Starting phenix.real_space_refine on Sun Sep 13 09:30:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.map" model { file = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2026/7rdy_24427.cif" } resolution = 3.1 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= 0.012 sd= 1.106 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 84 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13561 2.51 5 N 3680 2.21 5 O 4351 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21846 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 178} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4570 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 934 Classifications: {'RNAv2': 44} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 4, 'rna3p': 39} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 127 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 3, 'ADP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 62.106 45.789 115.707 1.00 41.22 S ATOM 2495 SG CYS A 306 62.060 46.963 119.484 1.00 37.19 S ATOM 2527 SG CYS A 310 63.654 43.696 118.430 1.00 32.94 S ATOM 3935 SG CYS A 487 64.686 61.094 102.015 1.00 43.02 S ATOM 5188 SG CYS A 645 63.591 62.902 105.190 1.00 50.04 S ATOM 5194 SG CYS A 646 62.677 59.303 104.524 1.00 47.24 S ATOM 10896 SG CYS E 5 113.227 64.615 52.394 1.00 74.74 S ATOM 10917 SG CYS E 8 116.514 64.781 53.678 1.00 79.45 S ATOM 11055 SG CYS E 26 114.610 68.068 53.500 1.00 77.30 S ATOM 11076 SG CYS E 29 115.928 66.820 50.476 1.00 81.66 S ATOM 11241 SG CYS E 50 93.963 82.419 48.935 1.00 92.08 S ATOM 11271 SG CYS E 55 92.816 82.744 45.208 1.00101.11 S ATOM 11404 SG CYS E 72 95.446 85.167 46.649 1.00 94.15 S ATOM 10978 SG CYS E 16 105.749 67.409 45.042 1.00 76.77 S ATOM 10993 SG CYS E 19 106.018 64.069 43.240 1.00 80.95 S ATOM 15466 SG CYS F 5 61.179 64.236 54.799 1.00111.78 S ATOM 15487 SG CYS F 8 64.099 64.826 52.749 1.00115.39 S ATOM 15625 SG CYS F 26 63.355 67.628 54.682 1.00114.39 S ATOM 15646 SG CYS F 29 60.950 67.399 52.404 1.00118.98 S ATOM 15811 SG CYS F 50 54.005 80.679 74.901 1.00127.65 S ATOM 15841 SG CYS F 55 50.269 81.168 74.675 1.00134.09 S ATOM 15974 SG CYS F 72 52.344 83.796 73.213 1.00132.86 S ATOM 15548 SG CYS F 16 51.755 67.264 60.933 1.00113.89 S ATOM 15563 SG CYS F 19 50.479 64.123 59.031 1.00123.51 S Time building chain proxies: 4.68, per 1000 atoms: 0.21 Number of scatterers: 21846 At special positions: 0 Unit cell: (145.52, 150.87, 178.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 84 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4351 8.00 N 3680 7.00 C 13561 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: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 8 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 26 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 5 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 29 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 72 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 55 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 50 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E1002 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 19 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 25 sheets defined 42.9% alpha, 13.8% beta 34 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.781A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.530A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.757A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.570A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.549A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.832A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.507A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.755A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 318 removed outlier: 3.526A pdb=" N CYS A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.878A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.688A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.316A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.125A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.555A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.179A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.667A pdb=" N ASN A 600 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.753A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.741A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.778A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 874 through 902 removed outlier: 4.513A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 4.144A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.251A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.889A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 97 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.346A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'C' and resid 2 through 20 removed outlier: 3.750A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.645A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 3.744A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 32 through 82 Processing helix chain 'D' and resid 83 through 99 removed outlier: 3.926A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 3.952A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 removed outlier: 3.642A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR E 37 " --> pdb=" O HIS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 104 removed outlier: 3.580A pdb=" N THR E 104 " --> pdb=" O ASP E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 101 through 104' Processing helix chain 'E' and resid 105 through 112 Processing helix chain 'E' and resid 117 through 123 removed outlier: 4.035A pdb=" N ILE E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 146 removed outlier: 3.838A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 261 through 264 removed outlier: 4.445A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 264' Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.540A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 325 Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 432 Processing helix chain 'E' and resid 445 through 453 Processing helix chain 'E' and resid 489 through 502 removed outlier: 3.562A pdb=" N ILE E 493 " --> pdb=" O ASN E 489 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR E 501 " --> pdb=" O ARG E 497 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 502 " --> pdb=" O GLU E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 509 removed outlier: 3.517A pdb=" N TRP E 506 " --> pdb=" O ASN E 503 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 522 Processing helix chain 'E' and resid 534 through 537 removed outlier: 4.158A pdb=" N GLN E 537 " --> pdb=" O ASP E 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 534 through 537' Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 578 through 585 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.522A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 116 through 123 removed outlier: 4.180A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 3.557A pdb=" N SER F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'F' and resid 265 through 275 removed outlier: 3.715A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 310 through 324 removed outlier: 3.816A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 379 Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 430 Processing helix chain 'F' and resid 445 through 456 Processing helix chain 'F' and resid 489 through 499 Processing helix chain 'F' and resid 515 through 526 removed outlier: 3.533A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 526 " --> pdb=" O ALA F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 578 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.382A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 56 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.110A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 338 through 343 removed outlier: 9.345A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 338 through 343 Processing sheet with id=AA7, first strand: chain 'A' and resid 345 through 348 Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.397A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 removed outlier: 4.391A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.203A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.203A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.917A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 69 through 71 Processing sheet with id=AB8, first strand: chain 'E' and resid 152 through 159 removed outlier: 6.567A pdb=" N ARG E 155 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER E 166 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL E 157 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS E 164 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 355 through 359 removed outlier: 6.244A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 471 through 475 removed outlier: 7.143A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N TYR E 541 " --> pdb=" O LYS E 569 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY E 571 " --> pdb=" O TYR E 541 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR E 543 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU E 573 " --> pdb=" O TYR E 543 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE E 545 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE E 575 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR E 547 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC3, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.815A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AC5, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.067A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 347 through 348 removed outlier: 3.874A pdb=" N LYS F 347 " --> pdb=" O CYS F 330 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 305 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N THR F 367 " --> pdb=" O ALA F 393 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N HIS F 395 " --> pdb=" O THR F 367 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASP F 369 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL F 397 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY F 400 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU F 280 " --> pdb=" O GLY F 400 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 510 through 512 removed outlier: 6.253A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP F 542 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU F 573 " --> pdb=" O ASP F 542 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 544 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE F 575 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE F 546 " --> pdb=" O ILE F 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 846 hydrogen bonds defined for protein. 2343 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4558 1.32 - 1.45: 5643 1.45 - 1.57: 11836 1.57 - 1.69: 218 1.69 - 1.81: 220 Bond restraints: 22475 Sorted by residual: bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" F3 AF3 E1005 " pdb="AL AF3 E1005 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.794 -0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" F1 AF3 E1005 " pdb="AL AF3 E1005 " ideal model delta sigma weight residual 1.637 1.791 -0.154 2.00e-02 2.50e+03 5.96e+01 ... (remaining 22470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 30371 3.29 - 6.59: 507 6.59 - 9.88: 48 9.88 - 13.17: 4 13.17 - 16.46: 2 Bond angle restraints: 30932 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 138.16 -16.46 1.80e+00 3.09e-01 8.36e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 135.43 -13.73 1.80e+00 3.09e-01 5.82e+01 angle pdb=" C SER F 80 " pdb=" N PHE F 81 " pdb=" CA PHE F 81 " ideal model delta sigma weight residual 121.70 131.57 -9.87 1.80e+00 3.09e-01 3.01e+01 angle pdb=" N ALA E 454 " pdb=" CA ALA E 454 " pdb=" C ALA E 454 " ideal model delta sigma weight residual 114.56 108.81 5.75 1.27e+00 6.20e-01 2.05e+01 angle pdb=" N LYS F 345 " pdb=" CA LYS F 345 " pdb=" C LYS F 345 " ideal model delta sigma weight residual 114.39 108.06 6.33 1.45e+00 4.76e-01 1.91e+01 ... (remaining 30927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 12765 35.18 - 70.37: 438 70.37 - 105.55: 27 105.55 - 140.73: 6 140.73 - 175.91: 4 Dihedral angle restraints: 13240 sinusoidal: 5682 harmonic: 7558 Sorted by residual: dihedral pdb=" C4' C T 6 " pdb=" C3' C T 6 " pdb=" C2' C T 6 " pdb=" C1' C T 6 " ideal model delta sinusoidal sigma weight residual 36.34 -38.78 75.12 1 3.10e+00 1.04e-01 7.42e+02 dihedral pdb=" C4' A P 35 " pdb=" C3' A P 35 " pdb=" C2' A P 35 " pdb=" C1' A P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.09 72.44 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" CA SER D 31 " pdb=" C SER D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta harmonic sigma weight residual -180.00 -49.12 -130.88 0 5.00e+00 4.00e-02 6.85e+02 ... (remaining 13237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.041: 3602 1.041 - 2.081: 0 2.081 - 3.122: 0 3.122 - 4.163: 0 4.163 - 5.203: 2 Chirality restraints: 3604 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.77 -5.20 2.00e-01 2.50e+01 6.77e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.63 5.17 2.00e-01 2.50e+01 6.67e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.83 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 3601 not shown) Planarity restraints: 3630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 491 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 407 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO E 408 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 408 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 408 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 444 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO F 445 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 445 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 445 " -0.041 5.00e-02 4.00e+02 ... (remaining 3627 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 195 2.50 - 3.10: 15451 3.10 - 3.70: 34567 3.70 - 4.30: 48997 4.30 - 4.90: 81073 Nonbonded interactions: 180283 Sorted by model distance: nonbonded pdb=" N SER F 289 " pdb="MG MG F1004 " model vdw 1.894 2.250 nonbonded pdb=" OG SER E 289 " pdb="MG MG E1004 " model vdw 1.980 2.170 nonbonded pdb=" OG SER F 289 " pdb="MG MG F1004 " model vdw 2.019 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1B ADP A1004 " model vdw 2.053 2.170 nonbonded pdb=" O3B ADP E1003 " pdb="MG MG E1004 " model vdw 2.063 2.170 ... (remaining 180278 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 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 474 or (resid 475 through 476 and (name N or nam \ e CA or name C or name O or name CB )) or resid 477 through 1005)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 26.010 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.015 0.163 22507 Z= 0.654 Angle : 1.086 17.417 30958 Z= 0.557 Chirality : 0.142 5.203 3604 Planarity : 0.006 0.080 3630 Dihedral : 16.875 175.913 8366 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 10.18 % Allowed : 12.14 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.87 (0.15), residues: 2541 helix: -1.74 (0.14), residues: 1037 sheet: -1.25 (0.28), residues: 328 loop : -2.18 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.031 0.003 TYR A 788 PHE 0.029 0.003 PHE B 147 TRP 0.021 0.003 TRP A 916 HIS 0.011 0.002 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.01528 / 0.65 (22475) covalent geometry : angle 1.06547 / 0.56 (30932) hydrogen bonds : bond 0.14784 / 9.67 ( 914) hydrogen bonds : angle 6.68592 / 4.64 ( 2505) metal coordination : bond 0.02712 / 1.74 ( 32) metal coordination : angle 7.27926 / 5.02 ( 26) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 209 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8188 (t80) cc_final: 0.7925 (t80) REVERT: A 388 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8521 (tp) REVERT: A 477 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7878 (t70) REVERT: A 723 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 815 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: A 891 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 911 ASN cc_start: 0.7810 (t0) cc_final: 0.6718 (t0) REVERT: B 62 MET cc_start: 0.8121 (tmm) cc_final: 0.7733 (tmm) REVERT: B 65 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 174 MET cc_start: 0.8307 (tpp) cc_final: 0.8104 (tpt) REVERT: C 69 ASN cc_start: 0.7905 (t0) cc_final: 0.7656 (t0) REVERT: D 12 TYR cc_start: 0.7070 (t80) cc_final: 0.6739 (t80) REVERT: D 32 GLU cc_start: 0.6369 (mm-30) cc_final: 0.6088 (mm-30) REVERT: D 55 MET cc_start: 0.8576 (tpp) cc_final: 0.8311 (tpp) REVERT: D 80 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: D 185 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8149 (mt) REVERT: E 105 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7992 (t0) REVERT: E 122 LEU cc_start: 0.8922 (tp) cc_final: 0.8421 (tp) REVERT: E 197 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: E 227 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8084 (tt) REVERT: E 320 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8039 (mtmt) REVERT: E 411 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8699 (mm) REVERT: E 510 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8300 (p) REVERT: E 562 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (t0) REVERT: F 95 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7702 (p0) REVERT: F 107 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6682 (t0) REVERT: F 304 ILE cc_start: 0.5950 (OUTLIER) cc_final: 0.5748 (mp) REVERT: F 576 MET cc_start: 0.2636 (mmm) cc_final: 0.2288 (mmt) REVERT: F 590 LEU cc_start: -0.0578 (OUTLIER) cc_final: -0.0959 (mt) outliers start: 224 outliers final: 112 residues processed: 417 average time/residue: 0.1529 time to fit residues: 100.4265 Evaluate side-chains 285 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 156 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 51 ASN E 311 HIS E 361 ASN E 404 GLN E 464 HIS ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.136113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094166 restraints weight = 35926.718| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.49 r_work: 0.3273 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22507 Z= 0.151 Angle : 0.726 16.038 30958 Z= 0.340 Chirality : 0.049 0.664 3604 Planarity : 0.005 0.073 3630 Dihedral : 13.079 171.509 3974 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.82 % Allowed : 15.95 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 2541 helix: -0.29 (0.16), residues: 1034 sheet: -1.24 (0.29), residues: 317 loop : -1.79 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 567 TYR 0.013 0.001 TYR E 224 PHE 0.023 0.001 PHE A 652 TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (22475) covalent geometry : angle 0.71359 / 0.34 (30932) hydrogen bonds : bond 0.04441 / 2.77 ( 914) hydrogen bonds : angle 4.59099 / 3.15 ( 2505) metal coordination : bond 0.00951 / 0.56 ( 32) metal coordination : angle 4.64240 / 3.21 ( 26) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 172 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7852 (tp40) cc_final: 0.7561 (tp-100) REVERT: A 105 ARG cc_start: 0.7897 (tpp80) cc_final: 0.7346 (tpp80) REVERT: A 790 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8173 (t0) REVERT: A 891 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 62 MET cc_start: 0.8260 (tmm) cc_final: 0.7931 (tmm) REVERT: B 69 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 171 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8596 (mm-30) REVERT: C 34 GLN cc_start: 0.8503 (tp40) cc_final: 0.7942 (tp40) REVERT: C 69 ASN cc_start: 0.7926 (t0) cc_final: 0.7705 (t0) REVERT: D 75 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7952 (tpp80) REVERT: D 180 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8689 (mm) REVERT: E 163 LEU cc_start: 0.8596 (mt) cc_final: 0.8094 (mt) REVERT: E 227 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8347 (tt) REVERT: E 260 ASP cc_start: 0.8801 (p0) cc_final: 0.8418 (t0) REVERT: E 474 MET cc_start: 0.6113 (ptp) cc_final: 0.5858 (ppp) REVERT: E 562 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8301 (t0) REVERT: F 546 PHE cc_start: 0.6929 (t80) cc_final: 0.6639 (t80) outliers start: 106 outliers final: 66 residues processed: 273 average time/residue: 0.1619 time to fit residues: 68.5685 Evaluate side-chains 219 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 148 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 210 GLN A 611 ASN B 158 GLN E 270 GLN F 88 GLN F 349 ASN F 470 GLN F 503 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095299 restraints weight = 35883.699| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.49 r_work: 0.3295 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22507 Z= 0.127 Angle : 0.637 13.883 30958 Z= 0.301 Chirality : 0.045 0.465 3604 Planarity : 0.004 0.071 3630 Dihedral : 11.207 170.798 3852 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.23 % Allowed : 16.68 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.16), residues: 2541 helix: 0.36 (0.16), residues: 1043 sheet: -1.05 (0.29), residues: 317 loop : -1.63 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 178 TYR 0.012 0.001 TYR E 224 PHE 0.017 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.003 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (22475) covalent geometry : angle 0.62697 / 0.30 (30932) hydrogen bonds : bond 0.03935 / 2.43 ( 914) hydrogen bonds : angle 4.12740 / 2.82 ( 2505) metal coordination : bond 0.00748 / 0.45 ( 32) metal coordination : angle 4.02719 / 2.77 ( 26) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 164 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8012 (tp40) cc_final: 0.7743 (tp40) REVERT: A 105 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7367 (tpp80) REVERT: A 450 ILE cc_start: 0.8942 (tp) cc_final: 0.8537 (tp) REVERT: B 62 MET cc_start: 0.8379 (tmm) cc_final: 0.8156 (tmm) REVERT: B 69 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 70 MET cc_start: 0.8147 (ttm) cc_final: 0.7935 (mtt) REVERT: B 171 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8655 (mm-30) REVERT: C 34 GLN cc_start: 0.8592 (tp40) cc_final: 0.8165 (tp40) REVERT: C 69 ASN cc_start: 0.8049 (t0) cc_final: 0.7795 (t0) REVERT: E 9 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8324 (t0) REVERT: E 227 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8390 (tt) REVERT: E 562 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8151 (t0) REVERT: F 345 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6481 (mtmm) REVERT: F 498 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5013 (pt0) outliers start: 93 outliers final: 55 residues processed: 247 average time/residue: 0.1568 time to fit residues: 61.4137 Evaluate side-chains 208 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 148 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain E residue 576 MET Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 345 LYS Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 181 optimal weight: 0.0270 chunk 214 optimal weight: 30.0000 chunk 77 optimal weight: 0.6980 chunk 212 optimal weight: 0.3980 chunk 218 optimal weight: 4.9990 chunk 242 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 822 GLN C 19 GLN E 464 HIS E 519 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.138254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096415 restraints weight = 35988.715| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.51 r_work: 0.3287 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22507 Z= 0.105 Angle : 0.605 13.832 30958 Z= 0.284 Chirality : 0.043 0.359 3604 Planarity : 0.004 0.068 3630 Dihedral : 10.648 177.441 3816 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.27 % Allowed : 17.45 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.17), residues: 2541 helix: 0.72 (0.17), residues: 1040 sheet: -0.85 (0.30), residues: 312 loop : -1.47 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 212 TYR 0.011 0.001 TYR E 224 PHE 0.015 0.001 PHE F 561 TRP 0.009 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (22475) covalent geometry : angle 0.59500 / 0.28 (30932) hydrogen bonds : bond 0.03585 / 2.17 ( 914) hydrogen bonds : angle 3.89501 / 2.66 ( 2505) metal coordination : bond 0.00525 / 0.31 ( 32) metal coordination : angle 3.77500 / 2.60 ( 26) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 171 time to evaluate : 0.822 Fit side-chains REVERT: A 5 GLN cc_start: 0.7766 (tp40) cc_final: 0.7492 (tp40) REVERT: A 77 PHE cc_start: 0.7830 (t80) cc_final: 0.7581 (t80) REVERT: A 105 ARG cc_start: 0.7882 (tpp80) cc_final: 0.7187 (tpp80) REVERT: A 110 MET cc_start: 0.8405 (mmt) cc_final: 0.7978 (mmm) REVERT: A 450 ILE cc_start: 0.8954 (tp) cc_final: 0.8625 (tp) REVERT: A 463 MET cc_start: 0.8299 (ttt) cc_final: 0.7912 (ttt) REVERT: B 51 ARG cc_start: 0.8143 (mmm-85) cc_final: 0.7919 (mtm-85) REVERT: B 55 MET cc_start: 0.6504 (tpt) cc_final: 0.6074 (tpt) REVERT: B 62 MET cc_start: 0.8305 (tmm) cc_final: 0.8086 (tmm) REVERT: B 67 MET cc_start: 0.7511 (tpp) cc_final: 0.7307 (tpp) REVERT: B 69 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 70 MET cc_start: 0.8044 (ttm) cc_final: 0.7830 (mtt) REVERT: B 171 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8596 (mm-30) REVERT: C 34 GLN cc_start: 0.8465 (tp40) cc_final: 0.7901 (tp40) REVERT: C 69 ASN cc_start: 0.8064 (t0) cc_final: 0.7805 (t0) REVERT: E 163 LEU cc_start: 0.8518 (mt) cc_final: 0.8121 (mt) REVERT: E 227 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8409 (tt) REVERT: E 262 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: E 562 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8185 (t0) REVERT: F 531 GLN cc_start: 0.6590 (pp30) cc_final: 0.5866 (tp40) outliers start: 72 outliers final: 53 residues processed: 231 average time/residue: 0.1649 time to fit residues: 59.4155 Evaluate side-chains 206 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 18 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 270 GLN E 404 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 HIS F 404 GLN F 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.129998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087703 restraints weight = 36333.984| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.48 r_work: 0.3120 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 22507 Z= 0.357 Angle : 0.775 13.896 30958 Z= 0.374 Chirality : 0.051 0.361 3604 Planarity : 0.005 0.069 3630 Dihedral : 10.730 174.921 3805 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.23 % Allowed : 17.50 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2541 helix: 0.33 (0.16), residues: 1038 sheet: -0.89 (0.29), residues: 319 loop : -1.61 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 443 TYR 0.029 0.002 TYR A 788 PHE 0.022 0.002 PHE E 373 TRP 0.010 0.002 TRP E 114 HIS 0.009 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.36 (22475) covalent geometry : angle 0.76256 / 0.37 (30932) hydrogen bonds : bond 0.04888 / 3.20 ( 914) hydrogen bonds : angle 4.44074 / 3.07 ( 2505) metal coordination : bond 0.01895 / 1.23 ( 32) metal coordination : angle 4.77791 / 3.26 ( 26) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 156 time to evaluate : 0.728 Fit side-chains REVERT: A 5 GLN cc_start: 0.7880 (tp40) cc_final: 0.7546 (tp-100) REVERT: A 105 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7201 (tpp80) REVERT: A 110 MET cc_start: 0.8463 (mmt) cc_final: 0.8014 (mmm) REVERT: A 160 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8400 (ptmm) REVERT: A 857 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: B 51 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7917 (mtm180) REVERT: B 62 MET cc_start: 0.8615 (tmm) cc_final: 0.8337 (tmm) REVERT: B 69 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 70 MET cc_start: 0.8138 (ttm) cc_final: 0.7875 (mtt) REVERT: B 171 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8876 (mt-10) REVERT: C 69 ASN cc_start: 0.8125 (t0) cc_final: 0.7869 (t0) REVERT: E 9 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8185 (t0) REVERT: E 163 LEU cc_start: 0.8593 (mt) cc_final: 0.8335 (mt) REVERT: E 227 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8405 (tt) REVERT: E 262 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: E 474 MET cc_start: 0.7058 (ppp) cc_final: 0.6690 (ppp) REVERT: E 562 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8534 (t0) REVERT: F 474 MET cc_start: 0.1599 (OUTLIER) cc_final: 0.1147 (mmm) REVERT: F 498 GLU cc_start: 0.5696 (OUTLIER) cc_final: 0.5009 (pt0) REVERT: F 576 MET cc_start: 0.2629 (mmp) cc_final: 0.2346 (mmm) outliers start: 93 outliers final: 67 residues processed: 243 average time/residue: 0.1574 time to fit residues: 60.0237 Evaluate side-chains 223 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 148 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 232 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN E 270 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092683 restraints weight = 35796.879| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.50 r_work: 0.3253 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22507 Z= 0.136 Angle : 0.624 13.859 30958 Z= 0.297 Chirality : 0.044 0.332 3604 Planarity : 0.004 0.067 3630 Dihedral : 10.409 176.120 3800 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.68 % Allowed : 19.09 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2541 helix: 0.71 (0.17), residues: 1033 sheet: -0.84 (0.30), residues: 301 loop : -1.44 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.011 0.001 TYR A 884 PHE 0.022 0.001 PHE F 262 TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (22475) covalent geometry : angle 0.61141 / 0.30 (30932) hydrogen bonds : bond 0.03796 / 2.35 ( 914) hydrogen bonds : angle 4.02962 / 2.77 ( 2505) metal coordination : bond 0.00746 / 0.45 ( 32) metal coordination : angle 4.26455 / 3.01 ( 26) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.641 Fit side-chains REVERT: A 5 GLN cc_start: 0.7868 (tp40) cc_final: 0.7624 (tp40) REVERT: A 77 PHE cc_start: 0.7961 (t80) cc_final: 0.7752 (t80) REVERT: A 105 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7321 (tpp80) REVERT: A 110 MET cc_start: 0.8448 (mmt) cc_final: 0.7913 (mmm) REVERT: A 160 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8399 (ptmm) REVERT: A 450 ILE cc_start: 0.8973 (tp) cc_final: 0.8705 (tp) REVERT: A 463 MET cc_start: 0.8562 (ttt) cc_final: 0.8129 (ttt) REVERT: B 51 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7978 (mtm-85) REVERT: B 55 MET cc_start: 0.6491 (tpt) cc_final: 0.6074 (tpt) REVERT: B 69 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 70 MET cc_start: 0.8139 (ttm) cc_final: 0.7885 (mtt) REVERT: B 171 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8913 (mt-10) REVERT: C 34 GLN cc_start: 0.8440 (tp40) cc_final: 0.8002 (tp40) REVERT: C 38 ASP cc_start: 0.8034 (m-30) cc_final: 0.7324 (m-30) REVERT: C 69 ASN cc_start: 0.8118 (t0) cc_final: 0.7876 (t0) REVERT: E 9 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8212 (t0) REVERT: E 163 LEU cc_start: 0.8622 (mt) cc_final: 0.8415 (mt) REVERT: E 227 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8398 (tt) REVERT: E 474 MET cc_start: 0.6976 (ppp) cc_final: 0.6609 (ppp) REVERT: E 562 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8316 (t0) REVERT: F 95 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7937 (p0) REVERT: F 474 MET cc_start: 0.2006 (mmt) cc_final: 0.1562 (mmm) REVERT: F 498 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.4913 (pt0) outliers start: 59 outliers final: 44 residues processed: 213 average time/residue: 0.1714 time to fit residues: 56.1470 Evaluate side-chains 201 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 234 optimal weight: 0.0970 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 ASN ** 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 = 0.3989 r_free = 0.3989 target = 0.135065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.093342 restraints weight = 35896.913| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.50 r_work: 0.3268 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22507 Z= 0.130 Angle : 0.606 13.802 30958 Z= 0.286 Chirality : 0.043 0.324 3604 Planarity : 0.004 0.067 3630 Dihedral : 10.082 177.673 3794 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.09 % Allowed : 18.64 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2541 helix: 0.89 (0.17), residues: 1036 sheet: -0.68 (0.30), residues: 303 loop : -1.36 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 178 TYR 0.012 0.001 TYR A 748 PHE 0.023 0.001 PHE F 262 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (22475) covalent geometry : angle 0.59433 / 0.29 (30932) hydrogen bonds : bond 0.03702 / 2.28 ( 914) hydrogen bonds : angle 3.91319 / 2.69 ( 2505) metal coordination : bond 0.00665 / 0.41 ( 32) metal coordination : angle 4.10828 / 2.90 ( 26) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 151 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7904 (tp40) cc_final: 0.7669 (tp40) REVERT: A 105 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7188 (tpp80) REVERT: A 110 MET cc_start: 0.8419 (mmt) cc_final: 0.7970 (mmm) REVERT: A 160 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8387 (ptmm) REVERT: A 450 ILE cc_start: 0.8900 (tp) cc_final: 0.8621 (tp) REVERT: A 463 MET cc_start: 0.8535 (ttt) cc_final: 0.8133 (ttt) REVERT: A 761 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.7984 (m-30) REVERT: A 906 MET cc_start: 0.8495 (mtm) cc_final: 0.8101 (pmm) REVERT: B 55 MET cc_start: 0.6459 (tpt) cc_final: 0.6039 (tpt) REVERT: B 69 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 70 MET cc_start: 0.8107 (ttm) cc_final: 0.7891 (mtt) REVERT: C 34 GLN cc_start: 0.8479 (tp40) cc_final: 0.8032 (tp40) REVERT: C 69 ASN cc_start: 0.8122 (t0) cc_final: 0.7846 (t0) REVERT: E 9 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8245 (t0) REVERT: E 163 LEU cc_start: 0.8534 (mt) cc_final: 0.8274 (mt) REVERT: E 227 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8431 (tt) REVERT: E 474 MET cc_start: 0.6982 (ppp) cc_final: 0.6591 (ppp) REVERT: E 562 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8371 (t0) REVERT: F 95 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7943 (p0) REVERT: F 474 MET cc_start: 0.1736 (mmt) cc_final: 0.1222 (mmm) REVERT: F 498 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.4790 (pt0) REVERT: F 531 GLN cc_start: 0.6700 (pp30) cc_final: 0.5728 (tp40) outliers start: 68 outliers final: 49 residues processed: 210 average time/residue: 0.1661 time to fit residues: 54.2574 Evaluate side-chains 201 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 145 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 109 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 217 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN C 19 GLN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 ASN ** 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 = 0.3994 r_free = 0.3994 target = 0.135529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093724 restraints weight = 35694.840| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.50 r_work: 0.3242 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22507 Z= 0.125 Angle : 0.599 13.757 30958 Z= 0.282 Chirality : 0.044 0.323 3604 Planarity : 0.004 0.066 3630 Dihedral : 9.940 177.280 3792 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.05 % Allowed : 18.95 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2541 helix: 1.00 (0.17), residues: 1035 sheet: -0.59 (0.30), residues: 301 loop : -1.28 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.011 0.001 TYR A 788 PHE 0.016 0.001 PHE F 262 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (22475) covalent geometry : angle 0.58751 / 0.28 (30932) hydrogen bonds : bond 0.03629 / 2.23 ( 914) hydrogen bonds : angle 3.86156 / 2.65 ( 2505) metal coordination : bond 0.00618 / 0.38 ( 32) metal coordination : angle 4.03250 / 2.88 ( 26) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 154 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7792 (tp40) cc_final: 0.7511 (tp40) REVERT: A 105 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7172 (tpp80) REVERT: A 110 MET cc_start: 0.8342 (mmt) cc_final: 0.7906 (mmm) REVERT: A 160 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8377 (ptmm) REVERT: A 450 ILE cc_start: 0.8887 (tp) cc_final: 0.8636 (tp) REVERT: A 463 MET cc_start: 0.8568 (ttt) cc_final: 0.8172 (ttt) REVERT: A 761 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 906 MET cc_start: 0.8502 (mtm) cc_final: 0.8127 (pmm) REVERT: B 55 MET cc_start: 0.6442 (tpt) cc_final: 0.5944 (tpt) REVERT: B 69 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 70 MET cc_start: 0.8081 (ttm) cc_final: 0.7856 (mtt) REVERT: B 171 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8767 (mm-30) REVERT: C 34 GLN cc_start: 0.8381 (tp40) cc_final: 0.7954 (tp40) REVERT: C 69 ASN cc_start: 0.8101 (t0) cc_final: 0.7835 (t0) REVERT: E 9 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8186 (t0) REVERT: E 163 LEU cc_start: 0.8482 (mt) cc_final: 0.8241 (mt) REVERT: E 227 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8417 (tt) REVERT: E 474 MET cc_start: 0.6899 (ppp) cc_final: 0.6466 (ppp) REVERT: E 513 SER cc_start: 0.9208 (t) cc_final: 0.8680 (p) REVERT: E 562 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8277 (t0) REVERT: F 95 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7936 (p0) REVERT: F 474 MET cc_start: 0.1546 (mmt) cc_final: 0.1004 (mmm) REVERT: F 498 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4427 (pt0) REVERT: F 531 GLN cc_start: 0.6751 (pp30) cc_final: 0.5763 (tp40) outliers start: 67 outliers final: 47 residues processed: 212 average time/residue: 0.1570 time to fit residues: 52.0735 Evaluate side-chains 201 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 140 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 158 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 178 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 51 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.133411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091475 restraints weight = 36081.821| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.51 r_work: 0.3227 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22507 Z= 0.190 Angle : 0.637 13.752 30958 Z= 0.301 Chirality : 0.045 0.334 3604 Planarity : 0.004 0.067 3630 Dihedral : 9.952 175.416 3791 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.68 % Allowed : 19.05 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.17), residues: 2541 helix: 0.93 (0.17), residues: 1037 sheet: -0.50 (0.30), residues: 301 loop : -1.29 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.016 0.001 TYR A 788 PHE 0.018 0.001 PHE F 262 TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (22475) covalent geometry : angle 0.62470 / 0.30 (30932) hydrogen bonds : bond 0.03922 / 2.47 ( 914) hydrogen bonds : angle 3.96092 / 2.73 ( 2505) metal coordination : bond 0.01017 / 0.63 ( 32) metal coordination : angle 4.28542 / 3.04 ( 26) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7905 (tp40) cc_final: 0.7656 (tp-100) REVERT: A 105 ARG cc_start: 0.8135 (tpp80) cc_final: 0.7223 (tpp80) REVERT: A 110 MET cc_start: 0.8370 (mmt) cc_final: 0.7951 (mmm) REVERT: A 160 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8402 (ptmm) REVERT: A 450 ILE cc_start: 0.8962 (tp) cc_final: 0.8661 (tp) REVERT: A 761 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: A 791 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8544 (m-40) REVERT: B 55 MET cc_start: 0.6466 (tpt) cc_final: 0.5955 (tpt) REVERT: B 69 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 70 MET cc_start: 0.8112 (ttm) cc_final: 0.7881 (mtt) REVERT: B 171 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8814 (mm-30) REVERT: C 34 GLN cc_start: 0.8536 (tp40) cc_final: 0.8104 (tp40) REVERT: C 69 ASN cc_start: 0.8170 (t0) cc_final: 0.7888 (t0) REVERT: E 9 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8234 (t0) REVERT: E 163 LEU cc_start: 0.8524 (mt) cc_final: 0.8284 (mt) REVERT: E 227 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8479 (tt) REVERT: E 474 MET cc_start: 0.6986 (ppp) cc_final: 0.6586 (ppp) REVERT: F 95 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7978 (p0) REVERT: F 474 MET cc_start: 0.1698 (mmt) cc_final: 0.1193 (mmm) REVERT: F 498 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.4464 (pt0) REVERT: F 531 GLN cc_start: 0.6795 (pp30) cc_final: 0.5797 (tp40) outliers start: 59 outliers final: 45 residues processed: 201 average time/residue: 0.1673 time to fit residues: 52.1763 Evaluate side-chains 198 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 256 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 133 optimal weight: 0.1980 chunk 158 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 51 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.135301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093277 restraints weight = 35781.574| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.60 r_work: 0.3197 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22507 Z= 0.110 Angle : 0.592 13.666 30958 Z= 0.278 Chirality : 0.043 0.318 3604 Planarity : 0.004 0.066 3630 Dihedral : 9.772 174.626 3789 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.09 % Allowed : 19.55 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2541 helix: 1.15 (0.17), residues: 1033 sheet: -0.59 (0.30), residues: 303 loop : -1.20 (0.18), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 178 TYR 0.013 0.001 TYR B 71 PHE 0.021 0.001 PHE A 340 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (22475) covalent geometry : angle 0.58037 / 0.28 (30932) hydrogen bonds : bond 0.03484 / 2.13 ( 914) hydrogen bonds : angle 3.78744 / 2.60 ( 2505) metal coordination : bond 0.00544 / 0.32 ( 32) metal coordination : angle 4.07026 / 2.91 ( 26) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7657 (tp40) cc_final: 0.7321 (tp40) REVERT: A 105 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7143 (tpp80) REVERT: A 110 MET cc_start: 0.8129 (mmt) cc_final: 0.7706 (mmm) REVERT: A 160 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8382 (ptmm) REVERT: A 450 ILE cc_start: 0.8787 (tp) cc_final: 0.8564 (tp) REVERT: A 633 MET cc_start: 0.8826 (ttp) cc_final: 0.8479 (ttp) REVERT: A 791 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: A 906 MET cc_start: 0.8563 (mtm) cc_final: 0.8069 (pmm) REVERT: B 55 MET cc_start: 0.6313 (tpt) cc_final: 0.5835 (tpt) REVERT: B 65 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8314 (pt0) REVERT: B 69 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 70 MET cc_start: 0.7986 (ttm) cc_final: 0.7746 (mtt) REVERT: B 171 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8681 (mm-30) REVERT: C 34 GLN cc_start: 0.8259 (tp40) cc_final: 0.7800 (tp40) REVERT: C 69 ASN cc_start: 0.8066 (t0) cc_final: 0.7817 (t0) REVERT: E 9 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8245 (t0) REVERT: E 163 LEU cc_start: 0.8376 (mt) cc_final: 0.8142 (mt) REVERT: E 178 ARG cc_start: 0.8798 (ptt90) cc_final: 0.8428 (ptt90) REVERT: E 227 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8398 (tt) REVERT: E 474 MET cc_start: 0.6803 (ppp) cc_final: 0.6332 (ppp) REVERT: E 513 SER cc_start: 0.9225 (t) cc_final: 0.8635 (p) REVERT: F 474 MET cc_start: 0.1441 (mmt) cc_final: 0.0922 (mmm) REVERT: F 498 GLU cc_start: 0.5282 (OUTLIER) cc_final: 0.4445 (pt0) REVERT: F 531 GLN cc_start: 0.6612 (pp30) cc_final: 0.5695 (tp40) REVERT: F 532 THR cc_start: 0.7677 (t) cc_final: 0.6959 (p) outliers start: 46 outliers final: 36 residues processed: 194 average time/residue: 0.1563 time to fit residues: 47.4722 Evaluate side-chains 189 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 219 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 51 ASN ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.133305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091243 restraints weight = 35795.952| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.59 r_work: 0.3164 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22507 Z= 0.155 Angle : 0.613 13.689 30958 Z= 0.289 Chirality : 0.044 0.326 3604 Planarity : 0.004 0.066 3630 Dihedral : 9.706 172.627 3789 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.05 % Allowed : 19.82 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2541 helix: 1.12 (0.17), residues: 1031 sheet: -0.43 (0.31), residues: 293 loop : -1.22 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.017 0.001 TYR B 71 PHE 0.021 0.001 PHE A 340 TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (22475) covalent geometry : angle 0.60159 / 0.29 (30932) hydrogen bonds : bond 0.03717 / 2.33 ( 914) hydrogen bonds : angle 3.85267 / 2.65 ( 2505) metal coordination : bond 0.00758 / 0.48 ( 32) metal coordination : angle 4.14809 / 2.95 ( 26) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7649.19 seconds wall clock time: 131 minutes 20.07 seconds (7880.07 seconds total)