Starting phenix.real_space_refine on Fri Sep 19 02:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rdy_24427/09_2025/7rdy_24427.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rdy_24427/09_2025/7rdy_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2025/7rdy_24427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2025/7rdy_24427.map" model { file = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2025/7rdy_24427.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rdy_24427/09_2025/7rdy_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: {'RNA': 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: {'RNA': 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: 26 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: 5.37, per 1000 atoms: 0.25 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: 2.01 Conformation dependent library (CDL) restraints added in 960.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.40 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: 5.02 Time building geometry restraints manager: 2.65 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: 30432 3.29 - 6.59: 446 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=" O3' C P 24 " pdb=" C3' C P 24 " pdb=" C2' C P 24 " ideal model delta sigma weight residual 113.70 120.53 -6.83 1.50e+00 4.44e-01 2.07e+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 ... (remaining 30927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13085 35.18 - 70.37: 536 70.37 - 105.55: 71 105.55 - 140.73: 13 140.73 - 175.91: 4 Dihedral angle restraints: 13709 sinusoidal: 6151 harmonic: 7558 Sorted by residual: 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 dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 140.29 39.71 0 5.00e+00 4.00e-02 6.31e+01 dihedral pdb=" CA LYS F 189 " pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta harmonic sigma weight residual 0.00 38.22 -38.22 0 5.00e+00 4.00e-02 5.84e+01 ... (remaining 13706 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.310 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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= 0.656 Angle : 1.058 17.417 30958 Z= 0.556 Chirality : 0.138 5.203 3604 Planarity : 0.006 0.080 3630 Dihedral : 18.955 175.913 8835 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 aren 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 covalent geometry : bond 0.01527 (22475) covalent geometry : angle 1.03761 (30932) hydrogen bonds : bond 0.14784 ( 914) hydrogen bonds : angle 6.68592 ( 2505) metal coordination : bond 0.02712 ( 32) metal coordination : angle 7.27926 ( 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 : 0.833 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: 0.8542 (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: 0.1618 time to fit residues: 105.2141 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 : 0.822 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 611 ASN E 51 ASN E 311 HIS E 404 GLN E 464 HIS F 257 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.136214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094218 restraints weight = 35964.668| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.51 r_work: 0.3278 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1488 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= 0.134 Angle : 0.632 13.849 30958 Z= 0.317 Chirality : 0.041 0.244 3604 Planarity : 0.005 0.073 3630 Dihedral : 16.352 171.089 4443 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.91 % Allowed : 16.00 % Favored : 79.09 % 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 aren not related in a simple way. whole: -1.65 (0.16), residues: 2541 helix: -0.26 (0.16), residues: 1034 sheet: -1.23 (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 E 427 TYR 0.013 0.001 TYR B 138 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 covalent geometry : bond 0.00293 (22475) covalent geometry : angle 0.61860 (30932) hydrogen bonds : bond 0.04375 ( 914) hydrogen bonds : angle 4.57344 ( 2505) metal coordination : bond 0.00916 ( 32) metal coordination : angle 4.58590 ( 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 280 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 172 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7881 (tp40) cc_final: 0.7592 (tp-100) REVERT: A 105 ARG cc_start: 0.7932 (tpp80) cc_final: 0.7400 (tpp80) REVERT: A 790 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 891 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 62 MET cc_start: 0.8250 (tmm) cc_final: 0.7919 (tmm) REVERT: B 69 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 171 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8607 (mm-30) REVERT: C 34 GLN cc_start: 0.8504 (tp40) cc_final: 0.8062 (tp40) REVERT: C 69 ASN cc_start: 0.7934 (t0) cc_final: 0.7714 (t0) REVERT: D 75 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7947 (tpp80) REVERT: D 180 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8698 (mm) REVERT: E 163 LEU cc_start: 0.8589 (mt) cc_final: 0.8087 (mt) REVERT: E 227 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8346 (tt) REVERT: E 260 ASP cc_start: 0.8784 (p0) cc_final: 0.8402 (t0) REVERT: E 474 MET cc_start: 0.6125 (ptp) cc_final: 0.5872 (ppp) REVERT: E 562 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8304 (t0) REVERT: F 274 MET cc_start: 0.8687 (mmp) cc_final: 0.8428 (mmp) REVERT: F 531 GLN cc_start: 0.6662 (pp30) cc_final: 0.6080 (mt0) REVERT: F 546 PHE cc_start: 0.6912 (t80) cc_final: 0.6634 (t80) outliers start: 108 outliers final: 67 residues processed: 275 average time/residue: 0.1695 time to fit residues: 71.9846 Evaluate side-chains 225 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 153 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 759 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 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 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 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 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: 0.0670 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 210 GLN B 158 GLN E 464 HIS E 519 ASN F 88 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4006 r_free = 0.4006 target = 0.136335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.094434 restraints weight = 35851.259| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.49 r_work: 0.3281 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22507 Z= 0.129 Angle : 0.587 13.856 30958 Z= 0.290 Chirality : 0.040 0.361 3604 Planarity : 0.004 0.070 3630 Dihedral : 15.219 170.386 4319 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.36 % Allowed : 16.59 % Favored : 79.05 % 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 aren not related in a simple way. whole: -1.18 (0.16), residues: 2541 helix: 0.29 (0.16), residues: 1042 sheet: -1.04 (0.29), residues: 313 loop : -1.68 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.012 0.001 TYR E 224 PHE 0.018 0.001 PHE A 652 TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00287 (22475) covalent geometry : angle 0.57463 (30932) hydrogen bonds : bond 0.04006 ( 914) hydrogen bonds : angle 4.20457 ( 2505) metal coordination : bond 0.00808 ( 32) metal coordination : angle 4.13769 ( 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 260 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 164 time to evaluate : 0.820 Fit side-chains REVERT: A 5 GLN cc_start: 0.7855 (tp40) cc_final: 0.7540 (tp-100) REVERT: A 105 ARG cc_start: 0.7974 (tpp80) cc_final: 0.7331 (tpp80) REVERT: A 450 ILE cc_start: 0.9031 (tp) cc_final: 0.8620 (tp) REVERT: B 51 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7920 (mtm-85) REVERT: B 62 MET cc_start: 0.8310 (tmm) cc_final: 0.8060 (tmm) REVERT: B 69 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 171 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8589 (mm-30) REVERT: C 34 GLN cc_start: 0.8530 (tp40) cc_final: 0.7983 (tp40) REVERT: C 69 ASN cc_start: 0.7990 (t0) cc_final: 0.7740 (t0) REVERT: E 9 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8295 (t0) REVERT: E 227 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8355 (tt) REVERT: E 562 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8241 (t0) REVERT: F 274 MET cc_start: 0.8691 (mmp) cc_final: 0.8491 (mmp) REVERT: F 345 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6624 (mtmm) REVERT: F 474 MET cc_start: 0.1072 (mmt) cc_final: 0.0697 (mmm) REVERT: F 498 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.4966 (pt0) REVERT: F 590 LEU cc_start: -0.0174 (OUTLIER) cc_final: -0.0381 (mm) outliers start: 96 outliers final: 58 residues processed: 253 average time/residue: 0.1702 time to fit residues: 66.7511 Evaluate side-chains 212 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 148 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 361 LEU 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 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 157 GLN Chi-restraints excluded: chain B residue 177 SER 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 95 LEU 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 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 519 ASN 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 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 349 ASN 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 Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 107 optimal weight: 0.0870 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 181 optimal weight: 0.0270 chunk 214 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 218 optimal weight: 1.9990 chunk 242 optimal weight: 0.0670 chunk 102 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3998 r_free = 0.3998 target = 0.135667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093677 restraints weight = 36010.440| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.50 r_work: 0.3271 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22507 Z= 0.143 Angle : 0.581 13.872 30958 Z= 0.288 Chirality : 0.040 0.352 3604 Planarity : 0.004 0.069 3630 Dihedral : 14.884 173.177 4288 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.73 % Allowed : 17.55 % Favored : 78.73 % 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 aren not related in a simple way. whole: -0.91 (0.17), residues: 2541 helix: 0.55 (0.17), residues: 1043 sheet: -0.92 (0.30), residues: 312 loop : -1.57 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 178 TYR 0.013 0.001 TYR A 788 PHE 0.017 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00320 (22475) covalent geometry : angle 0.56939 (30932) hydrogen bonds : bond 0.03864 ( 914) hydrogen bonds : angle 4.05862 ( 2505) metal coordination : bond 0.00775 ( 32) metal coordination : angle 3.98212 ( 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 247 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 165 time to evaluate : 0.836 Fit side-chains REVERT: A 5 GLN cc_start: 0.7884 (tp40) cc_final: 0.7624 (tp40) REVERT: A 77 PHE cc_start: 0.7955 (t80) cc_final: 0.7642 (t80) REVERT: A 105 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7125 (tpp80) REVERT: A 110 MET cc_start: 0.8556 (mmt) cc_final: 0.8343 (mmt) REVERT: A 160 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (ptmm) REVERT: A 450 ILE cc_start: 0.9013 (tp) cc_final: 0.8590 (tp) REVERT: A 463 MET cc_start: 0.8498 (ttt) cc_final: 0.8102 (ttt) REVERT: B 51 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7969 (mtm-85) REVERT: B 62 MET cc_start: 0.8343 (tmm) cc_final: 0.8104 (tmm) REVERT: B 69 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 171 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8556 (mm-30) REVERT: C 34 GLN cc_start: 0.8487 (tp40) cc_final: 0.8056 (tp40) REVERT: C 69 ASN cc_start: 0.8105 (t0) cc_final: 0.7858 (t0) REVERT: E 163 LEU cc_start: 0.8570 (mt) cc_final: 0.8291 (mt) REVERT: E 227 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8357 (tt) REVERT: E 262 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8527 (m-80) REVERT: E 474 MET cc_start: 0.6675 (ppp) cc_final: 0.6349 (ppp) REVERT: E 562 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8233 (t0) REVERT: F 274 MET cc_start: 0.8733 (mmp) cc_final: 0.8515 (mmp) REVERT: F 345 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6405 (mtmm) outliers start: 82 outliers final: 62 residues processed: 236 average time/residue: 0.1758 time to fit residues: 63.4502 Evaluate side-chains 215 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 148 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 148 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU 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 361 LEU Chi-restraints excluded: chain A residue 447 ASN 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 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 B residue 157 GLN Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU 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 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 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 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 410 THR Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 519 ASN 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 37 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU 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 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 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: 0.9990 chunk 63 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 404 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.130650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088465 restraints weight = 36071.543| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.50 r_work: 0.3133 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 22507 Z= 0.298 Angle : 0.693 13.910 30958 Z= 0.345 Chirality : 0.045 0.340 3604 Planarity : 0.004 0.069 3630 Dihedral : 14.695 172.516 4280 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.68 % Allowed : 16.77 % Favored : 78.55 % 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 aren not related in a simple way. whole: -1.01 (0.16), residues: 2541 helix: 0.44 (0.16), residues: 1032 sheet: -0.80 (0.30), residues: 312 loop : -1.63 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 178 TYR 0.027 0.002 TYR A 80 PHE 0.019 0.002 PHE A 652 TRP 0.010 0.002 TRP E 114 HIS 0.007 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00697 (22475) covalent geometry : angle 0.67948 (30932) hydrogen bonds : bond 0.04649 ( 914) hydrogen bonds : angle 4.35104 ( 2505) metal coordination : bond 0.01549 ( 32) metal coordination : angle 4.72992 ( 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 261 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 158 time to evaluate : 0.793 Fit side-chains REVERT: A 5 GLN cc_start: 0.7835 (tp40) cc_final: 0.7511 (tp-100) REVERT: A 105 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7135 (tpp80) REVERT: A 110 MET cc_start: 0.8486 (mmt) cc_final: 0.8114 (mmm) REVERT: A 160 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8426 (ptmm) REVERT: A 450 ILE cc_start: 0.9195 (tp) cc_final: 0.8765 (tp) REVERT: A 857 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: B 51 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7919 (mtm180) REVERT: B 62 MET cc_start: 0.8570 (tmm) cc_final: 0.8274 (tmm) REVERT: B 69 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 171 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8855 (mt-10) REVERT: C 69 ASN cc_start: 0.8078 (t0) cc_final: 0.7868 (t0) REVERT: E 9 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8215 (t0) REVERT: E 163 LEU cc_start: 0.8562 (mt) cc_final: 0.8291 (mt) REVERT: E 227 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8404 (tt) REVERT: E 262 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8441 (m-80) REVERT: E 442 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8173 (mtt-85) REVERT: E 562 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.8385 (t0) REVERT: F 274 MET cc_start: 0.8676 (mmp) cc_final: 0.8397 (mmp) REVERT: F 345 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6347 (mtmm) REVERT: F 474 MET cc_start: 0.1453 (mmt) cc_final: 0.0950 (mmm) REVERT: F 498 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5028 (pt0) REVERT: F 535 SER cc_start: 0.6478 (OUTLIER) cc_final: 0.6141 (p) outliers start: 103 outliers final: 73 residues processed: 252 average time/residue: 0.1708 time to fit residues: 66.7903 Evaluate side-chains 233 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 150 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 114 ILE 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 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 351 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 573 GLN 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 776 VAL Chi-restraints excluded: chain A residue 820 VAL 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 C residue 74 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 37 LYS 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 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 E residue 9 ASN Chi-restraints excluded: chain E residue 56 ASP 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 410 THR Chi-restraints excluded: chain E residue 442 ARG Chi-restraints excluded: chain E residue 482 HIS 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 F residue 45 VAL Chi-restraints excluded: chain F residue 115 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 253 TYR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 345 LYS 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 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 535 SER 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: 0.7980 chunk 68 optimal weight: 0.8980 chunk 249 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 232 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.134220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092438 restraints weight = 35698.302| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.48 r_work: 0.3247 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22507 Z= 0.141 Angle : 0.579 13.877 30958 Z= 0.288 Chirality : 0.040 0.229 3604 Planarity : 0.004 0.068 3630 Dihedral : 14.305 175.003 4274 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.09 % Allowed : 18.73 % Favored : 78.18 % 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 aren not related in a simple way. whole: -0.74 (0.17), residues: 2541 helix: 0.72 (0.17), residues: 1033 sheet: -0.81 (0.31), residues: 301 loop : -1.49 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.013 0.001 TYR B 71 PHE 0.018 0.001 PHE A 652 TRP 0.010 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00323 (22475) covalent geometry : angle 0.56528 (30932) hydrogen bonds : bond 0.03840 ( 914) hydrogen bonds : angle 4.03377 ( 2505) metal coordination : bond 0.00759 ( 32) metal coordination : angle 4.30335 ( 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 224 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7895 (tp40) cc_final: 0.7660 (tp40) REVERT: A 77 PHE cc_start: 0.8082 (t80) cc_final: 0.7848 (t80) REVERT: A 110 MET cc_start: 0.8465 (mmt) cc_final: 0.8072 (mmm) REVERT: A 450 ILE cc_start: 0.9095 (tp) cc_final: 0.8646 (tp) REVERT: A 463 MET cc_start: 0.8570 (ttt) cc_final: 0.8109 (ttt) REVERT: A 791 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8573 (m-40) REVERT: B 51 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7937 (mtm-85) REVERT: B 55 MET cc_start: 0.6524 (tpt) cc_final: 0.6119 (tpt) REVERT: B 62 MET cc_start: 0.8568 (tmm) cc_final: 0.8352 (tmm) REVERT: B 69 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8260 (tm-30) REVERT: B 171 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8916 (mt-10) REVERT: C 34 GLN cc_start: 0.8467 (tp40) cc_final: 0.8032 (tp40) REVERT: C 69 ASN cc_start: 0.8091 (t0) cc_final: 0.7875 (t0) REVERT: E 9 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8218 (t0) REVERT: E 163 LEU cc_start: 0.8620 (mt) cc_final: 0.8290 (mt) REVERT: E 227 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8402 (tt) REVERT: E 474 MET cc_start: 0.7023 (ppp) cc_final: 0.6585 (ppp) REVERT: E 486 SER cc_start: 0.7666 (OUTLIER) cc_final: 0.7307 (p) REVERT: E 562 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8241 (t0) REVERT: F 95 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.7953 (p0) REVERT: F 274 MET cc_start: 0.8722 (mmp) cc_final: 0.8450 (mmp) REVERT: F 345 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6266 (mtmm) REVERT: F 474 MET cc_start: 0.1619 (mmt) cc_final: 0.1086 (mmm) REVERT: F 498 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.4909 (pt0) REVERT: F 576 MET cc_start: 0.2837 (mmp) cc_final: 0.2632 (mmm) outliers start: 68 outliers final: 49 residues processed: 215 average time/residue: 0.1742 time to fit residues: 57.4555 Evaluate side-chains 207 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 114 ILE Chi-restraints excluded: chain A residue 148 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 351 LEU 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 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 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN 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 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 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 441 CYS Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 486 SER 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 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 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: 3.9990 chunk 72 optimal weight: 2.9990 chunk 249 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 202 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 270 GLN ** 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 = 0.3980 r_free = 0.3980 target = 0.134240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092409 restraints weight = 35836.313| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.49 r_work: 0.3247 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22507 Z= 0.147 Angle : 0.574 13.813 30958 Z= 0.283 Chirality : 0.040 0.228 3604 Planarity : 0.004 0.067 3630 Dihedral : 14.105 176.632 4271 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.77 % Allowed : 18.18 % Favored : 78.05 % 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 aren not related in a simple way. whole: -0.57 (0.17), residues: 2541 helix: 0.84 (0.17), residues: 1038 sheet: -0.67 (0.31), residues: 298 loop : -1.40 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 75 TYR 0.015 0.001 TYR B 71 PHE 0.020 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 covalent geometry : bond 0.00339 (22475) covalent geometry : angle 0.56048 (30932) hydrogen bonds : bond 0.03780 ( 914) hydrogen bonds : angle 3.93865 ( 2505) metal coordination : bond 0.00771 ( 32) metal coordination : angle 4.25497 ( 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 233 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 150 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7882 (tp40) cc_final: 0.7625 (tp40) REVERT: A 105 ARG cc_start: 0.8067 (tpp80) cc_final: 0.7188 (tpp80) REVERT: A 110 MET cc_start: 0.8426 (mmt) cc_final: 0.8119 (mmm) REVERT: A 160 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8387 (ptmm) REVERT: A 450 ILE cc_start: 0.9097 (tp) cc_final: 0.8648 (tp) REVERT: A 463 MET cc_start: 0.8528 (ttt) cc_final: 0.8088 (ttt) REVERT: A 791 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8585 (m-40) REVERT: A 857 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: B 51 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7853 (mtm180) REVERT: B 55 MET cc_start: 0.6504 (tpt) cc_final: 0.6095 (tpt) REVERT: B 62 MET cc_start: 0.8599 (tmm) cc_final: 0.8383 (tmm) REVERT: B 69 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 171 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8906 (mt-10) REVERT: C 34 GLN cc_start: 0.8507 (tp40) cc_final: 0.8059 (tp40) REVERT: C 69 ASN cc_start: 0.8093 (t0) cc_final: 0.7874 (t0) REVERT: E 9 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8224 (t0) REVERT: E 163 LEU cc_start: 0.8559 (mt) cc_final: 0.8269 (mt) REVERT: E 227 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8424 (tt) REVERT: E 474 MET cc_start: 0.6975 (ppp) cc_final: 0.6545 (ppp) REVERT: E 486 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7326 (p) REVERT: E 562 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8338 (t0) REVERT: F 95 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7957 (p0) REVERT: F 274 MET cc_start: 0.8717 (mmp) cc_final: 0.8445 (mmp) REVERT: F 474 MET cc_start: 0.1732 (mmt) cc_final: 0.1210 (mmm) REVERT: F 498 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.4821 (pt0) REVERT: F 531 GLN cc_start: 0.6638 (pp30) cc_final: 0.5587 (tp40) outliers start: 83 outliers final: 61 residues processed: 223 average time/residue: 0.1709 time to fit residues: 58.3397 Evaluate side-chains 214 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 144 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 114 ILE 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 267 LYS 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 351 LEU Chi-restraints excluded: chain A residue 425 SER 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 776 VAL Chi-restraints excluded: chain A residue 791 ASN 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 153 LEU 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 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 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 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 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 486 SER 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 F residue 15 ARG 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 356 VAL Chi-restraints excluded: chain F residue 359 THR 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: 2.9990 chunk 214 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** F 281 GLN ** 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 = 0.135051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093387 restraints weight = 35534.225| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.48 r_work: 0.3263 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22507 Z= 0.125 Angle : 0.556 13.769 30958 Z= 0.274 Chirality : 0.039 0.224 3604 Planarity : 0.004 0.067 3630 Dihedral : 13.985 177.832 4268 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.23 % Allowed : 18.86 % Favored : 77.91 % 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 aren not related in a simple way. whole: -0.40 (0.17), residues: 2541 helix: 1.00 (0.17), residues: 1034 sheet: -0.50 (0.31), residues: 297 loop : -1.33 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.012 0.001 TYR B 71 PHE 0.019 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 covalent geometry : bond 0.00285 (22475) covalent geometry : angle 0.54357 (30932) hydrogen bonds : bond 0.03602 ( 914) hydrogen bonds : angle 3.85963 ( 2505) metal coordination : bond 0.00648 ( 32) metal coordination : angle 4.14391 ( 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 220 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 0.967 Fit side-chains REVERT: A 5 GLN cc_start: 0.7860 (tp40) cc_final: 0.7607 (tp40) REVERT: A 105 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7232 (tpp80) REVERT: A 110 MET cc_start: 0.8327 (mmt) cc_final: 0.8028 (mmm) REVERT: A 160 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8376 (ptmm) REVERT: A 450 ILE cc_start: 0.9051 (tp) cc_final: 0.8598 (tp) REVERT: A 463 MET cc_start: 0.8436 (ttt) cc_final: 0.8010 (ttt) REVERT: A 791 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8533 (m-40) REVERT: B 55 MET cc_start: 0.6488 (tpt) cc_final: 0.6080 (tpt) REVERT: B 62 MET cc_start: 0.8563 (tmm) cc_final: 0.8357 (tmm) REVERT: B 69 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 34 GLN cc_start: 0.8498 (tp40) cc_final: 0.8050 (tp40) REVERT: C 69 ASN cc_start: 0.8038 (t0) cc_final: 0.7747 (t0) REVERT: E 9 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8230 (t0) REVERT: E 163 LEU cc_start: 0.8525 (mt) cc_final: 0.8289 (mt) REVERT: E 227 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8464 (tt) REVERT: E 474 MET cc_start: 0.6876 (ppp) cc_final: 0.6412 (ppp) REVERT: E 486 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7273 (p) REVERT: E 562 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8208 (t0) REVERT: E 576 MET cc_start: 0.7552 (mmm) cc_final: 0.7230 (mmm) REVERT: F 95 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7934 (p0) REVERT: F 274 MET cc_start: 0.8737 (mmp) cc_final: 0.8476 (mmp) REVERT: F 474 MET cc_start: 0.1725 (mmt) cc_final: 0.1255 (mmm) REVERT: F 498 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.4715 (pt0) REVERT: F 531 GLN cc_start: 0.6461 (pp30) cc_final: 0.5561 (tp40) REVERT: F 532 THR cc_start: 0.7731 (t) cc_final: 0.7102 (p) outliers start: 71 outliers final: 54 residues processed: 212 average time/residue: 0.1504 time to fit residues: 50.0193 Evaluate side-chains 210 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 148 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 351 LEU Chi-restraints excluded: chain A residue 425 SER 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 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 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 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 180 LEU 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 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 486 SER 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 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 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 426 CYS 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: 8.9990 chunk 133 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 189 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN C 19 GLN ** 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 = 0.3972 r_free = 0.3972 target = 0.133582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091726 restraints weight = 35909.986| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.48 r_work: 0.3234 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22507 Z= 0.179 Angle : 0.582 13.763 30958 Z= 0.288 Chirality : 0.041 0.229 3604 Planarity : 0.004 0.067 3630 Dihedral : 13.938 176.639 4265 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.27 % Allowed : 19.00 % Favored : 77.73 % 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 aren not related in a simple way. whole: -0.40 (0.17), residues: 2541 helix: 0.96 (0.17), residues: 1035 sheet: -0.45 (0.31), residues: 291 loop : -1.32 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.019 0.001 TYR B 71 PHE 0.019 0.001 PHE F 262 TRP 0.009 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00418 (22475) covalent geometry : angle 0.56868 (30932) hydrogen bonds : bond 0.03830 ( 914) hydrogen bonds : angle 3.93009 ( 2505) metal coordination : bond 0.00918 ( 32) metal coordination : angle 4.31485 ( 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 223 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 151 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7880 (tp40) cc_final: 0.7598 (tp40) REVERT: A 105 ARG cc_start: 0.8128 (tpp80) cc_final: 0.7255 (tpp80) REVERT: A 110 MET cc_start: 0.8226 (mmt) cc_final: 0.7924 (mmm) REVERT: A 160 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8396 (ptmm) REVERT: A 450 ILE cc_start: 0.9111 (tp) cc_final: 0.8652 (tp) REVERT: A 791 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8543 (m-40) REVERT: A 857 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: B 55 MET cc_start: 0.6495 (tpt) cc_final: 0.6087 (tpt) REVERT: B 62 MET cc_start: 0.8613 (tmm) cc_final: 0.8389 (tmm) REVERT: B 69 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 171 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8773 (mm-30) REVERT: C 34 GLN cc_start: 0.8529 (tp40) cc_final: 0.8099 (tp40) REVERT: C 69 ASN cc_start: 0.8134 (t0) cc_final: 0.7826 (t0) REVERT: E 9 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8230 (t0) REVERT: E 163 LEU cc_start: 0.8523 (mt) cc_final: 0.8279 (mt) REVERT: E 227 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8490 (tt) REVERT: E 474 MET cc_start: 0.6871 (ppp) cc_final: 0.6423 (ppp) REVERT: E 562 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8338 (t0) REVERT: E 576 MET cc_start: 0.7645 (mmm) cc_final: 0.7391 (mmm) REVERT: F 95 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7947 (p0) REVERT: F 274 MET cc_start: 0.8725 (mmp) cc_final: 0.8447 (mmp) REVERT: F 474 MET cc_start: 0.1577 (mmt) cc_final: 0.1032 (mmm) REVERT: F 498 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.4464 (pt0) REVERT: F 531 GLN cc_start: 0.6598 (pp30) cc_final: 0.5772 (tp40) outliers start: 72 outliers final: 58 residues processed: 213 average time/residue: 0.1638 time to fit residues: 53.7513 Evaluate side-chains 217 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 267 LYS 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 351 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 425 SER 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 776 VAL Chi-restraints excluded: chain A residue 791 ASN 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 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 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 180 LEU 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 199 THR 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 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 115 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 319 GLU 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 426 CYS 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: 5.9990 chunk 158 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 221 optimal weight: 0.7980 chunk 202 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** 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 = 0.3994 r_free = 0.3994 target = 0.135349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093614 restraints weight = 35813.251| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.50 r_work: 0.3240 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22507 Z= 0.121 Angle : 0.556 13.706 30958 Z= 0.273 Chirality : 0.039 0.222 3604 Planarity : 0.004 0.066 3630 Dihedral : 13.840 175.454 4265 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.09 % Allowed : 18.82 % Favored : 78.09 % 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 aren not related in a simple way. whole: -0.28 (0.17), residues: 2541 helix: 1.09 (0.17), residues: 1034 sheet: -0.40 (0.31), residues: 291 loop : -1.27 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 75 TYR 0.028 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 covalent geometry : bond 0.00279 (22475) covalent geometry : angle 0.54334 (30932) hydrogen bonds : bond 0.03540 ( 914) hydrogen bonds : angle 3.81148 ( 2505) metal coordination : bond 0.00621 ( 32) metal coordination : angle 4.16053 ( 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 223 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 155 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7774 (tp40) cc_final: 0.7552 (tp40) REVERT: A 105 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7223 (tpp80) REVERT: A 110 MET cc_start: 0.8134 (mmt) cc_final: 0.7825 (mmm) REVERT: A 160 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8383 (ptmm) REVERT: A 450 ILE cc_start: 0.9050 (tp) cc_final: 0.8618 (tp) REVERT: A 463 MET cc_start: 0.8437 (ttt) cc_final: 0.7955 (ttt) REVERT: A 791 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8570 (m-40) REVERT: A 857 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: B 55 MET cc_start: 0.6455 (tpt) cc_final: 0.5967 (tpt) REVERT: B 62 MET cc_start: 0.8559 (tmm) cc_final: 0.8349 (tmm) REVERT: B 69 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 171 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8766 (mm-30) REVERT: C 34 GLN cc_start: 0.8396 (tp40) cc_final: 0.7956 (tp40) REVERT: C 69 ASN cc_start: 0.8199 (t0) cc_final: 0.7889 (t0) REVERT: D 99 ASP cc_start: 0.8899 (t0) cc_final: 0.8392 (t0) REVERT: E 9 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8202 (t0) REVERT: E 163 LEU cc_start: 0.8475 (mt) cc_final: 0.8229 (mt) REVERT: E 178 ARG cc_start: 0.8755 (ptt90) cc_final: 0.8407 (ptt90) REVERT: E 227 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8474 (tt) REVERT: E 474 MET cc_start: 0.6797 (ppp) cc_final: 0.6296 (ppp) REVERT: E 562 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8166 (t0) REVERT: E 576 MET cc_start: 0.7748 (mmm) cc_final: 0.7500 (mmm) REVERT: F 95 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7999 (p0) REVERT: F 274 MET cc_start: 0.8719 (mmp) cc_final: 0.8463 (mmp) REVERT: F 349 ASN cc_start: 0.8252 (t0) cc_final: 0.7918 (m-40) REVERT: F 474 MET cc_start: 0.1480 (mmt) cc_final: 0.0918 (mmm) REVERT: F 498 GLU cc_start: 0.5253 (OUTLIER) cc_final: 0.4415 (pt0) REVERT: F 531 GLN cc_start: 0.6494 (pp30) cc_final: 0.5686 (tp40) REVERT: F 532 THR cc_start: 0.7702 (t) cc_final: 0.7129 (p) outliers start: 68 outliers final: 55 residues processed: 213 average time/residue: 0.1552 time to fit residues: 51.0685 Evaluate side-chains 214 residues out of total 2230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 151 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 114 ILE 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 267 LYS Chi-restraints excluded: chain A residue 325 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 425 SER 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 776 VAL Chi-restraints excluded: chain A residue 791 ASN 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 160 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 130 VAL Chi-restraints excluded: chain D residue 131 VAL 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 98 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 199 THR 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 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 15 ARG 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 319 GLU 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 371 VAL Chi-restraints excluded: chain F residue 426 CYS Chi-restraints excluded: chain F residue 461 LEU 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: 2.9990 chunk 90 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** F 281 GLN ** 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 = 0.4003 r_free = 0.4003 target = 0.136062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094521 restraints weight = 35789.375| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.49 r_work: 0.3257 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 22507 Z= 0.110 Angle : 0.551 13.691 30958 Z= 0.270 Chirality : 0.039 0.220 3604 Planarity : 0.004 0.066 3630 Dihedral : 13.692 173.048 4262 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.95 % Allowed : 19.00 % Favored : 78.05 % 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 aren not related in a simple way. whole: -0.19 (0.17), residues: 2541 helix: 1.17 (0.17), residues: 1036 sheet: -0.38 (0.31), residues: 293 loop : -1.21 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 75 TYR 0.011 0.001 TYR A 788 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 covalent geometry : bond 0.00248 (22475) covalent geometry : angle 0.53856 (30932) hydrogen bonds : bond 0.03442 ( 914) hydrogen bonds : angle 3.75486 ( 2505) metal coordination : bond 0.00542 ( 32) metal coordination : angle 4.10889 ( 26) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7751.63 seconds wall clock time: 132 minutes 55.98 seconds (7975.98 seconds total)