Starting phenix.real_space_refine on Mon Jul 6 17:26:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3d_47479/07_2026/9e3d_47479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3d_47479/07_2026/9e3d_47479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e3d_47479/07_2026/9e3d_47479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3d_47479/07_2026/9e3d_47479.map" model { file = "/net/cci-nas-00/data/ceres_data/9e3d_47479/07_2026/9e3d_47479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3d_47479/07_2026/9e3d_47479.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 640 5.49 5 S 135 5.16 5 C 21182 2.51 5 N 6767 2.21 5 O 8032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 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: 36765 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "O" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "Q" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 762 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "R" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 752 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 6594 Classifications: {'DNA': 320} Link IDs: {'rna3p': 319} Chain: "J" Number of atoms: 6526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 6526 Classifications: {'DNA': 320} Link IDs: {'rna3p': 319} Chain: "V" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2682 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Chain: "Z" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1470 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 4 Chain: "U" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "Y" Number of atoms: 4451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4451 Classifications: {'peptide': 555} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 523} Chain breaks: 3 Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24860 SG CYS V 415 76.501 87.076 80.485 1.00418.70 S ATOM 24880 SG CYS V 418 79.381 88.261 82.857 1.00354.61 S ATOM 25010 SG CYS V 435 79.840 89.421 79.468 1.00422.80 S ATOM 25032 SG CYS V 438 80.321 86.096 80.056 1.00369.46 S ATOM 25214 SG CYS V 458 78.990 74.206 77.650 1.00348.37 S ATOM 25234 SG CYS V 461 79.166 76.654 81.025 1.00344.71 S ATOM 25376 SG CYS V 480 78.762 73.255 81.494 1.00344.20 S ATOM 25398 SG CYS V 483 76.171 75.376 80.528 1.00396.66 S ATOM 25303 SG CYS V 470 76.833 64.668 68.921 1.00488.48 S ATOM 25336 SG CYS V 475 77.767 68.252 67.074 1.00503.08 S ATOM 25551 SG CYS V 504 75.056 68.087 69.216 1.00512.50 S ATOM 25577 SG CYS V 507 74.660 66.743 66.103 1.00570.53 S ATOM 29016 SG CYS U 494 131.747 73.900 74.391 1.00411.03 S ATOM 29036 SG CYS U 497 128.423 71.555 75.088 1.00469.40 S ATOM 29158 SG CYS U 514 128.390 74.068 72.112 1.00390.60 S ATOM 29181 SG CYS U 517 128.097 74.981 75.040 1.00368.41 S ATOM 29349 SG CYS U 537 130.257 78.323 85.619 1.00401.89 S ATOM 29370 SG CYS U 540 128.578 75.518 83.147 1.00392.32 S ATOM 29507 SG CYS U 559 129.790 74.878 86.744 1.00369.15 S ATOM 29529 SG CYS U 562 131.802 74.613 84.316 1.00381.59 S ATOM 29433 SG CYS U 549 135.742 86.982 92.966 1.00433.09 S ATOM 29467 SG CYS U 554 134.940 88.999 90.090 1.00411.40 S ATOM 29680 SG CYS U 583 136.829 85.675 89.714 1.00443.64 S ATOM 29706 SG CYS U 586 138.425 88.973 90.183 1.00428.28 S ATOM 33467 SG CYS Y 494 77.898 140.701 123.539 1.00349.57 S ATOM 33487 SG CYS Y 497 76.918 137.195 125.892 1.00368.59 S ATOM 33609 SG CYS Y 514 80.104 139.116 126.328 1.00356.49 S ATOM 33632 SG CYS Y 517 79.523 136.958 124.189 1.00379.70 S ATOM 33800 SG CYS Y 537 76.861 133.699 113.766 1.00352.46 S ATOM 33821 SG CYS Y 540 76.124 132.845 117.496 1.00414.97 S ATOM 33958 SG CYS Y 559 73.594 131.928 114.790 1.00369.40 S ATOM 33980 SG CYS Y 562 73.882 135.234 116.136 1.00428.41 S ATOM 33884 SG CYS Y 549 79.305 134.410 101.052 1.00287.44 S ATOM 33918 SG CYS Y 554 82.510 135.137 102.093 1.00310.20 S ATOM 34131 SG CYS Y 583 79.352 137.614 102.861 1.00329.47 S ATOM 34157 SG CYS Y 586 81.051 138.316 100.138 1.00304.92 S Time building chain proxies: 8.14, per 1000 atoms: 0.22 Number of scatterers: 36765 At special positions: 0 Unit cell: (158.148, 160.632, 211.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 135 16.00 P 640 15.00 O 8032 8.00 N 6767 7.00 C 21182 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=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U1001 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 517 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 494 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 497 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 514 " pdb=" ZN U1002 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 537 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 562 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 540 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 559 " pdb=" ZN U1003 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 583 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 554 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 549 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 586 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 418 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 435 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 415 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 438 " pdb=" ZN V1002 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 458 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 480 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 483 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 461 " pdb=" ZN V1003 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 504 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 475 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 470 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 507 " pdb=" ZN Y1001 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 497 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 494 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 514 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 517 " pdb=" ZN Y1002 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 537 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 562 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 540 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 559 " pdb=" ZN Y1003 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 583 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 549 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 554 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 586 " Number of angles added : 54 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5488 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 32 sheets defined 55.4% alpha, 6.8% beta 319 base pairs and 540 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.623A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.736A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.033A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.610A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.654A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.644A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.595A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.320A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.532A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.602A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.824A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.559A pdb=" N ILE E 74 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.729A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.601A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.895A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.619A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.527A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.722A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.365A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.603A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.540A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.610A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.601A pdb=" N GLN M 55 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS M 56 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 77 removed outlier: 3.635A pdb=" N PHE M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP M 77 " --> pdb=" O GLU M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.541A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA M 114 " --> pdb=" O CYS M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 25 through 29 removed outlier: 3.837A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.860A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 92 removed outlier: 3.623A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 38 removed outlier: 3.635A pdb=" N VAL O 30 " --> pdb=" O PRO O 26 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN O 38 " --> pdb=" O LEU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 73 removed outlier: 3.636A pdb=" N ALA O 53 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE O 62 " --> pdb=" O LEU O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 89 removed outlier: 3.578A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'P' and resid 34 through 46 removed outlier: 3.501A pdb=" N VAL P 38 " --> pdb=" O TYR P 34 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 81 removed outlier: 3.507A pdb=" N ASN P 81 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 99 removed outlier: 3.579A pdb=" N ILE P 91 " --> pdb=" O THR P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.550A pdb=" N HIS P 106 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS P 113 " --> pdb=" O SER P 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 removed outlier: 3.515A pdb=" N ARG Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 79 removed outlier: 3.544A pdb=" N PHE Q 67 " --> pdb=" O ARG Q 63 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE Q 78 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.508A pdb=" N VAL Q 89 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Q 114 " --> pdb=" O CYS Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.658A pdb=" N ARG Q 131 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 42 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.913A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR R 71 " --> pdb=" O ARG R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 92 removed outlier: 3.640A pdb=" N VAL R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.669A pdb=" N VAL S 30 " --> pdb=" O PRO S 26 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG S 32 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG S 35 " --> pdb=" O HIS S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 73 Processing helix chain 'S' and resid 79 through 90 removed outlier: 3.735A pdb=" N LEU S 83 " --> pdb=" O ILE S 79 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 97 removed outlier: 3.590A pdb=" N LYS S 95 " --> pdb=" O GLU S 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 46 removed outlier: 3.586A pdb=" N LYS T 40 " --> pdb=" O ILE T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 81 Processing helix chain 'T' and resid 87 through 99 removed outlier: 3.642A pdb=" N ALA T 94 " --> pdb=" O GLU T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 119 removed outlier: 3.671A pdb=" N LYS T 105 " --> pdb=" O GLY T 101 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 396 through 407 removed outlier: 3.881A pdb=" N ALA V 405 " --> pdb=" O ALA V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 445 Processing helix chain 'V' and resid 481 through 487 Processing helix chain 'V' and resid 491 through 499 removed outlier: 3.501A pdb=" N GLU V 495 " --> pdb=" O GLY V 491 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU V 498 " --> pdb=" O ALA V 494 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 532 removed outlier: 3.502A pdb=" N SER V 532 " --> pdb=" O ALA V 528 " (cutoff:3.500A) Processing helix chain 'V' and resid 565 through 575 Processing helix chain 'V' and resid 589 through 598 removed outlier: 3.787A pdb=" N VAL V 593 " --> pdb=" O GLU V 589 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL V 596 " --> pdb=" O ALA V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 613 through 620 removed outlier: 3.803A pdb=" N GLU V 617 " --> pdb=" O LYS V 613 " (cutoff:3.500A) Processing helix chain 'V' and resid 650 through 663 removed outlier: 3.509A pdb=" N GLU V 654 " --> pdb=" O ARG V 650 " (cutoff:3.500A) Processing helix chain 'V' and resid 683 through 695 Processing helix chain 'V' and resid 751 through 760 removed outlier: 4.429A pdb=" N VAL V 755 " --> pdb=" O TRP V 751 " (cutoff:3.500A) Processing helix chain 'V' and resid 760 through 766 removed outlier: 3.874A pdb=" N LYS V 764 " --> pdb=" O PHE V 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP V 765 " --> pdb=" O ALA V 761 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR V 766 " --> pdb=" O PRO V 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 760 through 766' Processing helix chain 'Z' and resid 565 through 574 Processing helix chain 'Z' and resid 587 through 598 removed outlier: 3.683A pdb=" N ILE Z 591 " --> pdb=" O CYS Z 587 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS Z 598 " --> pdb=" O GLY Z 594 " (cutoff:3.500A) Processing helix chain 'Z' and resid 612 through 620 Processing helix chain 'Z' and resid 645 through 663 Processing helix chain 'Z' and resid 683 through 695 Processing helix chain 'Z' and resid 753 through 760 Processing helix chain 'Z' and resid 760 through 767 Processing helix chain 'U' and resid 477 through 485 Processing helix chain 'U' and resid 489 through 493 removed outlier: 3.530A pdb=" N ILE U 493 " --> pdb=" O ILE U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 514 through 525 Processing helix chain 'U' and resid 560 through 567 Processing helix chain 'U' and resid 570 through 578 Processing helix chain 'U' and resid 600 through 611 removed outlier: 3.606A pdb=" N PHE U 609 " --> pdb=" O LEU U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 631 removed outlier: 3.560A pdb=" N ARG U 631 " --> pdb=" O ALA U 628 " (cutoff:3.500A) Processing helix chain 'U' and resid 644 through 654 Processing helix chain 'U' and resid 666 through 677 Processing helix chain 'U' and resid 691 through 698 Processing helix chain 'U' and resid 729 through 742 Processing helix chain 'U' and resid 762 through 774 Processing helix chain 'U' and resid 814 through 819 removed outlier: 3.673A pdb=" N CYS U 818 " --> pdb=" O GLU U 814 " (cutoff:3.500A) Processing helix chain 'U' and resid 860 through 868 Processing helix chain 'U' and resid 881 through 892 Processing helix chain 'U' and resid 894 through 903 Processing helix chain 'U' and resid 904 through 908 removed outlier: 3.540A pdb=" N GLU U 907 " --> pdb=" O PRO U 904 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 88 Processing helix chain 'Y' and resid 88 through 107 removed outlier: 3.743A pdb=" N ARG Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 125 through 138 Proline residue: Y 131 - end of helix Processing helix chain 'Y' and resid 144 through 149 Processing helix chain 'Y' and resid 477 through 484 Processing helix chain 'Y' and resid 489 through 493 removed outlier: 3.636A pdb=" N ILE Y 493 " --> pdb=" O ILE Y 490 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 525 Processing helix chain 'Y' and resid 560 through 566 Processing helix chain 'Y' and resid 571 through 578 Processing helix chain 'Y' and resid 600 through 611 removed outlier: 3.724A pdb=" N GLN Y 606 " --> pdb=" O PRO Y 602 " (cutoff:3.500A) Processing helix chain 'Y' and resid 644 through 654 removed outlier: 3.682A pdb=" N LEU Y 648 " --> pdb=" O ALA Y 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 666 through 677 Processing helix chain 'Y' and resid 691 through 698 Processing helix chain 'Y' and resid 729 through 742 removed outlier: 3.861A pdb=" N GLU Y 733 " --> pdb=" O ARG Y 729 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Y' and resid 814 through 819 removed outlier: 3.752A pdb=" N CYS Y 818 " --> pdb=" O GLU Y 814 " (cutoff:3.500A) Processing helix chain 'Y' and resid 860 through 869 Processing helix chain 'Y' and resid 881 through 892 Processing helix chain 'Y' and resid 894 through 903 Processing helix chain 'Y' and resid 904 through 908 removed outlier: 3.785A pdb=" N GLU Y 907 " --> pdb=" O PRO Y 904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.184A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.246A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.831A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.643A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 83 through 84 removed outlier: 7.151A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AB3, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.493A pdb=" N ARG O 42 " --> pdb=" O ILE P 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'O' and resid 100 through 102 removed outlier: 7.217A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.073A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.667A pdb=" N ARG S 42 " --> pdb=" O ILE T 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'V' and resid 467 through 469 removed outlier: 3.702A pdb=" N PHE V 479 " --> pdb=" O LEU V 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 512 through 513 Processing sheet with id=AC2, first strand: chain 'V' and resid 578 through 584 removed outlier: 5.611A pdb=" N ILE V 555 " --> pdb=" O VAL V 578 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS V 580 " --> pdb=" O ILE V 555 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL V 625 " --> pdb=" O MET V 675 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLU V 677 " --> pdb=" O VAL V 625 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY V 627 " --> pdb=" O GLU V 677 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL V 679 " --> pdb=" O GLY V 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 603 through 605 removed outlier: 8.960A pdb=" N LYS Z 603 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR Z 581 " --> pdb=" O LYS Z 603 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL Z 605 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 605 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE Z 555 " --> pdb=" O VAL Z 578 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS Z 580 " --> pdb=" O ILE Z 555 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL Z 557 " --> pdb=" O LYS Z 580 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL Z 582 " --> pdb=" O VAL Z 557 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL Z 625 " --> pdb=" O MET Z 675 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU Z 677 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N GLY Z 627 " --> pdb=" O GLU Z 677 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 504 through 505 Processing sheet with id=AC5, first strand: chain 'U' and resid 546 through 548 Processing sheet with id=AC6, first strand: chain 'U' and resid 591 through 592 Processing sheet with id=AC7, first strand: chain 'U' and resid 682 through 684 removed outlier: 8.988A pdb=" N MET U 682 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR U 660 " --> pdb=" O MET U 682 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL U 684 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA U 662 " --> pdb=" O VAL U 684 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE U 634 " --> pdb=" O VAL U 657 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG U 659 " --> pdb=" O ILE U 634 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY U 707 " --> pdb=" O LEU U 639 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL U 704 " --> pdb=" O LEU U 754 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLU U 756 " --> pdb=" O VAL U 704 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLY U 706 " --> pdb=" O GLU U 756 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N VAL U 758 " --> pdb=" O GLY U 706 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 823 through 825 removed outlier: 4.318A pdb=" N VAL U 850 " --> pdb=" O ASP U 857 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 62 through 66 removed outlier: 5.190A pdb=" N SER Y 30 " --> pdb=" O LEU Y 26 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU Y 26 " --> pdb=" O SER Y 30 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 504 through 505 Processing sheet with id=AD2, first strand: chain 'Y' and resid 546 through 548 Processing sheet with id=AD3, first strand: chain 'Y' and resid 591 through 592 Processing sheet with id=AD4, first strand: chain 'Y' and resid 682 through 684 removed outlier: 7.721A pdb=" N ILE Y 634 " --> pdb=" O ASP Y 658 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TYR Y 660 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL Y 636 " --> pdb=" O TYR Y 660 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ALA Y 662 " --> pdb=" O VAL Y 636 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER Y 638 " --> pdb=" O ALA Y 662 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY Y 707 " --> pdb=" O LEU Y 639 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL Y 704 " --> pdb=" O LEU Y 754 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N GLU Y 756 " --> pdb=" O VAL Y 704 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY Y 706 " --> pdb=" O GLU Y 756 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N VAL Y 758 " --> pdb=" O GLY Y 706 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 824 through 825 removed outlier: 3.944A pdb=" N VAL Y 850 " --> pdb=" O ASP Y 857 " (cutoff:3.500A) 1131 hydrogen bonds defined for protein. 3318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 820 hydrogen bonds 1628 hydrogen bond angles 0 basepair planarities 319 basepair parallelities 540 stacking parallelities Total time for adding SS restraints: 12.09 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6098 1.33 - 1.45: 12962 1.45 - 1.58: 18275 1.58 - 1.70: 1279 1.70 - 1.82: 196 Bond restraints: 38810 Sorted by residual: bond pdb=" N PRO H 100 " pdb=" CA PRO H 100 " ideal model delta sigma weight residual 1.469 1.589 -0.120 1.28e-02 6.10e+03 8.83e+01 bond pdb=" N VAL U 785 " pdb=" CA VAL U 785 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.39e+01 bond pdb=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.32e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.483 -0.030 8.30e-03 1.45e+04 1.30e+01 bond pdb=" N ASP U 579 " pdb=" CA ASP U 579 " ideal model delta sigma weight residual 1.463 1.488 -0.025 6.90e-03 2.10e+04 1.28e+01 ... (remaining 38805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 52818 2.81 - 5.63: 2352 5.63 - 8.44: 8 8.44 - 11.25: 0 11.25 - 14.06: 1 Bond angle restraints: 55179 Sorted by residual: angle pdb=" C LEU H 99 " pdb=" N PRO H 100 " pdb=" CA PRO H 100 " ideal model delta sigma weight residual 119.84 133.90 -14.06 1.25e+00 6.40e-01 1.27e+02 angle pdb=" C SER V 752 " pdb=" N VAL V 753 " pdb=" CA VAL V 753 " ideal model delta sigma weight residual 120.33 125.12 -4.79 8.00e-01 1.56e+00 3.58e+01 angle pdb=" CA PRO H 100 " pdb=" N PRO H 100 " pdb=" CD PRO H 100 " ideal model delta sigma weight residual 112.00 104.38 7.62 1.40e+00 5.10e-01 2.97e+01 angle pdb=" C4' DT I 173 " pdb=" O4' DT I 173 " pdb=" C1' DT I 173 " ideal model delta sigma weight residual 110.10 104.83 5.27 1.00e+00 1.00e+00 2.78e+01 angle pdb=" C GLU D 102 " pdb=" N LEU D 103 " pdb=" CA LEU D 103 " ideal model delta sigma weight residual 120.54 127.21 -6.67 1.35e+00 5.49e-01 2.44e+01 ... (remaining 55174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 18627 35.14 - 70.28: 2852 70.28 - 105.41: 50 105.41 - 140.55: 1 140.55 - 175.69: 4 Dihedral angle restraints: 21534 sinusoidal: 13009 harmonic: 8525 Sorted by residual: dihedral pdb=" CA GLU U 523 " pdb=" C GLU U 523 " pdb=" N CYS U 524 " pdb=" CA CYS U 524 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ASN V 422 " pdb=" C ASN V 422 " pdb=" N PRO V 423 " pdb=" CA PRO V 423 " ideal model delta harmonic sigma weight residual 180.00 158.33 21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA SER V 752 " pdb=" C SER V 752 " pdb=" N VAL V 753 " pdb=" CA VAL V 753 " ideal model delta harmonic sigma weight residual 180.00 -160.19 -19.81 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 21531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4514 0.078 - 0.157: 1520 0.157 - 0.235: 76 0.235 - 0.314: 2 0.314 - 0.392: 4 Chirality restraints: 6116 Sorted by residual: chirality pdb=" C3' DC I 290 " pdb=" C4' DC I 290 " pdb=" O3' DC I 290 " pdb=" C2' DC I 290 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" C3' DG I 316 " pdb=" C4' DG I 316 " pdb=" O3' DG I 316 " pdb=" C2' DG I 316 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C3' DG I 3 " pdb=" C4' DG I 3 " pdb=" O3' DG I 3 " pdb=" C2' DG I 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 6113 not shown) Planarity restraints: 4819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 157 " 0.021 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" N1 DT J 157 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT J 157 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DT J 157 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DT J 157 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT J 157 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT J 157 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT J 157 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT J 157 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT J 157 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 153 " 0.023 2.00e-02 2.50e+03 1.36e-02 4.17e+00 pdb=" N1 DC J 153 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DC J 153 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DC J 153 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DC J 153 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 153 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 153 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC J 153 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 153 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 100 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C PRO D 100 " 0.034 2.00e-02 2.50e+03 pdb=" O PRO D 100 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY D 101 " -0.012 2.00e-02 2.50e+03 ... (remaining 4816 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 381 2.63 - 3.20: 27692 3.20 - 3.77: 64104 3.77 - 4.33: 83346 4.33 - 4.90: 122058 Nonbonded interactions: 297581 Sorted by model distance: nonbonded pdb=" NH2 ARG S 35 " pdb=" OP2 DA I 277 " model vdw 2.067 3.120 nonbonded pdb=" OH TYR P 37 " pdb=" OP1 DG J 132 " model vdw 2.137 3.040 nonbonded pdb=" CD1 LEU G 65 " pdb=" OD2 ASP G 90 " model vdw 2.205 3.460 nonbonded pdb=" CE1 TYR V 714 " pdb=" CH2 TRP V 716 " model vdw 2.208 3.640 nonbonded pdb=" NH2 ARG G 35 " pdb=" OP2 DA I 122 " model vdw 2.220 3.120 ... (remaining 297576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 42 through 134) selection = (chain 'E' and resid 42 through 134) selection = (chain 'M' and resid 42 through 134) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' selection = chain 'N' selection = chain 'R' } ncs_group { reference = (chain 'C' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = (chain 'G' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = (chain 'O' and (resid 14 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 111)) selection = chain 'S' } ncs_group { reference = (chain 'D' and resid 31 through 121) selection = (chain 'H' and resid 31 through 121) selection = chain 'P' selection = (chain 'T' and resid 31 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 46.850 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 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 : 0.010 0.120 38846 Z= 0.766 Angle : 1.352 27.932 55233 Z= 0.984 Chirality : 0.069 0.392 6116 Planarity : 0.003 0.024 4819 Dihedral : 23.537 175.690 16046 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.08 % Allowed : 0.72 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.12), residues: 2889 helix: -1.66 (0.10), residues: 1548 sheet: -1.38 (0.37), residues: 158 loop : -1.83 (0.15), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 45 TYR 0.021 0.002 TYR A 99 PHE 0.021 0.002 PHE Z 652 TRP 0.015 0.002 TRP V 716 HIS 0.006 0.001 HIS V 758 Details of bonding type rmsd/Z covalent geometry : bond 0.01036 / 0.77 (38810) covalent geometry : angle 1.27612 / 0.98 (55179) hydrogen bonds : bond 0.15584 / 10.66 ( 1951) hydrogen bonds : angle 6.23021 / 4.52 ( 4946) metal coordination : bond 0.01402 / 0.89 ( 36) metal coordination : angle 14.32342 / 9.90 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 394 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.8880 (m) cc_final: 0.8601 (t) REVERT: A 130 ILE cc_start: 0.9516 (mt) cc_final: 0.9288 (mm) REVERT: C 68 ASN cc_start: 0.7584 (m-40) cc_final: 0.7270 (m-40) REVERT: O 81 ARG cc_start: 0.8889 (tpt170) cc_final: 0.8538 (tpm170) REVERT: O 96 LEU cc_start: 0.8811 (tp) cc_final: 0.8532 (mt) REVERT: R 90 LEU cc_start: 0.9303 (mt) cc_final: 0.9061 (mt) REVERT: R 98 TYR cc_start: 0.7979 (m-10) cc_final: 0.7351 (m-10) REVERT: V 700 MET cc_start: 0.0129 (ptm) cc_final: -0.1248 (ttt) REVERT: U 852 MET cc_start: 0.3920 (ttt) cc_final: 0.3603 (tpt) REVERT: U 880 MET cc_start: -0.0526 (ptp) cc_final: -0.1134 (ptp) REVERT: Y 71 MET cc_start: 0.1574 (mtm) cc_final: 0.1368 (ttt) REVERT: Y 880 MET cc_start: 0.2591 (ptp) cc_final: 0.2286 (ptp) outliers start: 2 outliers final: 0 residues processed: 395 average time/residue: 0.2648 time to fit residues: 161.0796 Evaluate side-chains 160 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 298 optimal weight: 30.0000 overall best weight: 5.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 106 HIS E 68 GLN F 25 ASN G 31 HIS H 81 ASN M 39 HIS M 68 GLN N 25 ASN O 31 HIS O 73 ASN Q 68 GLN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS T 106 HIS V 657 HIS V 678 ASN U 789 HIS U 873 HIS U 900 HIS Y 129 ASN Y 789 HIS Y 821 HIS Y 900 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.108855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.076904 restraints weight = 306770.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.076138 restraints weight = 173963.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.075722 restraints weight = 123829.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.075164 restraints weight = 98499.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.074975 restraints weight = 95396.479| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 38846 Z= 0.253 Angle : 0.745 11.008 55233 Z= 0.406 Chirality : 0.044 0.247 6116 Planarity : 0.005 0.066 4819 Dihedral : 29.012 175.894 10249 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.12 % Allowed : 6.15 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 2889 helix: 0.32 (0.12), residues: 1576 sheet: -0.76 (0.37), residues: 158 loop : -1.20 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG U 688 TYR 0.033 0.002 TYR Q 54 PHE 0.021 0.002 PHE R 61 TRP 0.016 0.002 TRP Y 53 HIS 0.016 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (38810) covalent geometry : angle 0.72885 / 0.41 (55179) hydrogen bonds : bond 0.07080 / 4.82 ( 1951) hydrogen bonds : angle 4.10009 / 3.00 ( 4946) metal coordination : bond 0.00607 / 0.44 ( 36) metal coordination : angle 4.94431 / 3.62 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8605 (mmm) cc_final: 0.8400 (mmm) REVERT: E 50 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8566 (tt0) REVERT: E 60 LEU cc_start: 0.8768 (mt) cc_final: 0.8359 (mp) REVERT: O 92 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8431 (tt0) REVERT: O 96 LEU cc_start: 0.8313 (tp) cc_final: 0.8083 (mt) REVERT: R 62 LEU cc_start: 0.9819 (mt) cc_final: 0.9574 (tt) REVERT: T 99 LEU cc_start: 0.6970 (tp) cc_final: 0.6694 (tp) REVERT: V 700 MET cc_start: -0.0222 (ptm) cc_final: -0.1162 (ttt) REVERT: U 864 MET cc_start: 0.5411 (mmp) cc_final: 0.5139 (mmm) REVERT: U 880 MET cc_start: 0.2911 (ptp) cc_final: 0.1676 (ptp) outliers start: 28 outliers final: 14 residues processed: 190 average time/residue: 0.2151 time to fit residues: 67.3714 Evaluate side-chains 142 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 62 PHE Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain V residue 725 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 180 optimal weight: 50.0000 chunk 64 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 287 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 163 optimal weight: 50.0000 chunk 347 optimal weight: 8.9990 chunk 283 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 513 HIS V 678 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.074336 restraints weight = 303993.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.071529 restraints weight = 206731.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.071187 restraints weight = 158948.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070936 restraints weight = 115098.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.070816 restraints weight = 107104.628| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 38846 Z= 0.307 Angle : 0.776 10.399 55233 Z= 0.424 Chirality : 0.047 0.297 6116 Planarity : 0.006 0.071 4819 Dihedral : 29.968 177.136 10249 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.04 % Allowed : 6.66 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 2889 helix: 0.74 (0.12), residues: 1603 sheet: -0.57 (0.38), residues: 163 loop : -0.94 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 35 TYR 0.070 0.003 TYR P 118 PHE 0.025 0.002 PHE E 84 TRP 0.018 0.001 TRP Y 32 HIS 0.020 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.31 (38810) covalent geometry : angle 0.76294 / 0.42 (55179) hydrogen bonds : bond 0.09271 / 6.24 ( 1951) hydrogen bonds : angle 4.16998 / 3.04 ( 4946) metal coordination : bond 0.00562 / 0.40 ( 36) metal coordination : angle 4.59448 / 3.59 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8742 (mmm) cc_final: 0.8380 (mmm) REVERT: D 68 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8408 (tm-30) REVERT: E 50 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8561 (tt0) REVERT: H 56 MET cc_start: 0.9447 (tpp) cc_final: 0.9196 (tpp) REVERT: H 77 LEU cc_start: 0.9760 (OUTLIER) cc_final: 0.9509 (tp) REVERT: O 92 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8582 (tt0) REVERT: Q 106 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (t0) REVERT: T 99 LEU cc_start: 0.7226 (tp) cc_final: 0.7007 (tp) REVERT: V 700 MET cc_start: 0.0054 (ptm) cc_final: -0.1136 (ttt) REVERT: U 513 MET cc_start: -0.2923 (tpt) cc_final: -0.6321 (ptt) REVERT: U 548 MET cc_start: 0.2655 (ppp) cc_final: 0.1718 (mmt) REVERT: U 864 MET cc_start: 0.4983 (mmp) cc_final: 0.4680 (mmm) REVERT: U 880 MET cc_start: 0.1498 (ptp) cc_final: 0.0272 (ptp) outliers start: 51 outliers final: 27 residues processed: 183 average time/residue: 0.2122 time to fit residues: 64.0954 Evaluate side-chains 150 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain M residue 77 ASP Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 64 ASN Chi-restraints excluded: chain Q residue 99 TYR Chi-restraints excluded: chain Q residue 106 ASP Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 59 MET Chi-restraints excluded: chain V residue 725 ILE Chi-restraints excluded: chain U residue 877 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 272 optimal weight: 0.3980 chunk 247 optimal weight: 0.0570 chunk 137 optimal weight: 30.0000 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 154 optimal weight: 50.0000 chunk 80 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 46 HIS ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 847 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.107957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.076874 restraints weight = 303130.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.074947 restraints weight = 176975.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.074339 restraints weight = 149017.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.074223 restraints weight = 107590.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.074173 restraints weight = 107200.484| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38846 Z= 0.131 Angle : 0.605 12.284 55233 Z= 0.341 Chirality : 0.042 0.268 6116 Planarity : 0.004 0.082 4819 Dihedral : 29.751 178.878 10249 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.00 % Allowed : 7.78 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.15), residues: 2889 helix: 1.44 (0.13), residues: 1586 sheet: -0.53 (0.38), residues: 165 loop : -0.74 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 55 TYR 0.035 0.001 TYR T 80 PHE 0.018 0.001 PHE R 100 TRP 0.011 0.001 TRP Y 23 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.13 (38810) covalent geometry : angle 0.59573 / 0.34 (55179) hydrogen bonds : bond 0.04719 / 3.19 ( 1951) hydrogen bonds : angle 3.55008 / 2.60 ( 4946) metal coordination : bond 0.00426 / 0.31 ( 36) metal coordination : angle 3.44374 / 2.47 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8689 (mmm) cc_final: 0.8373 (mmm) REVERT: B 84 MET cc_start: 0.8418 (mmm) cc_final: 0.8069 (mmm) REVERT: D 68 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8316 (tm-30) REVERT: Q 90 MET cc_start: 0.9477 (tmm) cc_final: 0.9186 (ppp) REVERT: V 700 MET cc_start: -0.0076 (ptm) cc_final: -0.1149 (ttt) REVERT: U 513 MET cc_start: -0.2587 (tpt) cc_final: -0.6045 (ptt) REVERT: U 864 MET cc_start: 0.4707 (mmp) cc_final: 0.4297 (tpp) REVERT: U 880 MET cc_start: 0.2547 (ptp) cc_final: 0.1162 (ptp) REVERT: Y 607 MET cc_start: 0.3724 (tpt) cc_final: 0.3022 (tmm) REVERT: Y 674 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5578 (tmm) REVERT: Y 880 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.3793 (ppp) outliers start: 25 outliers final: 15 residues processed: 158 average time/residue: 0.2158 time to fit residues: 55.9167 Evaluate side-chains 140 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain Q residue 99 TYR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Chi-restraints excluded: chain Y residue 880 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 76 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 256 optimal weight: 50.0000 chunk 164 optimal weight: 50.0000 chunk 70 optimal weight: 30.0000 chunk 185 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 155 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.104329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.073212 restraints weight = 296513.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.071369 restraints weight = 179879.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.071169 restraints weight = 166426.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.070896 restraints weight = 141562.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.070817 restraints weight = 128315.875| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 38846 Z= 0.313 Angle : 0.757 12.304 55233 Z= 0.410 Chirality : 0.045 0.268 6116 Planarity : 0.006 0.086 4819 Dihedral : 30.052 178.490 10249 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.80 % Allowed : 8.02 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 2889 helix: 1.13 (0.13), residues: 1599 sheet: -0.58 (0.38), residues: 164 loop : -0.68 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG M 134 TYR 0.052 0.002 TYR R 88 PHE 0.027 0.002 PHE E 84 TRP 0.012 0.001 TRP Y 23 HIS 0.017 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.31 (38810) covalent geometry : angle 0.74940 / 0.41 (55179) hydrogen bonds : bond 0.10146 / 6.88 ( 1951) hydrogen bonds : angle 4.05428 / 2.94 ( 4946) metal coordination : bond 0.00499 / 0.38 ( 36) metal coordination : angle 3.61180 / 2.75 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 1.353 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 120 MET cc_start: 0.8732 (mmm) cc_final: 0.8484 (mmm) REVERT: B 84 MET cc_start: 0.8796 (mmm) cc_final: 0.8251 (mmm) REVERT: D 68 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8352 (tm-30) REVERT: Q 90 MET cc_start: 0.9343 (tmm) cc_final: 0.8999 (ppp) REVERT: R 88 TYR cc_start: 0.8872 (m-80) cc_final: 0.8432 (m-80) REVERT: V 700 MET cc_start: 0.0422 (ptm) cc_final: -0.0883 (ttt) REVERT: U 513 MET cc_start: -0.2991 (tpt) cc_final: -0.6407 (ptt) REVERT: U 548 MET cc_start: 0.1611 (ppp) cc_final: 0.0082 (mmt) REVERT: U 864 MET cc_start: 0.4912 (mmp) cc_final: 0.4511 (tpp) REVERT: U 880 MET cc_start: -0.0162 (ptp) cc_final: -0.1088 (ptp) REVERT: Y 607 MET cc_start: 0.3917 (tpt) cc_final: 0.2995 (ptt) REVERT: Y 674 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5514 (tmm) REVERT: Y 880 MET cc_start: 0.4707 (OUTLIER) cc_final: 0.4178 (ppp) outliers start: 45 outliers final: 32 residues processed: 158 average time/residue: 0.2114 time to fit residues: 56.1506 Evaluate side-chains 149 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain P residue 62 PHE Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 99 TYR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain V residue 725 ILE Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Chi-restraints excluded: chain Y residue 880 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 225 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 chunk 269 optimal weight: 30.0000 chunk 271 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 162 optimal weight: 50.0000 chunk 52 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 203 optimal weight: 0.0570 overall best weight: 1.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.106553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.073429 restraints weight = 301416.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.072466 restraints weight = 153377.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.071859 restraints weight = 106782.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.071892 restraints weight = 79492.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.071351 restraints weight = 68146.220| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38846 Z= 0.139 Angle : 0.602 11.478 55233 Z= 0.339 Chirality : 0.042 0.271 6116 Planarity : 0.004 0.068 4819 Dihedral : 30.006 179.933 10249 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.08 % Allowed : 8.94 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2889 helix: 1.61 (0.13), residues: 1595 sheet: -0.59 (0.38), residues: 164 loop : -0.55 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.020 0.001 TYR R 98 PHE 0.019 0.001 PHE P 62 TRP 0.010 0.001 TRP Y 23 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (38810) covalent geometry : angle 0.59388 / 0.34 (55179) hydrogen bonds : bond 0.05010 / 3.39 ( 1951) hydrogen bonds : angle 3.53741 / 2.59 ( 4946) metal coordination : bond 0.00414 / 0.32 ( 36) metal coordination : angle 3.24978 / 2.37 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.184 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 106 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8696 (t70) REVERT: A 120 MET cc_start: 0.8689 (mmm) cc_final: 0.8421 (mmm) REVERT: B 84 MET cc_start: 0.8535 (mmm) cc_final: 0.8012 (mmm) REVERT: D 68 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8284 (tm-30) REVERT: Q 90 MET cc_start: 0.9491 (tmm) cc_final: 0.9249 (ppp) REVERT: Q 125 GLN cc_start: 0.9328 (mt0) cc_final: 0.9116 (pp30) REVERT: S 95 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7173 (ptpt) REVERT: V 700 MET cc_start: 0.0125 (ptm) cc_final: -0.0884 (ttt) REVERT: U 513 MET cc_start: -0.1318 (tpt) cc_final: -0.5317 (ptt) REVERT: U 548 MET cc_start: 0.1739 (ppp) cc_final: 0.0569 (mmt) REVERT: U 864 MET cc_start: 0.4727 (mmp) cc_final: 0.4437 (tpp) REVERT: U 880 MET cc_start: 0.1833 (ptp) cc_final: 0.0608 (ptp) REVERT: Y 607 MET cc_start: 0.3973 (tpt) cc_final: 0.3151 (ptt) REVERT: Y 674 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5683 (tmm) REVERT: Y 880 MET cc_start: 0.5271 (OUTLIER) cc_final: 0.4939 (ppp) outliers start: 27 outliers final: 15 residues processed: 150 average time/residue: 0.2235 time to fit residues: 55.9470 Evaluate side-chains 141 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Chi-restraints excluded: chain Y residue 880 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 311 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 288 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 345 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 168 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.106379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.074350 restraints weight = 304149.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.072107 restraints weight = 177639.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.071730 restraints weight = 152456.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.071661 restraints weight = 106733.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.071646 restraints weight = 101392.499| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38846 Z= 0.145 Angle : 0.597 12.121 55233 Z= 0.335 Chirality : 0.041 0.255 6116 Planarity : 0.004 0.064 4819 Dihedral : 29.831 179.280 10249 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.00 % Allowed : 9.42 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.16), residues: 2889 helix: 1.85 (0.13), residues: 1590 sheet: -0.50 (0.39), residues: 161 loop : -0.44 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 35 TYR 0.016 0.001 TYR V 505 PHE 0.019 0.001 PHE R 61 TRP 0.011 0.001 TRP Y 23 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (38810) covalent geometry : angle 0.58877 / 0.33 (55179) hydrogen bonds : bond 0.05183 / 3.52 ( 1951) hydrogen bonds : angle 3.41594 / 2.49 ( 4946) metal coordination : bond 0.00494 / 0.40 ( 36) metal coordination : angle 3.22257 / 2.31 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.997 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 106 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8633 (t70) REVERT: A 120 MET cc_start: 0.8675 (mmm) cc_final: 0.8420 (mmm) REVERT: B 84 MET cc_start: 0.8500 (mmm) cc_final: 0.7920 (mmm) REVERT: D 68 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8319 (tm-30) REVERT: E 110 CYS cc_start: 0.9256 (m) cc_final: 0.9049 (t) REVERT: E 129 ARG cc_start: 0.9249 (tpp80) cc_final: 0.9006 (tpp80) REVERT: Q 90 MET cc_start: 0.9451 (tmm) cc_final: 0.9217 (ppp) REVERT: Q 125 GLN cc_start: 0.9307 (mt0) cc_final: 0.9099 (pp30) REVERT: R 88 TYR cc_start: 0.9058 (m-80) cc_final: 0.8793 (m-80) REVERT: S 72 ASP cc_start: 0.6639 (t0) cc_final: 0.5776 (m-30) REVERT: T 80 TYR cc_start: 0.7167 (t80) cc_final: 0.6959 (t80) REVERT: V 700 MET cc_start: 0.0277 (ptm) cc_final: -0.0722 (ttt) REVERT: U 513 MET cc_start: -0.1198 (tpt) cc_final: -0.5316 (ptt) REVERT: U 864 MET cc_start: 0.4703 (mmp) cc_final: 0.4430 (tpp) REVERT: U 880 MET cc_start: 0.2698 (ptp) cc_final: 0.1288 (ptp) REVERT: Y 607 MET cc_start: 0.4031 (tpt) cc_final: 0.3237 (ptt) REVERT: Y 674 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.5670 (tmm) outliers start: 25 outliers final: 16 residues processed: 144 average time/residue: 0.2222 time to fit residues: 53.7117 Evaluate side-chains 137 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain U residue 661 ILE Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 107 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 217 optimal weight: 30.0000 chunk 137 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 223 optimal weight: 40.0000 chunk 147 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 296 optimal weight: 0.9980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.106387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.075437 restraints weight = 290600.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.072871 restraints weight = 195795.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.072722 restraints weight = 151475.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.072572 restraints weight = 125428.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.072471 restraints weight = 118554.823| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 38846 Z= 0.145 Angle : 0.586 11.704 55233 Z= 0.331 Chirality : 0.041 0.256 6116 Planarity : 0.004 0.061 4819 Dihedral : 29.827 179.921 10249 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.88 % Allowed : 9.62 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 2889 helix: 1.91 (0.13), residues: 1595 sheet: -0.56 (0.40), residues: 155 loop : -0.35 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 604 TYR 0.013 0.001 TYR V 505 PHE 0.014 0.001 PHE R 61 TRP 0.012 0.001 TRP Y 23 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (38810) covalent geometry : angle 0.57910 / 0.33 (55179) hydrogen bonds : bond 0.04750 / 3.23 ( 1951) hydrogen bonds : angle 3.38759 / 2.48 ( 4946) metal coordination : bond 0.00384 / 0.29 ( 36) metal coordination : angle 2.94583 / 2.12 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.091 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: A 106 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8536 (t0) REVERT: A 120 MET cc_start: 0.8674 (mmm) cc_final: 0.8415 (mmm) REVERT: B 84 MET cc_start: 0.8559 (mmm) cc_final: 0.7996 (mmm) REVERT: D 68 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8066 (tm-30) REVERT: E 129 ARG cc_start: 0.9145 (tpp80) cc_final: 0.8910 (tpp80) REVERT: P 65 ASP cc_start: 0.9445 (t0) cc_final: 0.9125 (m-30) REVERT: Q 90 MET cc_start: 0.9298 (tmm) cc_final: 0.8989 (ppp) REVERT: Q 125 GLN cc_start: 0.9265 (mt0) cc_final: 0.9057 (pp30) REVERT: R 88 TYR cc_start: 0.8767 (m-80) cc_final: 0.8276 (m-80) REVERT: S 72 ASP cc_start: 0.6999 (t0) cc_final: 0.5966 (m-30) REVERT: T 80 TYR cc_start: 0.7825 (t80) cc_final: 0.7602 (t80) REVERT: T 99 LEU cc_start: 0.7697 (tp) cc_final: 0.7431 (tp) REVERT: V 511 ARG cc_start: 0.3593 (mtt180) cc_final: 0.3214 (ttp-170) REVERT: V 700 MET cc_start: 0.0648 (ptm) cc_final: -0.0693 (ttt) REVERT: U 548 MET cc_start: 0.1439 (ppp) cc_final: -0.0131 (mmt) REVERT: U 607 MET cc_start: 0.3108 (ppp) cc_final: 0.2179 (ppp) REVERT: U 880 MET cc_start: -0.0460 (ptp) cc_final: -0.1531 (ptp) REVERT: Y 607 MET cc_start: 0.3960 (tpt) cc_final: 0.3052 (ptt) REVERT: Y 674 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.5642 (tmm) REVERT: Y 761 MET cc_start: 0.1607 (tmm) cc_final: 0.0953 (mmm) outliers start: 22 outliers final: 14 residues processed: 146 average time/residue: 0.2230 time to fit residues: 54.8954 Evaluate side-chains 136 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 76 optimal weight: 6.9990 chunk 232 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 263 optimal weight: 40.0000 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 325 optimal weight: 30.0000 chunk 227 optimal weight: 30.0000 chunk 265 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.105662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.073768 restraints weight = 298752.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.072543 restraints weight = 163495.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.072262 restraints weight = 135504.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.072194 restraints weight = 115319.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.071991 restraints weight = 107127.758| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38846 Z= 0.171 Angle : 0.608 11.259 55233 Z= 0.339 Chirality : 0.041 0.257 6116 Planarity : 0.004 0.061 4819 Dihedral : 29.891 179.741 10249 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.00 % Allowed : 9.58 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.16), residues: 2889 helix: 1.95 (0.13), residues: 1591 sheet: -0.52 (0.40), residues: 156 loop : -0.29 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.014 0.001 TYR U 533 PHE 0.019 0.001 PHE R 61 TRP 0.025 0.001 TRP V 522 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (38810) covalent geometry : angle 0.60082 / 0.34 (55179) hydrogen bonds : bond 0.05716 / 3.89 ( 1951) hydrogen bonds : angle 3.44572 / 2.52 ( 4946) metal coordination : bond 0.00396 / 0.30 ( 36) metal coordination : angle 3.00444 / 2.17 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.796 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 106 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8614 (t0) REVERT: A 120 MET cc_start: 0.8695 (mmm) cc_final: 0.8450 (mmm) REVERT: B 84 MET cc_start: 0.8656 (mmm) cc_final: 0.8013 (mmm) REVERT: D 68 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 129 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8888 (tpp80) REVERT: P 65 ASP cc_start: 0.9458 (t0) cc_final: 0.9179 (m-30) REVERT: Q 90 MET cc_start: 0.9427 (tmm) cc_final: 0.9138 (ppp) REVERT: Q 125 GLN cc_start: 0.9285 (mt0) cc_final: 0.9063 (pp30) REVERT: R 88 TYR cc_start: 0.8900 (m-80) cc_final: 0.8465 (m-80) REVERT: S 72 ASP cc_start: 0.6936 (t0) cc_final: 0.5967 (m-30) REVERT: T 80 TYR cc_start: 0.7643 (t80) cc_final: 0.7418 (t80) REVERT: T 99 LEU cc_start: 0.7330 (tp) cc_final: 0.7076 (tp) REVERT: V 448 MET cc_start: 0.2337 (mmm) cc_final: 0.1982 (mmm) REVERT: V 511 ARG cc_start: 0.3599 (mtt180) cc_final: 0.3327 (ttp-170) REVERT: V 700 MET cc_start: 0.0543 (ptm) cc_final: -0.0618 (ttt) REVERT: U 548 MET cc_start: 0.1501 (ppp) cc_final: 0.0190 (mmt) REVERT: U 607 MET cc_start: 0.3363 (ppp) cc_final: 0.2559 (ppp) REVERT: U 880 MET cc_start: 0.0600 (ptp) cc_final: -0.0695 (ptp) REVERT: Y 607 MET cc_start: 0.4050 (tpt) cc_final: 0.3214 (ptt) REVERT: Y 674 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5787 (tmm) REVERT: Y 761 MET cc_start: 0.1358 (tmm) cc_final: 0.0800 (mmm) outliers start: 25 outliers final: 20 residues processed: 141 average time/residue: 0.2128 time to fit residues: 50.4585 Evaluate side-chains 142 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 260 optimal weight: 50.0000 chunk 222 optimal weight: 0.0470 chunk 71 optimal weight: 10.0000 chunk 172 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 337 optimal weight: 30.0000 chunk 169 optimal weight: 50.0000 chunk 28 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 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 = 0.4453 r_free = 0.4453 target = 0.106393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.074102 restraints weight = 301414.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.072979 restraints weight = 161955.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.073161 restraints weight = 122021.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072454 restraints weight = 90967.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.072013 restraints weight = 86381.505| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 38846 Z= 0.130 Angle : 0.581 12.524 55233 Z= 0.327 Chirality : 0.041 0.258 6116 Planarity : 0.004 0.060 4819 Dihedral : 29.829 179.259 10249 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.56 % Allowed : 10.18 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.16), residues: 2889 helix: 2.04 (0.13), residues: 1583 sheet: -0.50 (0.40), residues: 156 loop : -0.25 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 129 TYR 0.016 0.001 TYR S 57 PHE 0.017 0.001 PHE R 61 TRP 0.016 0.001 TRP V 522 HIS 0.008 0.001 HIS T 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (38810) covalent geometry : angle 0.57432 / 0.33 (55179) hydrogen bonds : bond 0.04417 / 3.01 ( 1951) hydrogen bonds : angle 3.31331 / 2.43 ( 4946) metal coordination : bond 0.00374 / 0.28 ( 36) metal coordination : angle 2.81394 / 2.00 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5778 Ramachandran restraints generated. 2889 Oldfield, 0 Emsley, 2889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 1.044 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: A 106 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8559 (t70) REVERT: A 120 MET cc_start: 0.8640 (mmm) cc_final: 0.8394 (mmm) REVERT: B 84 MET cc_start: 0.8534 (mmm) cc_final: 0.7922 (mmm) REVERT: D 68 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8137 (tm-30) REVERT: P 65 ASP cc_start: 0.9473 (t0) cc_final: 0.9171 (m-30) REVERT: Q 90 MET cc_start: 0.9430 (tmm) cc_final: 0.9215 (ppp) REVERT: Q 125 GLN cc_start: 0.9279 (mt0) cc_final: 0.9073 (pp30) REVERT: R 88 TYR cc_start: 0.9011 (m-80) cc_final: 0.8631 (m-80) REVERT: S 72 ASP cc_start: 0.6796 (t0) cc_final: 0.5963 (m-30) REVERT: T 80 TYR cc_start: 0.7181 (t80) cc_final: 0.6904 (t80) REVERT: T 99 LEU cc_start: 0.7022 (tp) cc_final: 0.6821 (tp) REVERT: V 448 MET cc_start: 0.2643 (mmm) cc_final: 0.2276 (mmm) REVERT: V 511 ARG cc_start: 0.3457 (mtt180) cc_final: 0.3248 (ttp-170) REVERT: V 700 MET cc_start: 0.0374 (ptm) cc_final: -0.0602 (ttt) REVERT: U 548 MET cc_start: 0.1588 (ppp) cc_final: 0.0554 (mmt) REVERT: U 607 MET cc_start: 0.4012 (ppp) cc_final: 0.3271 (ppp) REVERT: U 880 MET cc_start: 0.2080 (ptp) cc_final: 0.0637 (ptp) REVERT: Y 607 MET cc_start: 0.4013 (tpt) cc_final: 0.3238 (ptt) REVERT: Y 674 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5760 (tmm) REVERT: Y 761 MET cc_start: 0.0905 (tmm) cc_final: 0.0503 (mmm) outliers start: 14 outliers final: 11 residues processed: 132 average time/residue: 0.2080 time to fit residues: 46.5244 Evaluate side-chains 134 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain M residue 99 TYR Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 97 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 102 optimal weight: 0.8980 chunk 320 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 132 optimal weight: 40.0000 chunk 97 optimal weight: 30.0000 chunk 334 optimal weight: 8.9990 chunk 217 optimal weight: 0.5980 chunk 170 optimal weight: 50.0000 chunk 45 optimal weight: 0.9980 chunk 339 optimal weight: 30.0000 chunk 152 optimal weight: 50.0000 overall best weight: 3.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.105339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.072351 restraints weight = 297396.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070905 restraints weight = 175004.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.070587 restraints weight = 139387.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.070487 restraints weight = 93944.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.070439 restraints weight = 91551.024| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38846 Z= 0.176 Angle : 0.613 11.338 55233 Z= 0.340 Chirality : 0.041 0.258 6116 Planarity : 0.004 0.062 4819 Dihedral : 29.909 179.356 10249 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.60 % Allowed : 10.06 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.16), residues: 2889 helix: 1.98 (0.13), residues: 1591 sheet: -0.44 (0.40), residues: 156 loop : -0.21 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 882 TYR 0.021 0.001 TYR S 57 PHE 0.018 0.001 PHE R 61 TRP 0.015 0.001 TRP V 522 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (38810) covalent geometry : angle 0.60666 / 0.34 (55179) hydrogen bonds : bond 0.05985 / 4.08 ( 1951) hydrogen bonds : angle 3.43536 / 2.52 ( 4946) metal coordination : bond 0.00388 / 0.29 ( 36) metal coordination : angle 2.85527 / 2.07 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10320.57 seconds wall clock time: 176 minutes 42.16 seconds (10602.16 seconds total)