0.040 2.00e-02 2.50e+03 pdb=" O5 PXZ M 6 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 244 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO A 245 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR M 7 " -0.013 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" C THR M 7 " 0.041 2.00e-02 2.50e+03 pdb=" O THR M 7 " -0.015 2.00e-02 2.50e+03 pdb=" N DVA M 8 " -0.014 2.00e-02 2.50e+03 ... (remaining 5726 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 500 2.65 - 3.22: 30969 3.22 - 3.78: 52064 3.78 - 4.34: 74140 4.34 - 4.90: 119884 Nonbonded interactions: 277557 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.093 2.170 nonbonded pdb=" NH2 ARG A 469 " pdb=" O GLY B 991 " model vdw 2.167 3.120 nonbonded pdb=" O LEU D 167 " pdb=" OG1 THR D 170 " model vdw 2.170 3.040 nonbonded pdb=" O ASN A 700 " pdb=" NZ LYS I 115 " model vdw 2.194 3.120 nonbonded pdb=" OD2 ASP B 896 " pdb=" OH TYR L 29 " model vdw 2.196 3.040 ... (remaining 277552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 40.190 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 33808 Z= 0.242 Angle : 0.566 13.865 45921 Z= 0.329 Chirality : 0.045 0.624 5161 Planarity : 0.004 0.071 5728 Dihedral : 15.309 175.743 13052 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.96 (0.14), residues: 3936 helix: 1.59 (0.14), residues: 1354 sheet: -0.05 (0.20), residues: 632 loop : 0.32 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 123 TYR 0.021 0.001 TYR B1092 PHE 0.025 0.001 PHE A 444 TRP 0.015 0.001 TRP B 31 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (33771) covalent geometry : angle 0.54546 / 0.33 (45873) hydrogen bonds : bond 0.13650 / 9.36 ( 1456) hydrogen bonds : angle 5.64773 / 4.07 ( 4074) metal coordination : bond 0.00606 / 0.38 ( 32) metal coordination : angle 4.80279 / 2.89 ( 45) Misc. bond : bond 0.00615 / 0.31 ( 4) link_TRANS : bond 0.00197 / 0.10 ( 1) link_TRANS : angle 0.48750 / 0.27 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7782 (tpm170) cc_final: 0.7507 (tpm170) REVERT: A 124 GLN cc_start: 0.9148 (mt0) cc_final: 0.8930 (mm110) REVERT: A 281 HIS cc_start: 0.9105 (t-90) cc_final: 0.8741 (t-90) REVERT: A 287 HIS cc_start: 0.8772 (t70) cc_final: 0.8559 (t70) REVERT: A 826 ASP cc_start: 0.8303 (t70) cc_final: 0.7932 (m-30) REVERT: A 900 ASP cc_start: 0.8110 (t0) cc_final: 0.7294 (p0) REVERT: A 1112 LYS cc_start: 0.8866 (mmpt) cc_final: 0.8586 (mmmm) REVERT: A 1124 HIS cc_start: 0.8786 (m-70) cc_final: 0.8524 (m-70) REVERT: A 1144 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8513 (ttmm) REVERT: A 1209 MET cc_start: 0.8080 (mmm) cc_final: 0.7864 (mmm) REVERT: A 1259 MET cc_start: 0.8844 (tpt) cc_final: 0.8589 (tpp) REVERT: A 1274 ARG cc_start: 0.7952 (ptp-110) cc_final: 0.7667 (ptt-90) REVERT: A 1281 ARG cc_start: 0.7643 (tmm-80) cc_final: 0.7298 (ttp80) REVERT: A 1315 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8483 (mp0) REVERT: A 1445 ILE cc_start: 0.8484 (mt) cc_final: 0.7963 (tt) REVERT: B 94 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8614 (ttpp) REVERT: B 134 LYS cc_start: 0.8253 (tttt) cc_final: 0.7655 (tmtt) REVERT: B 173 MET cc_start: 0.8774 (ptp) cc_final: 0.8465 (ptp) REVERT: B 199 MET cc_start: 0.8731 (pmm) cc_final: 0.8493 (pmm) REVERT: B 667 GLN cc_start: 0.7195 (tt0) cc_final: 0.6798 (tm-30) REVERT: B 908 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8115 (tp30) REVERT: C 16 ASP cc_start: 0.8330 (p0) cc_final: 0.8070 (m-30) REVERT: C 75 MET cc_start: 0.9062 (tpp) cc_final: 0.8787 (tpt) REVERT: C 264 GLN cc_start: 0.8254 (pt0) cc_final: 0.8051 (pp30) REVERT: D 51 ASN cc_start: 0.6795 (p0) cc_final: 0.5201 (p0) REVERT: D 58 VAL cc_start: 0.8024 (t) cc_final: 0.7374 (p) REVERT: E 25 ASP cc_start: 0.7987 (m-30) cc_final: 0.7686 (m-30) REVERT: E 58 MET cc_start: 0.8449 (ttt) cc_final: 0.8170 (ttp) REVERT: E 84 ASP cc_start: 0.7547 (m-30) cc_final: 0.7333 (m-30) REVERT: E 101 GLN cc_start: 0.9050 (tt0) cc_final: 0.8659 (tp-100) REVERT: E 116 ILE cc_start: 0.8555 (mm) cc_final: 0.8048 (pp) REVERT: F 116 ASP cc_start: 0.8773 (t0) cc_final: 0.8480 (t0) REVERT: G 71 ASN cc_start: 0.9120 (t0) cc_final: 0.8911 (t0) REVERT: G 151 ILE cc_start: 0.8476 (mt) cc_final: 0.8236 (pt) REVERT: H 14 GLU cc_start: 0.8594 (tt0) cc_final: 0.8275 (tm-30) REVERT: H 27 GLU cc_start: 0.8308 (mp0) cc_final: 0.8005 (mp0) REVERT: H 35 GLN cc_start: 0.8305 (mt0) cc_final: 0.8085 (pm20) REVERT: H 53 ASP cc_start: 0.8698 (t0) cc_final: 0.8372 (m-30) REVERT: H 87 ARG cc_start: 0.8429 (mmt-90) cc_final: 0.8092 (mmp80) REVERT: H 105 GLU cc_start: 0.8547 (tt0) cc_final: 0.8269 (tt0) REVERT: H 129 TYR cc_start: 0.8583 (p90) cc_final: 0.8271 (p90) REVERT: H 136 LYS cc_start: 0.8715 (ptpp) cc_final: 0.8362 (ptpp) REVERT: H 138 GLU cc_start: 0.8436 (pt0) cc_final: 0.8204 (pm20) REVERT: H 139 ASN cc_start: 0.9416 (m-40) cc_final: 0.9173 (m110) REVERT: I 11 ASN cc_start: 0.8656 (t0) cc_final: 0.7819 (t0) REVERT: I 50 THR cc_start: 0.8345 (m) cc_final: 0.8008 (p) REVERT: I 55 THR cc_start: 0.8534 (p) cc_final: 0.8289 (m) REVERT: I 90 GLN cc_start: 0.8552 (tt0) cc_final: 0.8292 (tt0) REVERT: J 28 ASP cc_start: 0.8911 (m-30) cc_final: 0.8500 (m-30) REVERT: J 29 GLU cc_start: 0.8088 (mp0) cc_final: 0.7731 (pp20) REVERT: K 108 GLU cc_start: 0.8854 (tp30) cc_final: 0.8534 (tp30) REVERT: L 27 LEU cc_start: 0.7734 (mt) cc_final: 0.7238 (mt) outliers start: 0 outliers final: 0 residues processed: 583 average time/residue: 0.8287 time to fit residues: 559.5076 Evaluate side-chains 361 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 4 GLN A 64 ASN A 92 HIS A 118 HIS A 171 GLN A1048 ASN A1078 GLN B 309 GLN B 433 GLN B1093 GLN B1104 HIS D 138 ASN D 200 ASN E 113 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.101773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.064651 restraints weight = 62945.673| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.63 r_work: 0.2848 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 33808 Z= 0.202 Angle : 0.650 33.835 45921 Z= 0.321 Chirality : 0.045 0.238 5161 Planarity : 0.005 0.108 5728 Dihedral : 14.089 177.384 5078 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.62 % Allowed : 9.12 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.90 (0.13), residues: 3936 helix: 1.50 (0.14), residues: 1374 sheet: -0.11 (0.20), residues: 662 loop : 0.33 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 135 TYR 0.018 0.001 TYR B1092 PHE 0.024 0.002 PHE A 444 TRP 0.009 0.001 TRP B 31 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (33771) covalent geometry : angle 0.59903 / 0.32 (45873) hydrogen bonds : bond 0.04868 / 3.29 ( 1456) hydrogen bonds : angle 4.89629 / 3.52 ( 4074) metal coordination : bond 0.01010 / 0.51 ( 32) metal coordination : angle 8.07095 / 4.64 ( 45) Misc. bond : bond 0.00116 / 0.05 ( 4) link_TRANS : bond 0.00220 / 0.12 ( 1) link_TRANS : angle 0.22703 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 385 time to evaluate : 1.312 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 63 ARG cc_start: 0.7962 (tpm170) cc_final: 0.7612 (tpm170) REVERT: A 124 GLN cc_start: 0.9244 (mt0) cc_final: 0.8991 (mm110) REVERT: A 281 HIS cc_start: 0.9225 (t-90) cc_final: 0.8849 (t-90) REVERT: A 317 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8666 (tptt) REVERT: A 481 ASP cc_start: 0.8091 (m-30) cc_final: 0.7856 (m-30) REVERT: A 826 ASP cc_start: 0.8375 (t70) cc_final: 0.7947 (m-30) REVERT: A 900 ASP cc_start: 0.8309 (t0) cc_final: 0.7251 (p0) REVERT: A 1112 LYS cc_start: 0.8991 (mmpt) cc_final: 0.8647 (mmmm) REVERT: A 1124 HIS cc_start: 0.8877 (m-70) cc_final: 0.8581 (m-70) REVERT: A 1144 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8482 (ttmm) REVERT: A 1209 MET cc_start: 0.7885 (mmm) cc_final: 0.7571 (tpp) REVERT: A 1274 ARG cc_start: 0.8067 (ptp-110) cc_final: 0.7567 (ptt-90) REVERT: A 1281 ARG cc_start: 0.7735 (tmm-80) cc_final: 0.7260 (ttp80) REVERT: A 1287 TYR cc_start: 0.7606 (m-10) cc_final: 0.7239 (m-80) REVERT: A 1315 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8494 (mp0) REVERT: A 1445 ILE cc_start: 0.8577 (mt) cc_final: 0.8104 (tt) REVERT: A 1448 GLU cc_start: 0.8929 (pt0) cc_final: 0.8644 (pp20) REVERT: B 94 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8511 (ttmt) REVERT: B 277 LYS cc_start: 0.9168 (ptpt) cc_final: 0.8959 (ptpt) REVERT: B 667 GLN cc_start: 0.7335 (tt0) cc_final: 0.6990 (tm-30) REVERT: B 708 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7741 (mm-30) REVERT: B 908 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8246 (tp30) REVERT: B 935 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7631 (ttp80) REVERT: B 1152 MET cc_start: 0.9108 (mmm) cc_final: 0.8721 (mmm) REVERT: B 1183 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8001 (mppt) REVERT: C 12 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8005 (tm-30) REVERT: C 16 ASP cc_start: 0.8298 (p0) cc_final: 0.7959 (m-30) REVERT: C 75 MET cc_start: 0.9122 (tpp) cc_final: 0.8772 (tpt) REVERT: C 137 LYS cc_start: 0.9335 (ptmm) cc_final: 0.8983 (pmmt) REVERT: C 264 GLN cc_start: 0.8274 (pt0) cc_final: 0.7967 (pp30) REVERT: D 50 LEU cc_start: 0.9348 (mp) cc_final: 0.9023 (tp) REVERT: D 51 ASN cc_start: 0.8993 (p0) cc_final: 0.8478 (p0) REVERT: D 54 GLU cc_start: 0.9369 (mt-10) cc_final: 0.9048 (mp0) REVERT: E 3 GLN cc_start: 0.8653 (mm110) cc_final: 0.8422 (pm20) REVERT: E 25 ASP cc_start: 0.7766 (m-30) cc_final: 0.7474 (m-30) REVERT: E 58 MET cc_start: 0.8448 (ttt) cc_final: 0.8201 (ttp) REVERT: E 101 GLN cc_start: 0.9190 (tt0) cc_final: 0.8940 (pt0) REVERT: E 113 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8148 (tp40) REVERT: E 116 ILE cc_start: 0.8568 (mm) cc_final: 0.8225 (pp) REVERT: F 76 LYS cc_start: 0.8916 (tttp) cc_final: 0.8659 (ttmm) REVERT: F 116 ASP cc_start: 0.8556 (t0) cc_final: 0.8337 (t0) REVERT: G 71 ASN cc_start: 0.9107 (t0) cc_final: 0.8735 (t0) REVERT: G 153 GLN cc_start: 0.7058 (mp10) cc_final: 0.6788 (mp10) REVERT: H 14 GLU cc_start: 0.8901 (tt0) cc_final: 0.8604 (tm-30) REVERT: H 33 GLN cc_start: 0.7849 (mp10) cc_final: 0.7592 (mp10) REVERT: H 37 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8049 (pttp) REVERT: H 87 ARG cc_start: 0.8673 (mmt-90) cc_final: 0.8295 (mmp80) REVERT: H 105 GLU cc_start: 0.8582 (tt0) cc_final: 0.8244 (tt0) REVERT: H 139 ASN cc_start: 0.9323 (m-40) cc_final: 0.9114 (m-40) REVERT: I 11 ASN cc_start: 0.8350 (t0) cc_final: 0.7506 (t0) REVERT: I 15 TYR cc_start: 0.4754 (p90) cc_final: 0.3901 (p90) REVERT: I 50 THR cc_start: 0.8123 (m) cc_final: 0.7840 (p) REVERT: I 55 THR cc_start: 0.8438 (p) cc_final: 0.8119 (m) REVERT: I 89 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: J 26 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8263 (tm-30) REVERT: J 58 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8645 (mm-30) REVERT: K 108 GLU cc_start: 0.8900 (tp30) cc_final: 0.8526 (tp30) REVERT: L 47 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8395 (mtp-110) outliers start: 57 outliers final: 17 residues processed: 418 average time/residue: 0.7814 time to fit residues: 382.8629 Evaluate side-chains 377 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 356 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 58 optimal weight: 7.9990 chunk 113 optimal weight: 0.2980 chunk 381 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 374 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 300 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 767 GLN B 309 GLN B1040 ASN B1093 GLN D 200 ASN E 101 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 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 = 0.3588 r_free = 0.3588 target = 0.099248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.061864 restraints weight = 63085.699| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.63 r_work: 0.2797 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 33808 Z= 0.331 Angle : 0.691 24.673 45921 Z= 0.346 Chirality : 0.048 0.275 5161 Planarity : 0.005 0.068 5728 Dihedral : 14.094 174.986 5078 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.62 % Allowed : 11.55 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.63 (0.13), residues: 3936 helix: 1.22 (0.14), residues: 1381 sheet: -0.19 (0.20), residues: 647 loop : 0.17 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 135 TYR 0.027 0.002 TYR B1092 PHE 0.029 0.002 PHE A 219 TRP 0.011 0.002 TRP A 954 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.33 (33771) covalent geometry : angle 0.65021 / 0.34 (45873) hydrogen bonds : bond 0.05110 / 3.44 ( 1456) hydrogen bonds : angle 4.88587 / 3.49 ( 4074) metal coordination : bond 0.01140 / 0.64 ( 32) metal coordination : angle 7.52031 / 4.45 ( 45) Misc. bond : bond 0.00058 / 0.03 ( 4) link_TRANS : bond 0.00327 / 0.17 ( 1) link_TRANS : angle 0.08770 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 364 time to evaluate : 1.278 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 22 PHE cc_start: 0.9660 (OUTLIER) cc_final: 0.8921 (m-80) REVERT: A 124 GLN cc_start: 0.9232 (mt0) cc_final: 0.9011 (mm110) REVERT: A 281 HIS cc_start: 0.9236 (t-90) cc_final: 0.8871 (t-90) REVERT: A 317 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8532 (tptt) REVERT: A 481 ASP cc_start: 0.8314 (m-30) cc_final: 0.7972 (m-30) REVERT: A 826 ASP cc_start: 0.8468 (t70) cc_final: 0.7977 (m-30) REVERT: A 900 ASP cc_start: 0.8325 (t0) cc_final: 0.7402 (p0) REVERT: A 977 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8134 (tmmm) REVERT: A 1112 LYS cc_start: 0.9055 (mmpt) cc_final: 0.8683 (mmmm) REVERT: A 1124 HIS cc_start: 0.8760 (m-70) cc_final: 0.8555 (m-70) REVERT: A 1144 LYS cc_start: 0.8952 (ttmt) cc_final: 0.8623 (ttmm) REVERT: A 1209 MET cc_start: 0.7647 (mmm) cc_final: 0.7388 (mmm) REVERT: A 1281 ARG cc_start: 0.7828 (tmm-80) cc_final: 0.7447 (ttp80) REVERT: A 1287 TYR cc_start: 0.7818 (m-10) cc_final: 0.7524 (m-80) REVERT: A 1315 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8511 (mp0) REVERT: A 1445 ILE cc_start: 0.8655 (mt) cc_final: 0.8220 (tt) REVERT: B 94 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8467 (ttmt) REVERT: B 134 LYS cc_start: 0.8206 (tttt) cc_final: 0.7771 (tptt) REVERT: B 135 ARG cc_start: 0.5978 (mmm160) cc_final: 0.4763 (mmm160) REVERT: B 667 GLN cc_start: 0.7376 (tt0) cc_final: 0.7026 (tm-30) REVERT: B 708 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 884 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8251 (mpp80) REVERT: B 908 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8254 (tp30) REVERT: B 935 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7633 (ttp80) REVERT: B 1152 MET cc_start: 0.9158 (mmm) cc_final: 0.8807 (mmm) REVERT: B 1183 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8184 (mppt) REVERT: C 12 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7964 (tm-30) REVERT: C 16 ASP cc_start: 0.8428 (p0) cc_final: 0.8013 (m-30) REVERT: C 75 MET cc_start: 0.9189 (tpp) cc_final: 0.8868 (tpt) REVERT: C 264 GLN cc_start: 0.8317 (pt0) cc_final: 0.7973 (pp30) REVERT: D 50 LEU cc_start: 0.9401 (mp) cc_final: 0.8952 (tp) REVERT: D 145 MET cc_start: 0.9306 (ttt) cc_final: 0.8899 (tmm) REVERT: E 25 ASP cc_start: 0.7776 (m-30) cc_final: 0.7484 (m-30) REVERT: E 41 ASP cc_start: 0.9009 (m-30) cc_final: 0.8705 (m-30) REVERT: E 46 TYR cc_start: 0.8063 (m-80) cc_final: 0.7838 (m-80) REVERT: E 84 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7110 (m-30) REVERT: E 101 GLN cc_start: 0.9140 (tt0) cc_final: 0.8784 (tp-100) REVERT: E 113 GLN cc_start: 0.8582 (tp40) cc_final: 0.8265 (mm110) REVERT: F 116 ASP cc_start: 0.8524 (t0) cc_final: 0.8308 (t0) REVERT: F 144 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8629 (mt-10) REVERT: G 35 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7637 (mm-30) REVERT: G 71 ASN cc_start: 0.9129 (t0) cc_final: 0.8793 (t0) REVERT: G 151 ILE cc_start: 0.8738 (mm) cc_final: 0.8444 (pt) REVERT: G 153 GLN cc_start: 0.7604 (mp10) cc_final: 0.7011 (mp10) REVERT: H 14 GLU cc_start: 0.8906 (tt0) cc_final: 0.8428 (tm-30) REVERT: H 27 GLU cc_start: 0.8702 (mp0) cc_final: 0.8124 (mp0) REVERT: H 33 GLN cc_start: 0.8265 (mp10) cc_final: 0.7317 (mp10) REVERT: H 105 GLU cc_start: 0.8628 (tt0) cc_final: 0.8287 (tt0) REVERT: H 138 GLU cc_start: 0.8431 (pt0) cc_final: 0.7748 (pm20) REVERT: H 146 ARG cc_start: 0.8898 (ttm-80) cc_final: 0.8515 (ttp-170) REVERT: I 11 ASN cc_start: 0.8223 (t0) cc_final: 0.7396 (t0) REVERT: I 55 THR cc_start: 0.8476 (p) cc_final: 0.8121 (m) REVERT: I 89 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: J 32 GLU cc_start: 0.8452 (mp0) cc_final: 0.8173 (mp0) REVERT: J 58 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8754 (mm-30) REVERT: K 54 ARG cc_start: 0.8657 (tpt90) cc_final: 0.8378 (tpp80) REVERT: K 108 GLU cc_start: 0.8956 (tp30) cc_final: 0.8608 (tp30) outliers start: 57 outliers final: 18 residues processed: 392 average time/residue: 0.8030 time to fit residues: 367.3323 Evaluate side-chains 372 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 349 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 977 LYS Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1183 LYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 33 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 180 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 341 optimal weight: 8.9990 chunk 345 optimal weight: 4.9990 chunk 169 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 340 optimal weight: 10.0000 chunk 387 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 515 GLN B 309 GLN B1093 GLN E 113 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.101196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.064058 restraints weight = 62346.820| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.62 r_work: 0.2841 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 33808 Z= 0.148 Angle : 0.593 20.971 45921 Z= 0.297 Chirality : 0.044 0.242 5161 Planarity : 0.004 0.067 5728 Dihedral : 14.016 178.183 5078 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.57 % Allowed : 12.86 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.73 (0.13), residues: 3936 helix: 1.39 (0.14), residues: 1375 sheet: -0.22 (0.19), residues: 674 loop : 0.22 (0.15), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 434 TYR 0.024 0.001 TYR H 129 PHE 0.025 0.001 PHE I 4 TRP 0.010 0.001 TRP A 954 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (33771) covalent geometry : angle 0.55712 / 0.29 (45873) hydrogen bonds : bond 0.04192 / 2.82 ( 1456) hydrogen bonds : angle 4.63996 / 3.32 ( 4074) metal coordination : bond 0.00645 / 0.37 ( 32) metal coordination : angle 6.52943 / 3.86 ( 45) Misc. bond : bond 0.00061 / 0.03 ( 4) link_TRANS : bond 0.00145 / 0.08 ( 1) link_TRANS : angle 0.04116 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 366 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9655 (OUTLIER) cc_final: 0.8948 (m-80) REVERT: A 41 MET cc_start: 0.9264 (mmp) cc_final: 0.8917 (mmp) REVERT: A 124 GLN cc_start: 0.9212 (mt0) cc_final: 0.8993 (mm110) REVERT: A 281 HIS cc_start: 0.9219 (t-90) cc_final: 0.8836 (t-90) REVERT: A 317 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8549 (tptt) REVERT: A 481 ASP cc_start: 0.8169 (m-30) cc_final: 0.7898 (m-30) REVERT: A 826 ASP cc_start: 0.8404 (t70) cc_final: 0.7995 (m-30) REVERT: A 900 ASP cc_start: 0.8302 (t0) cc_final: 0.7370 (p0) REVERT: A 1112 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8616 (mmmm) REVERT: A 1124 HIS cc_start: 0.8746 (m-70) cc_final: 0.8531 (m-70) REVERT: A 1144 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8523 (ttmm) REVERT: A 1199 ARG cc_start: 0.8758 (tpp80) cc_final: 0.8438 (tpp-160) REVERT: A 1209 MET cc_start: 0.7584 (mmm) cc_final: 0.7379 (mmm) REVERT: A 1281 ARG cc_start: 0.7766 (tmm-80) cc_final: 0.7351 (ttp80) REVERT: A 1315 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8478 (mp0) REVERT: A 1445 ILE cc_start: 0.8642 (mt) cc_final: 0.8167 (tt) REVERT: B 94 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8470 (ttmt) REVERT: B 277 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8866 (mtmm) REVERT: B 667 GLN cc_start: 0.7337 (tt0) cc_final: 0.6983 (tm-30) REVERT: B 708 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7760 (mm-30) REVERT: B 884 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8137 (mtm-85) REVERT: B 908 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8250 (tp30) REVERT: B 935 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7509 (ttp80) REVERT: C 12 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8028 (tm-30) REVERT: C 16 ASP cc_start: 0.8429 (p0) cc_final: 0.8019 (m-30) REVERT: C 75 MET cc_start: 0.9143 (tpp) cc_final: 0.8810 (tpt) REVERT: C 264 GLN cc_start: 0.8289 (pt0) cc_final: 0.7959 (pp30) REVERT: D 50 LEU cc_start: 0.9368 (mp) cc_final: 0.8942 (tp) REVERT: D 145 MET cc_start: 0.9343 (ttt) cc_final: 0.9114 (ttt) REVERT: E 25 ASP cc_start: 0.7793 (m-30) cc_final: 0.7481 (m-30) REVERT: E 41 ASP cc_start: 0.9024 (m-30) cc_final: 0.8687 (m-30) REVERT: E 57 MET cc_start: 0.7927 (ptm) cc_final: 0.7558 (ppp) REVERT: E 58 MET cc_start: 0.8128 (ttp) cc_final: 0.7774 (ttp) REVERT: E 101 GLN cc_start: 0.9109 (tt0) cc_final: 0.8797 (tp-100) REVERT: E 113 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8391 (tp-100) REVERT: F 116 ASP cc_start: 0.8521 (t0) cc_final: 0.8279 (t0) REVERT: F 144 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8568 (mt-10) REVERT: G 71 ASN cc_start: 0.9135 (t0) cc_final: 0.8828 (t0) REVERT: G 151 ILE cc_start: 0.8733 (mm) cc_final: 0.8352 (pt) REVERT: G 153 GLN cc_start: 0.8005 (mp10) cc_final: 0.7487 (mp10) REVERT: H 14 GLU cc_start: 0.8882 (tt0) cc_final: 0.8545 (tm-30) REVERT: H 37 LYS cc_start: 0.8508 (ptmm) cc_final: 0.8259 (ptpp) REVERT: H 105 GLU cc_start: 0.8613 (tt0) cc_final: 0.8267 (tt0) REVERT: H 138 GLU cc_start: 0.8418 (pt0) cc_final: 0.7788 (pm20) REVERT: H 139 ASN cc_start: 0.9327 (m-40) cc_final: 0.9087 (m-40) REVERT: I 11 ASN cc_start: 0.8225 (t0) cc_final: 0.7437 (t0) REVERT: I 50 THR cc_start: 0.8345 (m) cc_final: 0.7983 (p) REVERT: I 55 THR cc_start: 0.8467 (p) cc_final: 0.8135 (m) REVERT: I 59 VAL cc_start: 0.8747 (p) cc_final: 0.8479 (m) REVERT: J 32 GLU cc_start: 0.8374 (mp0) cc_final: 0.8088 (mp0) REVERT: J 58 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8688 (mm-30) REVERT: K 108 GLU cc_start: 0.8992 (tp30) cc_final: 0.8657 (tp30) outliers start: 55 outliers final: 21 residues processed: 394 average time/residue: 0.7911 time to fit residues: 365.7788 Evaluate side-chains 377 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 353 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 124 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 323 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1093 GLN C 252 GLN D 200 ASN E 113 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063648 restraints weight = 62485.602| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.61 r_work: 0.2832 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 33808 Z= 0.177 Angle : 0.588 19.442 45921 Z= 0.295 Chirality : 0.044 0.241 5161 Planarity : 0.004 0.067 5728 Dihedral : 13.962 178.031 5078 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.54 % Allowed : 13.51 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.76 (0.13), residues: 3936 helix: 1.43 (0.14), residues: 1376 sheet: -0.22 (0.19), residues: 674 loop : 0.23 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 135 TYR 0.024 0.001 TYR I 15 PHE 0.024 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (33771) covalent geometry : angle 0.55560 / 0.29 (45873) hydrogen bonds : bond 0.04180 / 2.81 ( 1456) hydrogen bonds : angle 4.58471 / 3.28 ( 4074) metal coordination : bond 0.00649 / 0.39 ( 32) metal coordination : angle 6.19607 / 3.70 ( 45) Misc. bond : bond 0.00065 / 0.03 ( 4) link_TRANS : bond 0.00180 / 0.09 ( 1) link_TRANS : angle 0.04354 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 366 time to evaluate : 1.165 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 22 PHE cc_start: 0.9645 (OUTLIER) cc_final: 0.8925 (m-80) REVERT: A 41 MET cc_start: 0.9298 (mmp) cc_final: 0.8919 (mmp) REVERT: A 63 ARG cc_start: 0.8570 (ttm110) cc_final: 0.8323 (tpm170) REVERT: A 124 GLN cc_start: 0.9204 (mt0) cc_final: 0.8996 (mm110) REVERT: A 281 HIS cc_start: 0.9220 (t-90) cc_final: 0.8806 (t-90) REVERT: A 317 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8460 (tmtt) REVERT: A 481 ASP cc_start: 0.8196 (m-30) cc_final: 0.7935 (m-30) REVERT: A 826 ASP cc_start: 0.8398 (t70) cc_final: 0.7912 (m-30) REVERT: A 900 ASP cc_start: 0.8310 (t0) cc_final: 0.7403 (p0) REVERT: A 1112 LYS cc_start: 0.9026 (mmpt) cc_final: 0.8612 (mmmm) REVERT: A 1144 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8596 (ttmm) REVERT: A 1198 ASP cc_start: 0.8377 (t0) cc_final: 0.8163 (t0) REVERT: A 1203 ASN cc_start: 0.9133 (m-40) cc_final: 0.8888 (m-40) REVERT: A 1281 ARG cc_start: 0.7859 (tmm-80) cc_final: 0.7409 (ttp80) REVERT: A 1315 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8484 (mp0) REVERT: B 134 LYS cc_start: 0.8093 (tttt) cc_final: 0.7650 (tptt) REVERT: B 135 ARG cc_start: 0.5789 (mmm160) cc_final: 0.5262 (mmm160) REVERT: B 667 GLN cc_start: 0.7313 (tt0) cc_final: 0.6969 (tm-30) REVERT: B 708 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8055 (pm20) REVERT: B 884 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8162 (mtm-85) REVERT: B 908 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8248 (tp30) REVERT: B 935 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7527 (ttp80) REVERT: B 1028 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.9022 (tt0) REVERT: C 12 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8052 (tm-30) REVERT: C 16 ASP cc_start: 0.8425 (p0) cc_final: 0.7975 (m-30) REVERT: C 75 MET cc_start: 0.9144 (tpp) cc_final: 0.8848 (tpt) REVERT: C 264 GLN cc_start: 0.8291 (pt0) cc_final: 0.7940 (pp30) REVERT: D 50 LEU cc_start: 0.9311 (mp) cc_final: 0.9001 (tp) REVERT: D 145 MET cc_start: 0.9358 (ttt) cc_final: 0.9126 (ttt) REVERT: E 25 ASP cc_start: 0.7797 (m-30) cc_final: 0.7492 (m-30) REVERT: E 41 ASP cc_start: 0.8990 (m-30) cc_final: 0.8633 (m-30) REVERT: E 52 ARG cc_start: 0.7716 (mmp80) cc_final: 0.7404 (mmp80) REVERT: E 57 MET cc_start: 0.7894 (ptm) cc_final: 0.7640 (ppp) REVERT: E 58 MET cc_start: 0.8216 (ttp) cc_final: 0.7827 (ttp) REVERT: E 101 GLN cc_start: 0.9112 (tt0) cc_final: 0.8823 (tp-100) REVERT: E 113 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8277 (tp40) REVERT: F 116 ASP cc_start: 0.8516 (t0) cc_final: 0.8261 (t0) REVERT: F 144 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8586 (mt-10) REVERT: G 71 ASN cc_start: 0.9157 (t0) cc_final: 0.8848 (t0) REVERT: G 151 ILE cc_start: 0.8742 (mm) cc_final: 0.8495 (tp) REVERT: G 153 GLN cc_start: 0.8066 (mp10) cc_final: 0.7707 (mp10) REVERT: H 14 GLU cc_start: 0.8859 (tt0) cc_final: 0.8567 (tm-30) REVERT: H 37 LYS cc_start: 0.8502 (ptmm) cc_final: 0.8241 (ptpp) REVERT: H 87 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8637 (mmp80) REVERT: H 105 GLU cc_start: 0.8635 (tt0) cc_final: 0.8298 (tt0) REVERT: H 138 GLU cc_start: 0.8426 (pt0) cc_final: 0.7753 (pm20) REVERT: H 139 ASN cc_start: 0.9331 (m-40) cc_final: 0.9105 (m-40) REVERT: I 11 ASN cc_start: 0.8208 (t0) cc_final: 0.7432 (t0) REVERT: I 50 THR cc_start: 0.8288 (m) cc_final: 0.7896 (p) REVERT: I 55 THR cc_start: 0.8476 (p) cc_final: 0.8132 (m) REVERT: I 59 VAL cc_start: 0.8784 (p) cc_final: 0.8520 (m) REVERT: J 32 GLU cc_start: 0.8346 (mp0) cc_final: 0.8066 (mp0) REVERT: J 58 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8690 (mm-30) REVERT: K 108 GLU cc_start: 0.8987 (tp30) cc_final: 0.8644 (tp30) outliers start: 54 outliers final: 30 residues processed: 391 average time/residue: 0.7799 time to fit residues: 356.8375 Evaluate side-chains 382 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 181 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 393 optimal weight: 50.0000 chunk 290 optimal weight: 30.0000 chunk 170 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1093 GLN C 135 GLN D 200 ASN E 113 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.100313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.063159 restraints weight = 62543.667| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.60 r_work: 0.2821 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 33808 Z= 0.207 Angle : 0.602 18.865 45921 Z= 0.302 Chirality : 0.045 0.398 5161 Planarity : 0.004 0.078 5728 Dihedral : 13.954 178.198 5078 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.88 % Allowed : 14.11 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.74 (0.13), residues: 3936 helix: 1.41 (0.14), residues: 1375 sheet: -0.23 (0.20), residues: 665 loop : 0.21 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 434 TYR 0.027 0.001 TYR H 129 PHE 0.025 0.001 PHE A 219 TRP 0.009 0.001 TRP B 31 HIS 0.005 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (33771) covalent geometry : angle 0.56955 / 0.30 (45873) hydrogen bonds : bond 0.04276 / 2.87 ( 1456) hydrogen bonds : angle 4.59661 / 3.29 ( 4074) metal coordination : bond 0.00698 / 0.42 ( 32) metal coordination : angle 6.20780 / 3.72 ( 45) Misc. bond : bond 0.00062 / 0.03 ( 4) link_TRANS : bond 0.00215 / 0.11 ( 1) link_TRANS : angle 0.07458 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 1.372 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 22 PHE cc_start: 0.9650 (OUTLIER) cc_final: 0.8932 (m-80) REVERT: A 41 MET cc_start: 0.9301 (mmp) cc_final: 0.8925 (mmp) REVERT: A 124 GLN cc_start: 0.9209 (mt0) cc_final: 0.9006 (mm110) REVERT: A 281 HIS cc_start: 0.9229 (t-90) cc_final: 0.8800 (t-90) REVERT: A 317 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8424 (tmtt) REVERT: A 481 ASP cc_start: 0.8224 (m-30) cc_final: 0.7961 (m-30) REVERT: A 826 ASP cc_start: 0.8401 (t70) cc_final: 0.7991 (m-30) REVERT: A 900 ASP cc_start: 0.8313 (t0) cc_final: 0.7471 (p0) REVERT: A 1112 LYS cc_start: 0.9041 (mmpt) cc_final: 0.8620 (mmmm) REVERT: A 1144 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8599 (ttmm) REVERT: A 1198 ASP cc_start: 0.8404 (t0) cc_final: 0.8201 (t0) REVERT: A 1203 ASN cc_start: 0.9142 (m-40) cc_final: 0.8879 (m-40) REVERT: A 1281 ARG cc_start: 0.7893 (tmm-80) cc_final: 0.7427 (ttp80) REVERT: A 1315 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8478 (mp0) REVERT: B 134 LYS cc_start: 0.8104 (tttt) cc_final: 0.7631 (tptt) REVERT: B 135 ARG cc_start: 0.5891 (mmm160) cc_final: 0.5460 (mmm160) REVERT: B 667 GLN cc_start: 0.7324 (tt0) cc_final: 0.6977 (tm-30) REVERT: B 708 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8057 (pm20) REVERT: B 884 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8203 (mtm-85) REVERT: B 908 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8244 (tp30) REVERT: B 935 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7573 (ttp80) REVERT: B 1028 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.9026 (tt0) REVERT: B 1152 MET cc_start: 0.9085 (mmm) cc_final: 0.8741 (mmm) REVERT: C 12 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8064 (tm-30) REVERT: C 16 ASP cc_start: 0.8453 (p0) cc_final: 0.7975 (m-30) REVERT: C 75 MET cc_start: 0.9166 (tpp) cc_final: 0.8864 (tpt) REVERT: C 264 GLN cc_start: 0.8317 (pt0) cc_final: 0.7954 (pp30) REVERT: D 50 LEU cc_start: 0.9375 (mp) cc_final: 0.8932 (tp) REVERT: D 145 MET cc_start: 0.9347 (ttt) cc_final: 0.9114 (ttt) REVERT: E 25 ASP cc_start: 0.7811 (m-30) cc_final: 0.7505 (m-30) REVERT: E 41 ASP cc_start: 0.9002 (m-30) cc_final: 0.8618 (m-30) REVERT: E 50 MET cc_start: 0.8671 (mpp) cc_final: 0.8396 (mpp) REVERT: E 52 ARG cc_start: 0.7735 (mmp80) cc_final: 0.7392 (mmp80) REVERT: E 57 MET cc_start: 0.7959 (ptm) cc_final: 0.7616 (ppp) REVERT: E 58 MET cc_start: 0.8209 (ttp) cc_final: 0.7823 (ttp) REVERT: E 101 GLN cc_start: 0.9123 (tt0) cc_final: 0.8840 (tp-100) REVERT: F 116 ASP cc_start: 0.8527 (t0) cc_final: 0.8244 (t0) REVERT: F 144 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8593 (mt-10) REVERT: G 71 ASN cc_start: 0.9147 (t0) cc_final: 0.8844 (t0) REVERT: G 151 ILE cc_start: 0.8741 (mm) cc_final: 0.8449 (tp) REVERT: G 153 GLN cc_start: 0.8141 (mp10) cc_final: 0.7684 (mp10) REVERT: H 14 GLU cc_start: 0.8876 (tt0) cc_final: 0.8575 (tm-30) REVERT: H 37 LYS cc_start: 0.8413 (ptmm) cc_final: 0.8149 (ptpp) REVERT: H 87 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8677 (mmp80) REVERT: H 105 GLU cc_start: 0.8647 (tt0) cc_final: 0.8307 (tt0) REVERT: H 138 GLU cc_start: 0.8428 (pt0) cc_final: 0.7725 (pm20) REVERT: H 139 ASN cc_start: 0.9349 (m-40) cc_final: 0.9120 (m-40) REVERT: I 11 ASN cc_start: 0.8102 (t0) cc_final: 0.7392 (t0) REVERT: I 47 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8264 (mp0) REVERT: I 50 THR cc_start: 0.8271 (m) cc_final: 0.7859 (p) REVERT: I 55 THR cc_start: 0.8476 (p) cc_final: 0.8109 (m) REVERT: I 59 VAL cc_start: 0.8805 (p) cc_final: 0.8553 (m) REVERT: I 87 GLN cc_start: 0.8329 (pt0) cc_final: 0.6994 (mt0) REVERT: I 89 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: J 32 GLU cc_start: 0.8342 (mp0) cc_final: 0.8060 (mp0) REVERT: J 58 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8723 (mm-30) REVERT: K 54 ARG cc_start: 0.8649 (tpt90) cc_final: 0.8337 (tpt90) REVERT: K 108 GLU cc_start: 0.8984 (tp30) cc_final: 0.8631 (tp30) outliers start: 66 outliers final: 33 residues processed: 387 average time/residue: 0.7862 time to fit residues: 356.1940 Evaluate side-chains 381 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 345 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 89 GLN Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 278 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 274 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1093 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.101265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.064206 restraints weight = 62308.328| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.61 r_work: 0.2845 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 33808 Z= 0.155 Angle : 0.591 18.123 45921 Z= 0.296 Chirality : 0.043 0.241 5161 Planarity : 0.004 0.067 5728 Dihedral : 13.925 179.630 5078 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.80 % Allowed : 14.82 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.80 (0.13), residues: 3936 helix: 1.48 (0.14), residues: 1374 sheet: -0.20 (0.20), residues: 667 loop : 0.22 (0.15), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 434 TYR 0.028 0.001 TYR I 15 PHE 0.033 0.001 PHE A1225 TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (33771) covalent geometry : angle 0.56117 / 0.29 (45873) hydrogen bonds : bond 0.04009 / 2.70 ( 1456) hydrogen bonds : angle 4.50370 / 3.23 ( 4074) metal coordination : bond 0.00562 / 0.34 ( 32) metal coordination : angle 5.90934 / 3.56 ( 45) Misc. bond : bond 0.00071 / 0.03 ( 4) link_TRANS : bond 0.00160 / 0.08 ( 1) link_TRANS : angle 0.04399 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 363 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.9636 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: A 41 MET cc_start: 0.9322 (mmp) cc_final: 0.8952 (mmp) REVERT: A 124 GLN cc_start: 0.9196 (mt0) cc_final: 0.8992 (mm110) REVERT: A 281 HIS cc_start: 0.9223 (t-90) cc_final: 0.8791 (t-90) REVERT: A 317 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8388 (tmtt) REVERT: A 481 ASP cc_start: 0.8183 (m-30) cc_final: 0.7918 (m-30) REVERT: A 593 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8434 (pp20) REVERT: A 826 ASP cc_start: 0.8377 (t70) cc_final: 0.7969 (m-30) REVERT: A 900 ASP cc_start: 0.8355 (t0) cc_final: 0.7462 (p0) REVERT: A 1112 LYS cc_start: 0.9027 (mmpt) cc_final: 0.8587 (mmmm) REVERT: A 1144 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8579 (ttmm) REVERT: A 1198 ASP cc_start: 0.8351 (t0) cc_final: 0.8110 (t0) REVERT: A 1203 ASN cc_start: 0.9130 (m-40) cc_final: 0.8857 (m-40) REVERT: A 1281 ARG cc_start: 0.7849 (tmm-80) cc_final: 0.7376 (ttp80) REVERT: A 1315 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8495 (mp0) REVERT: B 134 LYS cc_start: 0.8068 (tttt) cc_final: 0.7753 (tptt) REVERT: B 135 ARG cc_start: 0.5819 (mmm160) cc_final: 0.5588 (mmm160) REVERT: B 241 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8007 (tpp80) REVERT: B 667 GLN cc_start: 0.7315 (tt0) cc_final: 0.6964 (tm-30) REVERT: B 708 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8034 (pm20) REVERT: B 884 ARG cc_start: 0.8732 (mmm-85) cc_final: 0.8251 (mtm-85) REVERT: B 908 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8251 (tp30) REVERT: B 935 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7500 (ttp80) REVERT: B 1028 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8991 (tt0) REVERT: B 1152 MET cc_start: 0.9058 (mmm) cc_final: 0.8712 (mmm) REVERT: C 12 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8047 (tm-30) REVERT: C 16 ASP cc_start: 0.8435 (p0) cc_final: 0.7938 (m-30) REVERT: C 50 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: C 75 MET cc_start: 0.9159 (tpp) cc_final: 0.8846 (tpt) REVERT: C 264 GLN cc_start: 0.8262 (pt0) cc_final: 0.7926 (pp30) REVERT: D 50 LEU cc_start: 0.9327 (mp) cc_final: 0.8857 (tp) REVERT: D 145 MET cc_start: 0.9409 (ttt) cc_final: 0.9149 (ttt) REVERT: E 3 GLN cc_start: 0.8741 (mm110) cc_final: 0.8486 (pm20) REVERT: E 25 ASP cc_start: 0.7797 (m-30) cc_final: 0.7500 (m-30) REVERT: E 41 ASP cc_start: 0.9016 (m-30) cc_final: 0.8634 (m-30) REVERT: E 52 ARG cc_start: 0.7731 (mmp80) cc_final: 0.7385 (mmp80) REVERT: E 57 MET cc_start: 0.7945 (ptm) cc_final: 0.7622 (ppp) REVERT: E 58 MET cc_start: 0.8228 (ttp) cc_final: 0.7824 (ttp) REVERT: E 101 GLN cc_start: 0.9108 (tt0) cc_final: 0.8842 (tp-100) REVERT: E 113 GLN cc_start: 0.8717 (tp40) cc_final: 0.8486 (mm110) REVERT: F 114 GLU cc_start: 0.7712 (pm20) cc_final: 0.7325 (pm20) REVERT: F 116 ASP cc_start: 0.8556 (t0) cc_final: 0.8270 (t0) REVERT: F 144 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8525 (mt-10) REVERT: G 71 ASN cc_start: 0.9139 (t0) cc_final: 0.8849 (t0) REVERT: G 153 GLN cc_start: 0.8263 (mp10) cc_final: 0.7981 (mp10) REVERT: H 14 GLU cc_start: 0.8856 (tt0) cc_final: 0.8551 (tm-30) REVERT: H 87 ARG cc_start: 0.8971 (mmm-85) cc_final: 0.8703 (mmp80) REVERT: H 105 GLU cc_start: 0.8666 (tt0) cc_final: 0.8333 (tt0) REVERT: H 109 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9103 (tmmt) REVERT: H 138 GLU cc_start: 0.8431 (pt0) cc_final: 0.7746 (pm20) REVERT: H 139 ASN cc_start: 0.9340 (m-40) cc_final: 0.9107 (m-40) REVERT: I 11 ASN cc_start: 0.8084 (t0) cc_final: 0.7393 (t0) REVERT: I 47 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8275 (mp0) REVERT: I 50 THR cc_start: 0.8111 (m) cc_final: 0.7682 (p) REVERT: I 55 THR cc_start: 0.8468 (p) cc_final: 0.8104 (m) REVERT: I 59 VAL cc_start: 0.8786 (p) cc_final: 0.8552 (m) REVERT: I 87 GLN cc_start: 0.8316 (pt0) cc_final: 0.7577 (mt0) REVERT: J 32 GLU cc_start: 0.8313 (mp0) cc_final: 0.8045 (mp0) REVERT: J 58 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8698 (mm-30) REVERT: K 54 ARG cc_start: 0.8625 (tpt90) cc_final: 0.8317 (tpt90) REVERT: K 108 GLU cc_start: 0.8976 (tp30) cc_final: 0.8760 (tp30) outliers start: 63 outliers final: 32 residues processed: 400 average time/residue: 0.8058 time to fit residues: 377.4881 Evaluate side-chains 386 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 350 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 44 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 76 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 395 optimal weight: 50.0000 chunk 53 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 479 ASN B1093 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.099753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.062531 restraints weight = 62414.172| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.61 r_work: 0.2815 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.006 0.095 33808 Z= 0.260 Angle : 0.641 18.483 45921 Z= 0.321 Chirality : 0.046 0.241 5161 Planarity : 0.005 0.067 5728 Dihedral : 13.945 178.522 5078 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.57 % Allowed : 15.54 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.69 (0.13), residues: 3936 helix: 1.33 (0.14), residues: 1379 sheet: -0.19 (0.20), residues: 657 loop : 0.19 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 434 TYR 0.029 0.002 TYR I 15 PHE 0.035 0.002 PHE D 151 TRP 0.009 0.001 TRP B 31 HIS 0.007 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.26 (33771) covalent geometry : angle 0.60777 / 0.32 (45873) hydrogen bonds : bond 0.04424 / 2.96 ( 1456) hydrogen bonds : angle 4.60584 / 3.29 ( 4074) metal coordination : bond 0.00895 / 0.56 ( 32) metal coordination : angle 6.52053 / 3.92 ( 45) Misc. bond : bond 0.00063 / 0.03 ( 4) link_TRANS : bond 0.00257 / 0.14 ( 1) link_TRANS : angle 0.12018 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 1.301 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 22 PHE cc_start: 0.9651 (OUTLIER) cc_final: 0.8942 (m-80) REVERT: A 41 MET cc_start: 0.9323 (mmp) cc_final: 0.8946 (mmp) REVERT: A 281 HIS cc_start: 0.9220 (t-90) cc_final: 0.8813 (t-90) REVERT: A 317 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8442 (tmtt) REVERT: A 481 ASP cc_start: 0.8258 (m-30) cc_final: 0.7896 (m-30) REVERT: A 826 ASP cc_start: 0.8370 (t70) cc_final: 0.7902 (m-30) REVERT: A 900 ASP cc_start: 0.8362 (t0) cc_final: 0.7504 (p0) REVERT: A 1112 LYS cc_start: 0.9050 (mmpt) cc_final: 0.8614 (mmmm) REVERT: A 1144 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8614 (ttmm) REVERT: A 1203 ASN cc_start: 0.9125 (m-40) cc_final: 0.8826 (m-40) REVERT: A 1281 ARG cc_start: 0.7891 (tmm-80) cc_final: 0.7427 (ttp80) REVERT: A 1315 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8532 (mp0) REVERT: B 134 LYS cc_start: 0.8110 (tttt) cc_final: 0.7805 (tptt) REVERT: B 135 ARG cc_start: 0.5846 (mmm160) cc_final: 0.5632 (mmm160) REVERT: B 241 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.7955 (tpp80) REVERT: B 667 GLN cc_start: 0.7358 (tt0) cc_final: 0.7001 (tm-30) REVERT: B 708 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8069 (pm20) REVERT: B 884 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8261 (mtm-85) REVERT: B 908 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8259 (tp30) REVERT: B 935 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7634 (ttp80) REVERT: B 1028 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8999 (tt0) REVERT: B 1152 MET cc_start: 0.9115 (mmm) cc_final: 0.8757 (mmm) REVERT: C 12 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8038 (tm-30) REVERT: C 16 ASP cc_start: 0.8494 (p0) cc_final: 0.7976 (m-30) REVERT: C 50 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: C 75 MET cc_start: 0.9176 (tpp) cc_final: 0.8868 (tpt) REVERT: C 264 GLN cc_start: 0.8299 (pt0) cc_final: 0.7938 (pp30) REVERT: D 50 LEU cc_start: 0.9363 (mp) cc_final: 0.8979 (tp) REVERT: D 145 MET cc_start: 0.9405 (ttt) cc_final: 0.9156 (ttt) REVERT: E 3 GLN cc_start: 0.8762 (mm110) cc_final: 0.8497 (pm20) REVERT: E 25 ASP cc_start: 0.7825 (m-30) cc_final: 0.7510 (m-30) REVERT: E 41 ASP cc_start: 0.9018 (m-30) cc_final: 0.8624 (m-30) REVERT: E 101 GLN cc_start: 0.9116 (tt0) cc_final: 0.8860 (tp-100) REVERT: F 114 GLU cc_start: 0.7719 (pm20) cc_final: 0.7305 (pm20) REVERT: F 116 ASP cc_start: 0.8565 (t0) cc_final: 0.8288 (t0) REVERT: F 144 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8577 (mt-10) REVERT: G 71 ASN cc_start: 0.9140 (t0) cc_final: 0.8850 (t0) REVERT: H 14 GLU cc_start: 0.8856 (tt0) cc_final: 0.8556 (tm-30) REVERT: H 87 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8666 (mmp80) REVERT: H 105 GLU cc_start: 0.8702 (tt0) cc_final: 0.8375 (tt0) REVERT: H 136 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8358 (mtmm) REVERT: H 138 GLU cc_start: 0.8441 (pt0) cc_final: 0.7626 (pm20) REVERT: H 139 ASN cc_start: 0.9327 (m-40) cc_final: 0.9097 (m-40) REVERT: I 11 ASN cc_start: 0.8102 (t0) cc_final: 0.7455 (t0) REVERT: I 47 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8309 (mp0) REVERT: I 50 THR cc_start: 0.8115 (m) cc_final: 0.7676 (p) REVERT: I 55 THR cc_start: 0.8479 (p) cc_final: 0.8106 (m) REVERT: I 59 VAL cc_start: 0.8825 (p) cc_final: 0.8599 (m) REVERT: I 87 GLN cc_start: 0.8442 (pt0) cc_final: 0.7585 (mt0) REVERT: J 23 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8198 (m-40) REVERT: J 32 GLU cc_start: 0.8375 (mp0) cc_final: 0.8079 (mp0) REVERT: J 58 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8831 (mm-30) REVERT: K 108 GLU cc_start: 0.8928 (tp30) cc_final: 0.8672 (tp30) outliers start: 55 outliers final: 33 residues processed: 381 average time/residue: 0.7863 time to fit residues: 349.8370 Evaluate side-chains 378 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 341 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 238 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 204 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 169 ASN B1093 GLN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.063315 restraints weight = 61943.890| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.61 r_work: 0.2831 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 33808 Z= 0.182 Angle : 0.621 18.071 45921 Z= 0.311 Chirality : 0.044 0.240 5161 Planarity : 0.005 0.067 5728 Dihedral : 13.932 179.791 5078 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.54 % Allowed : 15.82 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.72 (0.13), residues: 3936 helix: 1.33 (0.14), residues: 1385 sheet: -0.13 (0.20), residues: 658 loop : 0.19 (0.15), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 434 TYR 0.031 0.001 TYR I 15 PHE 0.039 0.001 PHE A1225 TRP 0.009 0.001 TRP B 31 HIS 0.004 0.001 HIS G 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (33771) covalent geometry : angle 0.58973 / 0.31 (45873) hydrogen bonds : bond 0.04166 / 2.80 ( 1456) hydrogen bonds : angle 4.55136 / 3.26 ( 4074) metal coordination : bond 0.00629 / 0.39 ( 32) metal coordination : angle 6.28580 / 3.77 ( 45) Misc. bond : bond 0.00073 / 0.04 ( 4) link_TRANS : bond 0.00187 / 0.10 ( 1) link_TRANS : angle 0.06828 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 351 time to evaluate : 1.345 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 22 PHE cc_start: 0.9637 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: A 41 MET cc_start: 0.9321 (mmp) cc_final: 0.8917 (mmp) REVERT: A 281 HIS cc_start: 0.9209 (t-90) cc_final: 0.8767 (t-90) REVERT: A 317 LYS cc_start: 0.8888 (mmtt) cc_final: 0.8435 (tmtt) REVERT: A 481 ASP cc_start: 0.8184 (m-30) cc_final: 0.7925 (m-30) REVERT: A 826 ASP cc_start: 0.8345 (t70) cc_final: 0.7947 (m-30) REVERT: A 900 ASP cc_start: 0.8374 (t0) cc_final: 0.7478 (p0) REVERT: A 1112 LYS cc_start: 0.9026 (mmpt) cc_final: 0.8577 (mmmm) REVERT: A 1144 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8591 (ttmm) REVERT: A 1281 ARG cc_start: 0.7830 (tmm-80) cc_final: 0.7353 (ttp80) REVERT: A 1315 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8492 (mp0) REVERT: B 134 LYS cc_start: 0.8101 (tttt) cc_final: 0.7790 (tptt) REVERT: B 241 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.7937 (tpp80) REVERT: B 667 GLN cc_start: 0.7353 (tt0) cc_final: 0.6994 (tm-30) REVERT: B 708 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8036 (pm20) REVERT: B 884 ARG cc_start: 0.8741 (mmm-85) cc_final: 0.8248 (mtm-85) REVERT: B 908 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8265 (tp30) REVERT: B 935 ARG cc_start: 0.7961 (ttp80) cc_final: 0.7622 (ttp80) REVERT: B 1028 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8989 (tt0) REVERT: B 1093 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.9269 (pt0) REVERT: B 1152 MET cc_start: 0.9090 (mmm) cc_final: 0.8735 (mmm) REVERT: C 12 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8059 (tm-30) REVERT: C 16 ASP cc_start: 0.8495 (p0) cc_final: 0.7927 (m-30) REVERT: C 50 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: C 75 MET cc_start: 0.9169 (tpp) cc_final: 0.8863 (tpt) REVERT: C 264 GLN cc_start: 0.8290 (pt0) cc_final: 0.7940 (pp30) REVERT: D 50 LEU cc_start: 0.9361 (mp) cc_final: 0.9012 (tp) REVERT: D 145 MET cc_start: 0.9418 (ttt) cc_final: 0.9149 (ttt) REVERT: E 3 GLN cc_start: 0.8822 (mm110) cc_final: 0.8523 (pm20) REVERT: E 25 ASP cc_start: 0.7806 (m-30) cc_final: 0.7493 (m-30) REVERT: E 41 ASP cc_start: 0.9025 (m-30) cc_final: 0.8617 (m-30) REVERT: E 101 GLN cc_start: 0.9113 (tt0) cc_final: 0.8858 (tp-100) REVERT: F 114 GLU cc_start: 0.7710 (pm20) cc_final: 0.7276 (pm20) REVERT: F 116 ASP cc_start: 0.8562 (t0) cc_final: 0.8264 (t0) REVERT: F 144 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8532 (mt-10) REVERT: G 71 ASN cc_start: 0.9127 (t0) cc_final: 0.8848 (t0) REVERT: G 144 ARG cc_start: 0.7379 (ttm110) cc_final: 0.7096 (mtp-110) REVERT: G 153 GLN cc_start: 0.7556 (mp10) cc_final: 0.7323 (mp10) REVERT: H 14 GLU cc_start: 0.8853 (tt0) cc_final: 0.8575 (tm-30) REVERT: H 87 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8663 (mmp80) REVERT: H 105 GLU cc_start: 0.8684 (tt0) cc_final: 0.8404 (tt0) REVERT: H 109 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9089 (tmmt) REVERT: H 129 TYR cc_start: 0.8978 (p90) cc_final: 0.8769 (p90) REVERT: H 133 ASN cc_start: 0.8932 (p0) cc_final: 0.8658 (p0) REVERT: H 136 LYS cc_start: 0.8932 (ptpp) cc_final: 0.8374 (mtmm) REVERT: H 138 GLU cc_start: 0.8433 (pt0) cc_final: 0.7594 (pm20) REVERT: H 139 ASN cc_start: 0.9328 (m-40) cc_final: 0.9096 (m-40) REVERT: I 11 ASN cc_start: 0.8119 (t0) cc_final: 0.7504 (t0) REVERT: I 47 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8286 (mp0) REVERT: I 50 THR cc_start: 0.8098 (m) cc_final: 0.7657 (p) REVERT: I 55 THR cc_start: 0.8475 (p) cc_final: 0.8107 (m) REVERT: I 59 VAL cc_start: 0.8809 (p) cc_final: 0.8585 (m) REVERT: I 87 GLN cc_start: 0.8415 (pt0) cc_final: 0.7584 (mt0) REVERT: J 32 GLU cc_start: 0.8325 (mp0) cc_final: 0.8053 (mp0) REVERT: J 58 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8733 (mm-30) REVERT: K 54 ARG cc_start: 0.8690 (mmm-85) cc_final: 0.8385 (tpt90) REVERT: K 108 GLU cc_start: 0.8926 (tp30) cc_final: 0.8617 (tp30) REVERT: L 28 LYS cc_start: 0.8266 (mmpt) cc_final: 0.8051 (mmpt) outliers start: 54 outliers final: 33 residues processed: 378 average time/residue: 0.8157 time to fit residues: 360.8984 Evaluate side-chains 385 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 347 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 444 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1093 GLN Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 36 GLU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 195 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 375 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 298 optimal weight: 30.0000 chunk 190 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 358 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1093 GLN D 34 GLN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.063566 restraints weight = 62475.269| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.62 r_work: 0.2835 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33808 Z= 0.169 Angle : 0.626 18.001 45921 Z= 0.314 Chirality : 0.044 0.239 5161 Planarity : 0.005 0.126 5728 Dihedral : 13.921 179.827 5078 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.45 % Allowed : 16.05 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.74 (0.13), residues: 3936 helix: 1.35 (0.14), residues: 1379 sheet: -0.13 (0.20), residues: 658 loop : 0.21 (0.15), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 135 TYR 0.032 0.001 TYR I 15 PHE 0.024 0.001 PHE D 151 TRP 0.010 0.001 TRP B 31 HIS 0.004 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (33771) covalent geometry : angle 0.59585 / 0.31 (45873) hydrogen bonds : bond 0.04109 / 2.76 ( 1456) hydrogen bonds : angle 4.53659 / 3.25 ( 4074) metal coordination : bond 0.00606 / 0.38 ( 32) metal coordination : angle 6.12867 / 3.67 ( 45) Misc. bond : bond 0.00075 / 0.04 ( 4) link_TRANS : bond 0.00123 / 0.06 ( 1) link_TRANS : angle 0.03324 / 0.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 1.454 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 22 PHE cc_start: 0.9632 (OUTLIER) cc_final: 0.8912 (m-80) REVERT: A 41 MET cc_start: 0.9318 (mmp) cc_final: 0.8919 (mmp) REVERT: A 281 HIS cc_start: 0.9208 (t-90) cc_final: 0.8767 (t-90) REVERT: A 317 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8418 (tmtt) REVERT: A 481 ASP cc_start: 0.8173 (m-30) cc_final: 0.7916 (m-30) REVERT: A 593 GLU cc_start: 0.8640 (pp20) cc_final: 0.8215 (tm-30) REVERT: A 826 ASP cc_start: 0.8340 (t70) cc_final: 0.7942 (m-30) REVERT: A 900 ASP cc_start: 0.8371 (t0) cc_final: 0.7482 (p0) REVERT: A 1112 LYS cc_start: 0.9026 (mmpt) cc_final: 0.8577 (mmmm) REVERT: A 1144 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8581 (ttmm) REVERT: A 1281 ARG cc_start: 0.7800 (tmm-80) cc_final: 0.7317 (ttp80) REVERT: A 1315 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8494 (mp0) REVERT: B 241 ARG cc_start: 0.8513 (ttm-80) cc_final: 0.7934 (tpp80) REVERT: B 667 GLN cc_start: 0.7348 (tt0) cc_final: 0.6989 (tm-30) REVERT: B 708 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8055 (pm20) REVERT: B 810 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8973 (tm-30) REVERT: B 884 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8247 (mtm-85) REVERT: B 908 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8264 (tp30) REVERT: B 935 ARG cc_start: 0.7957 (ttp80) cc_final: 0.7620 (ttp80) REVERT: B 1028 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.9000 (tt0) REVERT: B 1152 MET cc_start: 0.9078 (mmm) cc_final: 0.8724 (mmm) REVERT: C 12 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8075 (tm-30) REVERT: C 50 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: C 75 MET cc_start: 0.9159 (tpp) cc_final: 0.8848 (tpt) REVERT: C 264 GLN cc_start: 0.8283 (pt0) cc_final: 0.7936 (pp30) REVERT: D 50 LEU cc_start: 0.9391 (mp) cc_final: 0.9005 (tp) REVERT: D 145 MET cc_start: 0.9422 (ttt) cc_final: 0.9157 (ttt) REVERT: E 3 GLN cc_start: 0.8822 (mm110) cc_final: 0.8524 (pm20) REVERT: E 25 ASP cc_start: 0.7808 (m-30) cc_final: 0.7495 (m-30) REVERT: E 41 ASP cc_start: 0.9029 (m-30) cc_final: 0.8736 (m-30) REVERT: E 50 MET cc_start: 0.7724 (ppp) cc_final: 0.6732 (pp-130) REVERT: E 52 ARG cc_start: 0.7852 (mmp80) cc_final: 0.7505 (mmp80) REVERT: E 101 GLN cc_start: 0.9118 (tt0) cc_final: 0.8870 (tp-100) REVERT: F 114 GLU cc_start: 0.7724 (pm20) cc_final: 0.7318 (pm20) REVERT: F 116 ASP cc_start: 0.8559 (t0) cc_final: 0.8263 (t0) REVERT: F 144 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8534 (mt-10) REVERT: G 71 ASN cc_start: 0.9128 (t0) cc_final: 0.8843 (t0) REVERT: G 144 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7166 (mtp-110) REVERT: H 14 GLU cc_start: 0.8884 (tt0) cc_final: 0.8594 (tm-30) REVERT: H 87 ARG cc_start: 0.8951 (mmm-85) cc_final: 0.8640 (mmp80) REVERT: H 105 GLU cc_start: 0.8674 (tt0) cc_final: 0.8402 (tt0) REVERT: H 109 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9108 (tmmt) REVERT: H 133 ASN cc_start: 0.8945 (p0) cc_final: 0.8671 (p0) REVERT: H 136 LYS cc_start: 0.8951 (ptpp) cc_final: 0.8386 (mtmm) REVERT: H 138 GLU cc_start: 0.8448 (pt0) cc_final: 0.7602 (pm20) REVERT: H 139 ASN cc_start: 0.9313 (m-40) cc_final: 0.9074 (m-40) REVERT: I 11 ASN cc_start: 0.8120 (t0) cc_final: 0.7509 (t0) REVERT: I 47 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8294 (mp0) REVERT: I 50 THR cc_start: 0.8036 (m) cc_final: 0.7602 (p) REVERT: I 55 THR cc_start: 0.8470 (p) cc_final: 0.8102 (m) REVERT: I 59 VAL cc_start: 0.8805 (p) cc_final: 0.8584 (m) REVERT: I 87 GLN cc_start: 0.8407 (pt0) cc_final: 0.7589 (mt0) REVERT: J 32 GLU cc_start: 0.8321 (mp0) cc_final: 0.8045 (mp0) REVERT: J 58 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8696 (mm-30) REVERT: K 54 ARG cc_start: 0.8661 (mmm-85) cc_final: 0.8372 (tpt90) REVERT: K 108 GLU cc_start: 0.8905 (tp30) cc_final: 0.8602 (tp30) REVERT: L 28 LYS cc_start: 0.8261 (mmpt) cc_final: 0.8042 (mmpt) outliers start: 51 outliers final: 33 residues processed: 379 average time/residue: 0.8087 time to fit residues: 358.1436 Evaluate side-chains 382 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 344 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 716 ASP Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 444 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain I residue 15 TYR Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 107 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain L residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 309 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 271 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 279 optimal weight: 0.0370 chunk 183 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 325 optimal weight: 0.1980 chunk 281 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1093 GLN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN G 24 GLN ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN L 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.064912 restraints weight = 62046.144| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.62 r_work: 0.2860 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 0.003 0.065 33808 Z= 0.126 Angle : 0.607 17.401 45921 Z= 0.305 Chirality : 0.043 0.237 5161 Planarity : 0.004 0.078 5728 Dihedral : 13.859 177.830 5078 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.34 % Allowed : 16.42 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.05 % 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: 0.77 (0.14), residues: 3936 helix: 1.41 (0.14), residues: 1386 sheet: -0.06 (0.20), residues: 661 loop : 0.18 (0.15), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 434 TYR 0.032 0.001 TYR I 15 PHE 0.042 0.001 PHE A1225 TRP 0.010 0.001 TRP C 201 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (33771) covalent geometry : angle 0.58107 / 0.30 (45873) hydrogen bonds : bond 0.03793 / 2.56 ( 1456) hydrogen bonds : angle 4.42046 / 3.18 ( 4074) metal coordination : bond 0.00473 / 0.30 ( 32) metal coordination : angle 5.66294 / 3.42 ( 45) Misc. bond : bond 0.00082 / 0.04 ( 4) link_TRANS : bond 0.00073 / 0.04 ( 1) link_TRANS : angle 0.06263 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15046.33 seconds wall clock time: 256 minutes 4.98 seconds (15364.98 seconds total)