Starting phenix.real_space_refine on Sat Mar 7 03:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3d_47479/03_2026/9e3d_47479.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3d_47479/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9e3d_47479/03_2026/9e3d_47479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3d_47479/03_2026/9e3d_47479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e3d_47479/03_2026/9e3d_47479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3d_47479/03_2026/9e3d_47479.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 7.87, per 1000 atoms: 0.21 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: 3.11 Conformation dependent library (CDL) restraints added in 1.0 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: 6.40 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: 14.08 Time building geometry restraints manager: 3.97 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: 52857 2.81 - 5.63: 2311 5.63 - 8.44: 10 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=" 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 angle pdb=" O3' DG J 314 " pdb=" C3' DG J 314 " pdb=" C2' DG J 314 " ideal model delta sigma weight residual 111.50 104.20 7.30 1.50e+00 4.44e-01 2.37e+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 - 0.064: 4059 0.064 - 0.129: 1767 0.129 - 0.193: 276 0.193 - 0.257: 10 0.257 - 0.322: 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 -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.58e+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 -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.06e+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 -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.92e+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: 10.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 46.950 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 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= 0.757 Angle : 1.356 27.932 55233 Z= 0.958 Chirality : 0.065 0.322 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 covalent geometry : bond 0.01046 (38810) covalent geometry : angle 1.28103 (55179) hydrogen bonds : bond 0.15584 ( 1951) hydrogen bonds : angle 6.23021 ( 4946) metal coordination : bond 0.01402 ( 36) metal coordination : angle 14.32342 ( 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 : 1.157 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: 0.2672 time to fit residues: 161.1716 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 : 1.079 ------------------------------------------------------------------------------- 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: 4.9990 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: 30.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 30.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 ** T 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS T 106 HIS U 789 HIS U 873 HIS U 900 HIS Y 129 ASN Y 613 HIS Y 789 HIS Y 900 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.110046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.078771 restraints weight = 308165.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.077563 restraints weight = 171545.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.077345 restraints weight = 122368.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.077116 restraints weight = 92396.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.077092 restraints weight = 88607.478| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 38846 Z= 0.182 Angle : 0.628 11.376 55233 Z= 0.347 Chirality : 0.036 0.162 6116 Planarity : 0.004 0.048 4819 Dihedral : 28.528 179.708 10249 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.88 % Allowed : 6.23 % Favored : 92.90 % 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: -0.31 (0.14), residues: 2889 helix: 0.57 (0.12), residues: 1575 sheet: -0.64 (0.38), residues: 156 loop : -1.15 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 596 TYR 0.019 0.001 TYR Q 54 PHE 0.026 0.001 PHE R 61 TRP 0.018 0.001 TRP Y 53 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (38810) covalent geometry : angle 0.61164 (55179) hydrogen bonds : bond 0.04945 ( 1951) hydrogen bonds : angle 3.74928 ( 4946) metal coordination : bond 0.00522 ( 36) metal coordination : angle 4.64415 ( 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 190 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.833 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 120 MET cc_start: 0.8537 (mmm) cc_final: 0.8177 (mmm) REVERT: E 97 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8364 (mt-10) REVERT: O 92 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8524 (tt0) REVERT: O 96 LEU cc_start: 0.8342 (tp) cc_final: 0.8119 (mt) REVERT: R 97 LEU cc_start: 0.8883 (pt) cc_final: 0.8471 (tp) REVERT: T 99 LEU cc_start: 0.7068 (tp) cc_final: 0.6846 (tp) REVERT: V 511 ARG cc_start: 0.3023 (mtt180) cc_final: 0.2733 (ptt180) REVERT: V 700 MET cc_start: -0.0235 (ptm) cc_final: -0.1188 (ttt) REVERT: U 682 MET cc_start: 0.5678 (ptt) cc_final: 0.5268 (ptt) REVERT: U 864 MET cc_start: 0.4901 (mmp) cc_final: 0.4627 (mmm) REVERT: U 875 THR cc_start: 0.7378 (OUTLIER) cc_final: 0.7033 (p) REVERT: U 880 MET cc_start: 0.2215 (ptp) cc_final: 0.0612 (ptp) REVERT: Y 880 MET cc_start: 0.3441 (ptp) cc_final: 0.3201 (ptm) outliers start: 22 outliers final: 11 residues processed: 186 average time/residue: 0.2130 time to fit residues: 65.0588 Evaluate side-chains 138 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU 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 Chi-restraints excluded: chain U residue 875 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 180 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 287 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 209 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 347 optimal weight: 7.9990 chunk 283 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN ** P 46 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** U 847 HIS Y 821 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.106689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.074312 restraints weight = 301868.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.072884 restraints weight = 169292.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.072756 restraints weight = 123638.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072572 restraints weight = 97135.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.072391 restraints weight = 95719.159| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 38846 Z= 0.263 Angle : 0.652 10.124 55233 Z= 0.365 Chirality : 0.038 0.195 6116 Planarity : 0.005 0.097 4819 Dihedral : 29.087 178.736 10249 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.12 % Allowed : 6.23 % Favored : 92.66 % 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: 0.48 (0.15), residues: 2889 helix: 1.23 (0.13), residues: 1592 sheet: -0.46 (0.38), residues: 163 loop : -0.84 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG S 99 TYR 0.031 0.002 TYR N 88 PHE 0.015 0.001 PHE E 84 TRP 0.014 0.001 TRP Y 32 HIS 0.016 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00570 (38810) covalent geometry : angle 0.63992 (55179) hydrogen bonds : bond 0.06892 ( 1951) hydrogen bonds : angle 3.72125 ( 4946) metal coordination : bond 0.00517 ( 36) metal coordination : angle 4.03950 ( 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 178 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.094 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: B 84 MET cc_start: 0.8643 (mmm) cc_final: 0.8121 (mmm) REVERT: E 60 LEU cc_start: 0.8729 (mt) cc_final: 0.8267 (mt) REVERT: E 97 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8128 (mt-10) REVERT: H 77 LEU cc_start: 0.9778 (OUTLIER) cc_final: 0.9574 (tp) REVERT: O 92 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8634 (tt0) REVERT: Q 101 VAL cc_start: 0.9562 (p) cc_final: 0.9357 (m) REVERT: Q 104 PHE cc_start: 0.9366 (m-10) cc_final: 0.9134 (m-80) REVERT: T 99 LEU cc_start: 0.7121 (tp) cc_final: 0.6910 (tp) REVERT: V 700 MET cc_start: -0.0015 (ptm) cc_final: -0.1113 (ttt) REVERT: U 513 MET cc_start: -0.3018 (tpt) cc_final: -0.6276 (ptt) REVERT: U 548 MET cc_start: 0.2315 (ppp) cc_final: 0.1168 (mmt) REVERT: U 682 MET cc_start: 0.5875 (ptt) cc_final: 0.5609 (ptt) REVERT: U 864 MET cc_start: 0.4747 (mmp) cc_final: 0.4315 (tpp) REVERT: U 880 MET cc_start: 0.1432 (ptp) cc_final: 0.0156 (ptp) REVERT: Y 607 MET cc_start: 0.3695 (tpt) cc_final: 0.3021 (tmm) REVERT: Y 880 MET cc_start: 0.3565 (ptp) cc_final: 0.3332 (ptm) outliers start: 28 outliers final: 20 residues processed: 172 average time/residue: 0.2047 time to fit residues: 58.5011 Evaluate side-chains 148 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 49 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain M residue 103 LEU 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 109 SER Chi-restraints excluded: chain U residue 674 MET 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: 50.0000 chunk 247 optimal weight: 0.0980 chunk 137 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 218 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.108576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.078494 restraints weight = 306703.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.076676 restraints weight = 196517.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.076504 restraints weight = 144648.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.076432 restraints weight = 121119.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.076410 restraints weight = 114244.295| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 38846 Z= 0.140 Angle : 0.558 10.393 55233 Z= 0.315 Chirality : 0.035 0.177 6116 Planarity : 0.004 0.077 4819 Dihedral : 29.038 178.107 10249 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.88 % Allowed : 7.46 % Favored : 91.66 % 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: 0.96 (0.16), residues: 2889 helix: 1.63 (0.13), residues: 1592 sheet: -0.36 (0.38), residues: 165 loop : -0.61 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 76 TYR 0.038 0.001 TYR R 88 PHE 0.012 0.001 PHE M 78 TRP 0.012 0.001 TRP Y 23 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00299 (38810) covalent geometry : angle 0.54793 (55179) hydrogen bonds : bond 0.03975 ( 1951) hydrogen bonds : angle 3.34465 ( 4946) metal coordination : bond 0.00418 ( 36) metal coordination : angle 3.34215 ( 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 166 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8616 (mmm) cc_final: 0.8256 (mmm) REVERT: E 60 LEU cc_start: 0.8725 (mt) cc_final: 0.8444 (mp) REVERT: E 97 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8352 (mt-10) REVERT: E 129 ARG cc_start: 0.9001 (tpp80) cc_final: 0.8793 (tpp80) REVERT: Q 104 PHE cc_start: 0.9234 (m-10) cc_final: 0.8993 (m-80) REVERT: V 700 MET cc_start: 0.0203 (ptm) cc_final: -0.1017 (ttt) REVERT: U 513 MET cc_start: -0.3314 (tpt) cc_final: -0.6472 (ptt) REVERT: U 682 MET cc_start: 0.5998 (ptt) cc_final: 0.5674 (ptt) REVERT: U 864 MET cc_start: 0.4715 (mmp) cc_final: 0.4395 (tpp) REVERT: U 875 THR cc_start: 0.7193 (OUTLIER) cc_final: 0.6843 (p) REVERT: U 880 MET cc_start: 0.1151 (ptp) cc_final: -0.0474 (ptp) REVERT: Y 607 MET cc_start: 0.3761 (tpt) cc_final: 0.2945 (ptt) REVERT: Y 674 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.5123 (tmm) REVERT: Y 880 MET cc_start: 0.3621 (ptp) cc_final: 0.3230 (ttp) outliers start: 22 outliers final: 14 residues processed: 162 average time/residue: 0.2091 time to fit residues: 56.2402 Evaluate side-chains 149 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 109 SER Chi-restraints excluded: chain V residue 474 SER Chi-restraints excluded: chain U residue 875 THR Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Chi-restraints excluded: chain Y residue 779 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 76 optimal weight: 0.9990 chunk 321 optimal weight: 20.0000 chunk 205 optimal weight: 8.9990 chunk 256 optimal weight: 50.0000 chunk 164 optimal weight: 30.0000 chunk 70 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 155 optimal weight: 40.0000 chunk 91 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4450 r_free = 0.4450 target = 0.106305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.074744 restraints weight = 304677.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.072443 restraints weight = 164634.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.072507 restraints weight = 112188.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.072101 restraints weight = 83166.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.071973 restraints weight = 81059.198| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 38846 Z= 0.226 Angle : 0.589 8.871 55233 Z= 0.333 Chirality : 0.036 0.153 6116 Planarity : 0.004 0.076 4819 Dihedral : 29.148 177.889 10249 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.60 % Allowed : 7.14 % Favored : 91.26 % 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: 1.12 (0.16), residues: 2889 helix: 1.75 (0.13), residues: 1599 sheet: -0.32 (0.38), residues: 165 loop : -0.53 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 76 TYR 0.041 0.001 TYR R 88 PHE 0.013 0.001 PHE Q 67 TRP 0.013 0.001 TRP Y 23 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00495 (38810) covalent geometry : angle 0.58163 (55179) hydrogen bonds : bond 0.06177 ( 1951) hydrogen bonds : angle 3.47181 ( 4946) metal coordination : bond 0.00401 ( 36) metal coordination : angle 3.12175 ( 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 182 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9185 (OUTLIER) cc_final: 0.8604 (t70) REVERT: A 120 MET cc_start: 0.8694 (mmm) cc_final: 0.8397 (mmm) REVERT: E 60 LEU cc_start: 0.8852 (mt) cc_final: 0.8324 (mt) REVERT: E 97 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8103 (mt-10) REVERT: O 92 GLU cc_start: 0.9026 (tt0) cc_final: 0.8603 (tt0) REVERT: Q 104 PHE cc_start: 0.9376 (m-10) cc_final: 0.9117 (m-80) REVERT: R 88 TYR cc_start: 0.9029 (m-80) cc_final: 0.8654 (m-80) REVERT: S 72 ASP cc_start: 0.6791 (t0) cc_final: 0.5836 (m-30) REVERT: V 700 MET cc_start: 0.0430 (ptm) cc_final: -0.0726 (ttt) REVERT: U 513 MET cc_start: -0.2441 (tpt) cc_final: -0.5992 (ptt) REVERT: U 682 MET cc_start: 0.6119 (ptt) cc_final: 0.5898 (ptt) REVERT: U 864 MET cc_start: 0.4726 (mmp) cc_final: 0.4396 (tpp) REVERT: U 880 MET cc_start: 0.1830 (ptp) cc_final: 0.0469 (ptp) REVERT: Y 607 MET cc_start: 0.3916 (tpt) cc_final: 0.3114 (ptt) REVERT: Y 880 MET cc_start: 0.3407 (ptp) cc_final: 0.3189 (ttp) outliers start: 40 outliers final: 22 residues processed: 167 average time/residue: 0.2138 time to fit residues: 58.8229 Evaluate side-chains 151 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU 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 67 PHE Chi-restraints excluded: chain R residue 49 LEU 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 V residue 474 SER Chi-restraints excluded: chain V residue 725 ILE Chi-restraints excluded: chain U residue 674 MET Chi-restraints excluded: chain U residue 877 VAL 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: 0.4980 chunk 289 optimal weight: 40.0000 chunk 269 optimal weight: 50.0000 chunk 271 optimal weight: 8.9990 chunk 226 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4457 r_free = 0.4457 target = 0.106920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.076050 restraints weight = 307768.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.074331 restraints weight = 185570.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.073601 restraints weight = 147339.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.073298 restraints weight = 105369.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.073268 restraints weight = 90550.457| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38846 Z= 0.170 Angle : 0.563 10.041 55233 Z= 0.318 Chirality : 0.035 0.157 6116 Planarity : 0.004 0.076 4819 Dihedral : 29.232 177.626 10249 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.04 % Allowed : 8.10 % Favored : 90.86 % 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: 1.32 (0.16), residues: 2889 helix: 1.92 (0.13), residues: 1603 sheet: -0.36 (0.39), residues: 156 loop : -0.44 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 39 TYR 0.029 0.001 TYR R 88 PHE 0.011 0.001 PHE Q 67 TRP 0.013 0.001 TRP Y 23 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00369 (38810) covalent geometry : angle 0.55570 (55179) hydrogen bonds : bond 0.04254 ( 1951) hydrogen bonds : angle 3.34499 ( 4946) metal coordination : bond 0.00388 ( 36) metal coordination : angle 3.01558 ( 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 168 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.944 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 106 ASP cc_start: 0.9251 (OUTLIER) cc_final: 0.8816 (t70) REVERT: A 120 MET cc_start: 0.8628 (mmm) cc_final: 0.8320 (mmm) REVERT: E 60 LEU cc_start: 0.8815 (mt) cc_final: 0.8307 (mt) REVERT: E 97 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8080 (mt-10) REVERT: M 90 MET cc_start: 0.9302 (mmm) cc_final: 0.8979 (mmp) REVERT: Q 104 PHE cc_start: 0.9384 (m-10) cc_final: 0.9150 (m-80) REVERT: R 97 LEU cc_start: 0.9057 (pt) cc_final: 0.8340 (tp) REVERT: S 72 ASP cc_start: 0.6922 (t0) cc_final: 0.6062 (m-30) REVERT: V 700 MET cc_start: 0.0475 (ptm) cc_final: -0.0679 (ttt) REVERT: U 513 MET cc_start: -0.2168 (tpt) cc_final: -0.5885 (ptt) REVERT: U 682 MET cc_start: 0.6236 (ptt) cc_final: 0.6031 (ptt) REVERT: U 864 MET cc_start: 0.4699 (mmp) cc_final: 0.4460 (tpp) REVERT: U 880 MET cc_start: 0.1555 (ptp) cc_final: 0.0149 (ptp) REVERT: Y 607 MET cc_start: 0.4024 (tpt) cc_final: 0.3259 (ptt) REVERT: Y 674 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.5206 (tmm) REVERT: Y 761 MET cc_start: 0.1177 (tmm) cc_final: 0.0805 (mmm) outliers start: 26 outliers final: 18 residues processed: 157 average time/residue: 0.2116 time to fit residues: 56.2071 Evaluate side-chains 148 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU 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 R residue 49 LEU Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain V residue 474 SER Chi-restraints excluded: chain U residue 674 MET Chi-restraints excluded: chain U residue 877 VAL Chi-restraints excluded: chain Y residue 674 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 311 optimal weight: 30.0000 chunk 66 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 345 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 168 optimal weight: 30.0000 chunk 212 optimal weight: 2.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.106378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.072913 restraints weight = 298964.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.072260 restraints weight = 143232.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.073230 restraints weight = 101596.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.071305 restraints weight = 87493.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.071314 restraints weight = 79453.724| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38846 Z= 0.182 Angle : 0.562 10.114 55233 Z= 0.319 Chirality : 0.035 0.169 6116 Planarity : 0.004 0.079 4819 Dihedral : 29.216 177.629 10249 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.08 % Allowed : 8.66 % Favored : 90.26 % 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: 1.43 (0.16), residues: 2889 helix: 1.99 (0.13), residues: 1602 sheet: -0.26 (0.40), residues: 156 loop : -0.35 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 40 TYR 0.019 0.001 TYR T 80 PHE 0.011 0.001 PHE Q 67 TRP 0.012 0.001 TRP Y 23 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00396 (38810) covalent geometry : angle 0.55506 (55179) hydrogen bonds : bond 0.04943 ( 1951) hydrogen bonds : angle 3.33706 ( 4946) metal coordination : bond 0.00375 ( 36) metal coordination : angle 2.91777 ( 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 161 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.989 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 106 ASP cc_start: 0.9147 (OUTLIER) cc_final: 0.8628 (t70) REVERT: A 120 MET cc_start: 0.8649 (mmm) cc_final: 0.8343 (mmm) REVERT: E 97 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8328 (mt-10) REVERT: R 97 LEU cc_start: 0.9023 (pt) cc_final: 0.8248 (tp) REVERT: S 72 ASP cc_start: 0.6610 (t0) cc_final: 0.5892 (m-30) REVERT: V 448 MET cc_start: 0.2445 (mmm) cc_final: 0.2197 (mmm) REVERT: V 484 LEU cc_start: 0.6360 (mt) cc_final: 0.5806 (tp) REVERT: V 700 MET cc_start: 0.0679 (ptm) cc_final: -0.0307 (ttt) REVERT: U 513 MET cc_start: 0.0317 (tpt) cc_final: -0.3922 (ptt) REVERT: U 548 MET cc_start: 0.2220 (ppp) cc_final: 0.1183 (mmt) REVERT: U 607 MET cc_start: 0.4909 (tmm) cc_final: 0.4707 (ppp) REVERT: U 880 MET cc_start: 0.2574 (ptp) cc_final: 0.1049 (ptp) REVERT: Y 607 MET cc_start: 0.3961 (tpt) cc_final: 0.3233 (ptt) REVERT: Y 674 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.5301 (tmm) REVERT: Y 880 MET cc_start: 0.5002 (OUTLIER) cc_final: 0.4023 (ppp) outliers start: 27 outliers final: 16 residues processed: 149 average time/residue: 0.2124 time to fit residues: 53.1837 Evaluate side-chains 145 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 34 LEU 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 R residue 49 LEU Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain U residue 674 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 107 optimal weight: 20.0000 chunk 271 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 40.0000 chunk 217 optimal weight: 0.0020 chunk 137 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 147 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 296 optimal weight: 3.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.4458 r_free = 0.4458 target = 0.106724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.073331 restraints weight = 298742.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.072933 restraints weight = 144278.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.073124 restraints weight = 109790.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.072397 restraints weight = 85716.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.071910 restraints weight = 77679.390| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38846 Z= 0.150 Angle : 0.548 10.801 55233 Z= 0.311 Chirality : 0.034 0.166 6116 Planarity : 0.003 0.074 4819 Dihedral : 29.169 177.499 10249 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.92 % Allowed : 9.02 % Favored : 90.06 % 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: 1.57 (0.16), residues: 2889 helix: 2.11 (0.13), residues: 1587 sheet: -0.18 (0.40), residues: 156 loop : -0.29 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.018 0.001 TYR Z 766 PHE 0.036 0.001 PHE Q 104 TRP 0.012 0.001 TRP Y 23 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00321 (38810) covalent geometry : angle 0.54135 (55179) hydrogen bonds : bond 0.04017 ( 1951) hydrogen bonds : angle 3.23735 ( 4946) metal coordination : bond 0.00361 ( 36) metal coordination : angle 2.76298 ( 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 158 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8621 (t70) REVERT: A 120 MET cc_start: 0.8625 (mmm) cc_final: 0.8315 (mmm) REVERT: E 97 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8341 (mt-10) REVERT: Q 104 PHE cc_start: 0.9394 (m-10) cc_final: 0.9193 (m-80) REVERT: R 97 LEU cc_start: 0.9044 (pt) cc_final: 0.8287 (tp) REVERT: S 72 ASP cc_start: 0.6804 (t0) cc_final: 0.6022 (m-30) REVERT: V 448 MET cc_start: 0.2434 (mmm) cc_final: 0.2164 (mmm) REVERT: V 484 LEU cc_start: 0.6383 (mt) cc_final: 0.5815 (tp) REVERT: V 700 MET cc_start: 0.0520 (ptm) cc_final: -0.0552 (ttt) REVERT: V 722 MET cc_start: 0.2646 (mmm) cc_final: 0.2435 (mmm) REVERT: U 513 MET cc_start: -0.1084 (tpt) cc_final: -0.5271 (ptt) REVERT: U 548 MET cc_start: 0.2062 (ppp) cc_final: 0.0919 (mmt) REVERT: U 607 MET cc_start: 0.4880 (tmm) cc_final: 0.4652 (ppp) REVERT: U 880 MET cc_start: 0.2041 (ptp) cc_final: 0.0403 (ptp) REVERT: Y 607 MET cc_start: 0.3881 (tpt) cc_final: 0.3124 (ptt) REVERT: Y 674 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.5298 (tmm) REVERT: Y 761 MET cc_start: 0.0953 (tmm) cc_final: -0.2711 (ptm) outliers start: 23 outliers final: 18 residues processed: 146 average time/residue: 0.2094 time to fit residues: 51.8803 Evaluate side-chains 147 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 34 LEU 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 R residue 49 LEU Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 62 PHE Chi-restraints excluded: chain U residue 674 MET 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: 0.0770 chunk 231 optimal weight: 1.9990 chunk 263 optimal weight: 30.0000 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 227 optimal weight: 40.0000 chunk 265 optimal weight: 0.0370 chunk 65 optimal weight: 0.8980 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.107345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.076235 restraints weight = 301515.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.074321 restraints weight = 162791.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.074236 restraints weight = 124541.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.074048 restraints weight = 94634.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.073836 restraints weight = 97713.995| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38846 Z= 0.133 Angle : 0.539 11.353 55233 Z= 0.306 Chirality : 0.034 0.151 6116 Planarity : 0.003 0.073 4819 Dihedral : 28.997 177.567 10249 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.96 % Allowed : 9.06 % 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: 1.67 (0.16), residues: 2889 helix: 2.17 (0.13), residues: 1589 sheet: -0.12 (0.40), residues: 156 loop : -0.20 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.015 0.001 TYR R 88 PHE 0.026 0.001 PHE Q 104 TRP 0.012 0.001 TRP Y 23 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00283 (38810) covalent geometry : angle 0.53305 (55179) hydrogen bonds : bond 0.03767 ( 1951) hydrogen bonds : angle 3.12730 ( 4946) metal coordination : bond 0.00342 ( 36) metal coordination : angle 2.62483 ( 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 167 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.179 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: A 106 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8558 (t70) REVERT: A 120 MET cc_start: 0.8611 (mmm) cc_final: 0.8302 (mmm) REVERT: C 38 ASN cc_start: 0.8264 (t0) cc_final: 0.8062 (t0) REVERT: E 97 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8356 (mt-10) REVERT: E 129 ARG cc_start: 0.9020 (tpp80) cc_final: 0.8624 (tpp80) REVERT: R 97 LEU cc_start: 0.9112 (pt) cc_final: 0.8347 (tp) REVERT: S 72 ASP cc_start: 0.6991 (t0) cc_final: 0.6203 (m-30) REVERT: S 95 LYS cc_start: 0.7953 (mmtt) cc_final: 0.6984 (pttt) REVERT: V 448 MET cc_start: 0.2418 (mmm) cc_final: 0.2142 (mmm) REVERT: V 506 MET cc_start: 0.4050 (ptt) cc_final: 0.1942 (mmp) REVERT: V 700 MET cc_start: 0.0569 (ptm) cc_final: -0.0620 (ttt) REVERT: U 548 MET cc_start: 0.1993 (ppp) cc_final: 0.0833 (mmt) REVERT: U 607 MET cc_start: 0.4773 (tmm) cc_final: 0.4392 (ppp) REVERT: U 880 MET cc_start: 0.1702 (ptp) cc_final: 0.0165 (ptp) REVERT: Y 607 MET cc_start: 0.3897 (tpt) cc_final: 0.3117 (ptt) REVERT: Y 674 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.5256 (tmm) REVERT: Y 761 MET cc_start: 0.0995 (tmm) cc_final: -0.2738 (ptm) REVERT: Y 880 MET cc_start: 0.5702 (ttp) cc_final: 0.5362 (ppp) outliers start: 24 outliers final: 16 residues processed: 156 average time/residue: 0.2011 time to fit residues: 52.4294 Evaluate side-chains 152 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 34 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 R residue 49 LEU Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 62 PHE Chi-restraints excluded: chain U residue 674 MET 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: 50.0000 chunk 71 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 337 optimal weight: 50.0000 chunk 169 optimal weight: 40.0000 chunk 28 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.106295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.072566 restraints weight = 301532.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.071723 restraints weight = 144246.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.072798 restraints weight = 102638.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.070877 restraints weight = 85251.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.070409 restraints weight = 72292.075| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38846 Z= 0.173 Angle : 0.565 11.052 55233 Z= 0.318 Chirality : 0.035 0.160 6116 Planarity : 0.004 0.073 4819 Dihedral : 29.082 177.452 10249 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.76 % Allowed : 9.26 % 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: 1.74 (0.16), residues: 2889 helix: 2.23 (0.13), residues: 1579 sheet: -0.13 (0.41), residues: 155 loop : -0.15 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 42 TYR 0.023 0.001 TYR T 80 PHE 0.028 0.001 PHE Q 104 TRP 0.011 0.001 TRP Y 23 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00378 (38810) covalent geometry : angle 0.55954 (55179) hydrogen bonds : bond 0.04710 ( 1951) hydrogen bonds : angle 3.24136 ( 4946) metal coordination : bond 0.00353 ( 36) metal coordination : angle 2.55465 ( 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 160 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.121 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: 0.9085 (OUTLIER) cc_final: 0.8625 (t70) REVERT: A 120 MET cc_start: 0.8658 (mmm) cc_final: 0.8356 (mmm) REVERT: C 38 ASN cc_start: 0.8425 (t0) cc_final: 0.8224 (t0) REVERT: E 97 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8384 (mt-10) REVERT: M 90 MET cc_start: 0.9366 (mmp) cc_final: 0.8662 (tmm) REVERT: R 97 LEU cc_start: 0.9059 (pt) cc_final: 0.8191 (tp) REVERT: S 72 ASP cc_start: 0.6766 (t0) cc_final: 0.6077 (m-30) REVERT: S 95 LYS cc_start: 0.7732 (mmtt) cc_final: 0.6761 (pttt) REVERT: V 448 MET cc_start: 0.2462 (mmm) cc_final: 0.2205 (mmm) REVERT: V 506 MET cc_start: 0.4527 (ptt) cc_final: 0.2478 (mmp) REVERT: V 700 MET cc_start: 0.0596 (ptm) cc_final: -0.0396 (ttt) REVERT: U 548 MET cc_start: 0.2022 (ppp) cc_final: 0.1096 (mmt) REVERT: U 607 MET cc_start: 0.5119 (tmm) cc_final: 0.4746 (ppp) REVERT: U 880 MET cc_start: 0.2968 (ptp) cc_final: 0.1369 (ptp) REVERT: Y 607 MET cc_start: 0.3834 (tpt) cc_final: 0.3146 (ptt) REVERT: Y 674 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.5354 (tmm) REVERT: Y 761 MET cc_start: 0.0774 (tmm) cc_final: -0.2786 (ptm) outliers start: 19 outliers final: 15 residues processed: 152 average time/residue: 0.2078 time to fit residues: 53.1059 Evaluate side-chains 148 residues out of total 2507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 34 LEU 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 R residue 49 LEU Chi-restraints excluded: chain R residue 61 PHE Chi-restraints excluded: chain S residue 101 THR Chi-restraints excluded: chain T residue 62 PHE Chi-restraints excluded: chain U residue 674 MET 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: 8.9990 chunk 320 optimal weight: 0.0370 chunk 329 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 217 optimal weight: 1.9990 chunk 170 optimal weight: 40.0000 chunk 45 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4430 r_free = 0.4430 target = 0.104523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.072099 restraints weight = 293260.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.070529 restraints weight = 154916.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.069927 restraints weight = 111124.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.069713 restraints weight = 85057.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.069568 restraints weight = 80414.415| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 38846 Z= 0.224 Angle : 0.622 23.049 55233 Z= 0.344 Chirality : 0.037 0.227 6116 Planarity : 0.004 0.072 4819 Dihedral : 29.449 177.164 10249 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.84 % Allowed : 9.50 % Favored : 89.66 % 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: 1.54 (0.16), residues: 2889 helix: 2.02 (0.13), residues: 1574 sheet: -0.08 (0.41), residues: 156 loop : -0.17 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 129 TYR 0.023 0.001 TYR T 80 PHE 0.041 0.001 PHE Q 104 TRP 0.011 0.001 TRP Z 674 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00492 (38810) covalent geometry : angle 0.61673 (55179) hydrogen bonds : bond 0.06136 ( 1951) hydrogen bonds : angle 3.54835 ( 4946) metal coordination : bond 0.00407 ( 36) metal coordination : angle 2.65153 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11271.91 seconds wall clock time: 192 minutes 9.94 seconds (11529.94 seconds total)