Starting phenix.real_space_refine on Mon Oct 26 15:53:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxm_30492/10_2026/7cxm_30492.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 57 5.49 5 S 149 5.16 5 C 13292 2.51 5 N 3614 2.21 5 O 4175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21295 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNAv2': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "L" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNAv2': 6} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 74.344 69.270 125.166 1.00 62.19 S ATOM 2487 SG CYS A 306 73.435 69.560 128.822 1.00 58.05 S ATOM 2519 SG CYS A 310 77.097 69.366 127.772 1.00 55.23 S ATOM 3927 SG CYS A 487 60.685 78.628 112.105 1.00 67.79 S ATOM 5180 SG CYS A 645 59.239 78.664 115.620 1.00 71.75 S ATOM 5186 SG CYS A 646 61.947 76.085 114.637 1.00 70.24 S ATOM 12225 SG CYS F 26 49.898 78.666 63.761 1.00190.17 S ATOM 12246 SG CYS F 29 49.806 75.743 64.680 1.00194.08 S ATOM 12411 SG CYS F 50 36.912 78.108 85.770 1.00190.06 S ATOM 12441 SG CYS F 55 34.226 75.460 85.717 1.00192.87 S ATOM 12574 SG CYS F 72 33.195 79.003 85.469 1.00192.04 S ATOM 12148 SG CYS F 16 46.438 69.826 70.994 1.00196.13 S ATOM 12163 SG CYS F 19 48.064 66.790 69.330 1.00210.35 S ATOM 16696 SG CYS E 5 77.788 123.283 59.514 1.00115.67 S ATOM 16717 SG CYS E 8 79.050 126.656 60.728 1.00121.11 S ATOM 16855 SG CYS E 26 75.358 125.977 60.766 1.00117.77 S ATOM 16876 SG CYS E 29 76.994 126.341 57.462 1.00119.90 S ATOM 17041 SG CYS E 50 52.174 115.275 57.500 1.00136.65 S ATOM 17071 SG CYS E 55 50.637 114.350 54.299 1.00142.27 S ATOM 17204 SG CYS E 72 51.452 118.089 54.796 1.00142.05 S ATOM 16778 SG CYS E 16 71.088 117.748 52.291 1.00118.66 S ATOM 16793 SG CYS E 19 74.090 116.581 50.242 1.00123.83 S Time building chain proxies: 4.11, per 1000 atoms: 0.19 Number of scatterers: 21295 At special positions: 0 Unit cell: (145.14, 151.7, 186.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 149 16.00 P 57 15.00 O 4175 8.00 N 3614 7.00 C 13292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 789.8 milliseconds 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 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " 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 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - 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 29 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 21 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 22 sheets defined 40.4% alpha, 12.2% beta 15 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.814A pdb=" N HIS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.720A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.795A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 157 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.539A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.649A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.722A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 removed outlier: 3.707A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.787A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.502A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.533A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.357A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.403A 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 518 removed outlier: 3.957A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.181A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.804A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.874A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 791 removed outlier: 3.702A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.608A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 875 through 903 removed outlier: 3.889A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 removed outlier: 3.808A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 917' Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.688A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.830A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 44 through 55 removed outlier: 4.528A pdb=" N GLU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 95 removed outlier: 3.660A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.586A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.775A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.582A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.819A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.089A pdb=" N ALA D 13 " --> pdb=" O LEU D 9 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.755A pdb=" N LEU D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.383A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.863A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 removed outlier: 4.037A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.544A pdb=" N ASN D 179 " --> pdb=" O ASN D 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 59 through 63 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.659A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 removed outlier: 3.686A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 270 removed outlier: 5.445A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN F 270 " --> pdb=" O VAL F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 289 through 299 removed outlier: 3.564A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 319 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.617A pdb=" N LEU F 391 " --> pdb=" O VAL F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 removed outlier: 3.523A pdb=" N PHE F 422 " --> pdb=" O PRO F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 516 through 525 removed outlier: 4.266A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 557 through 567 removed outlier: 4.356A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 removed outlier: 3.675A pdb=" N ASP F 583 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS F 584 " --> pdb=" O LEU F 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 580 through 584' Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.683A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.157A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 146 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 265 through 274 Processing helix chain 'E' and resid 289 through 299 Processing helix chain 'E' and resid 310 through 323 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 removed outlier: 3.622A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 456 removed outlier: 3.507A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'E' and resid 515 through 523 Processing helix chain 'E' and resid 557 through 566 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.233A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.445A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 347 removed outlier: 3.840A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.801A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.582A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.669A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.669A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 189 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'F' and resid 14 through 15 removed outlier: 4.137A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB5, first strand: chain 'F' and resid 152 through 156 removed outlier: 4.851A pdb=" N VAL F 154 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER F 166 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 277 through 281 removed outlier: 3.824A pdb=" N SER F 278 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR F 398 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N CYS F 330 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 9.822A pdb=" N THR F 359 " --> pdb=" O CYS F 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 511 through 512 Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.556A pdb=" N THR E 12 " --> pdb=" O GLY E 3 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.782A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AC2, first strand: chain 'E' and resid 152 through 156 removed outlier: 7.202A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 163 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP E 223 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.223A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS E 358 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 530 through 532 removed outlier: 5.945A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ASP E 542 " --> pdb=" O VAL E 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 747 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3348 1.28 - 1.41: 5834 1.41 - 1.55: 12357 1.55 - 1.68: 117 1.68 - 1.82: 210 Bond restraints: 21866 Sorted by residual: bond pdb=" CA SER A 343 " pdb=" C SER A 343 " ideal model delta sigma weight residual 1.524 1.422 0.101 1.33e-02 5.65e+03 5.80e+01 bond pdb=" C PHE A 348 " pdb=" O PHE A 348 " ideal model delta sigma weight residual 1.234 1.145 0.089 1.22e-02 6.72e+03 5.33e+01 bond pdb=" C VAL A 342 " pdb=" O VAL A 342 " ideal model delta sigma weight residual 1.235 1.162 0.072 1.02e-02 9.61e+03 5.03e+01 bond pdb=" C TYR A 346 " pdb=" O TYR A 346 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.20e-02 6.94e+03 4.93e+01 bond pdb=" CA ASN D 109 " pdb=" C ASN D 109 " ideal model delta sigma weight residual 1.524 1.441 0.084 1.24e-02 6.50e+03 4.55e+01 ... (remaining 21861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 29705 6.76 - 13.52: 194 13.52 - 20.28: 59 20.28 - 27.03: 14 27.03 - 33.79: 8 Bond angle restraints: 29980 Sorted by residual: angle pdb=" N ASP E 458 " pdb=" CA ASP E 458 " pdb=" C ASP E 458 " ideal model delta sigma weight residual 110.52 78.65 31.87 1.48e+00 4.57e-01 4.64e+02 angle pdb=" N SER F 36 " pdb=" CA SER F 36 " pdb=" C SER F 36 " ideal model delta sigma weight residual 114.31 140.70 -26.39 1.29e+00 6.01e-01 4.18e+02 angle pdb=" N CYS B 142 " pdb=" CA CYS B 142 " pdb=" C CYS B 142 " ideal model delta sigma weight residual 107.80 74.01 33.79 1.73e+00 3.34e-01 3.82e+02 angle pdb=" N THR A 344 " pdb=" CA THR A 344 " pdb=" C THR A 344 " ideal model delta sigma weight residual 109.96 79.88 30.08 1.58e+00 4.01e-01 3.63e+02 angle pdb=" N ALA D 126 " pdb=" CA ALA D 126 " pdb=" CB ALA D 126 " ideal model delta sigma weight residual 110.38 85.25 25.13 1.38e+00 5.25e-01 3.32e+02 ... (remaining 29975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.53: 11725 25.53 - 51.06: 1055 51.06 - 76.59: 187 76.59 - 102.11: 15 102.11 - 127.64: 2 Dihedral angle restraints: 12984 sinusoidal: 5398 harmonic: 7586 Sorted by residual: dihedral pdb=" C4' A J 100 " pdb=" C3' A J 100 " pdb=" C2' A J 100 " pdb=" C1' A J 100 " ideal model delta sinusoidal sigma weight residual 36.34 -38.46 74.81 1 3.10e+00 1.04e-01 7.37e+02 dihedral pdb=" C4' A L 2 " pdb=" C3' A L 2 " pdb=" C2' A L 2 " pdb=" C1' A L 2 " ideal model delta sinusoidal sigma weight residual 36.35 -36.86 73.20 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' G I 35 " pdb=" C3' G I 35 " pdb=" C2' G I 35 " pdb=" C1' G I 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.07 72.42 1 3.10e+00 1.04e-01 6.97e+02 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.333: 3406 0.333 - 0.666: 46 0.666 - 0.999: 10 0.999 - 1.332: 1 1.332 - 1.665: 2 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CA TRP B 182 " pdb=" N TRP B 182 " pdb=" C TRP B 182 " pdb=" CB TRP B 182 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.93e+01 chirality pdb=" CA PHE E 346 " pdb=" N PHE E 346 " pdb=" C PHE E 346 " pdb=" CB PHE E 346 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.64e+01 chirality pdb=" CA VAL A 257 " pdb=" N VAL A 257 " pdb=" C VAL A 257 " pdb=" CB VAL A 257 " both_signs ideal model delta sigma weight residual False 2.44 1.39 1.05 2.00e-01 2.50e+01 2.77e+01 ... (remaining 3462 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 460 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO A 461 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 183 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 115 " 0.070 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO D 116 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 116 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 116 " 0.060 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 43 2.24 - 2.90: 9450 2.90 - 3.57: 30266 3.57 - 4.23: 50635 4.23 - 4.90: 83125 Nonbonded interactions: 173519 Sorted by model distance: nonbonded pdb=" O SER D 177 " pdb=" CD2 LEU D 180 " model vdw 1.572 3.460 nonbonded pdb=" OD2 ASP A 260 " pdb=" NZ LYS A 263 " model vdw 1.709 3.120 nonbonded pdb=" SG CYS F 8 " pdb=" CG1 VAL F 98 " model vdw 1.795 3.820 nonbonded pdb=" O LEU A 900 " pdb=" O TYR A 903 " model vdw 1.819 3.040 nonbonded pdb=" CD2 HIS A 75 " pdb=" CG2 THR A 76 " model vdw 1.839 3.680 ... (remaining 173514 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 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 703)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 1002)) } 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: 7.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.740 Find NCS groups from input model: 0.260 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 21896 Z= 0.522 Angle : 1.604 33.794 30001 Z= 0.986 Chirality : 0.107 1.665 3465 Planarity : 0.006 0.118 3626 Dihedral : 18.689 127.642 8090 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.98 % Favored : 90.40 % Rotamer: Outliers : 12.89 % Allowed : 28.73 % Favored : 58.37 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.13), residues: 2551 helix: -2.30 (0.14), residues: 944 sheet: -2.30 (0.26), residues: 301 loop : -3.47 (0.14), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 21 TYR 0.024 0.002 TYR E 582 PHE 0.026 0.002 PHE A 348 TRP 0.020 0.002 TRP A 916 HIS 0.010 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00963 / 0.52 (21866) covalent geometry : angle 1.60228 / 0.99 (29980) hydrogen bonds : bond 0.18135 / 11.72 ( 775) hydrogen bonds : angle 7.37050 / 5.14 ( 2129) metal coordination : bond 0.01968 / 1.03 ( 30) metal coordination : angle 3.42528 / 2.17 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 151 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: A 183 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7475 (ttp-110) REVERT: A 411 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8668 (mtpt) REVERT: A 621 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8478 (mttp) REVERT: A 758 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 798 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8409 (mtmm) REVERT: A 815 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.8303 (mm-40) REVERT: B 56 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6530 (mm-40) REVERT: B 59 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6226 (tm) REVERT: B 60 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: B 67 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7596 (tpp) REVERT: B 77 GLU cc_start: 0.8774 (tt0) cc_final: 0.8542 (tm-30) REVERT: B 78 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8530 (t0) REVERT: C 50 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: D 32 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: D 39 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6145 (mtmm) REVERT: D 56 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7285 (pp30) REVERT: D 69 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 73 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8307 (tm-30) REVERT: F 30 CYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8403 (m) REVERT: F 474 MET cc_start: 0.1587 (mtm) cc_final: 0.1155 (mtp) REVERT: F 550 THR cc_start: 0.4109 (OUTLIER) cc_final: 0.3660 (m) REVERT: F 582 TYR cc_start: 0.4398 (OUTLIER) cc_final: 0.4038 (p90) REVERT: F 587 PHE cc_start: 0.3834 (OUTLIER) cc_final: 0.2117 (m-10) REVERT: E 168 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7016 (mm-30) REVERT: E 226 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (m) REVERT: E 243 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7339 (tp40) REVERT: E 250 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8169 (t) REVERT: E 348 VAL cc_start: 0.7264 (OUTLIER) cc_final: 0.6859 (t) REVERT: E 462 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8281 (mppt) REVERT: E 464 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4590 (p-80) REVERT: E 580 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7991 (p0) outliers start: 284 outliers final: 118 residues processed: 418 average time/residue: 0.4697 time to fit residues: 230.5296 Evaluate side-chains 267 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 122 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 621 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 136 ASN 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 180 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 214 THR Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 424 SER Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 475 PHE Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 575 ILE Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain F residue 587 PHE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 161 ARG Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 349 ASN Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 427 ARG Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 513 SER Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 580 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 790 ASN A 909 ASN B 56 GLN B 118 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS ** F 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN E 290 HIS E 311 HIS E 361 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.128184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068938 restraints weight = 48015.369| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.86 r_work: 0.2940 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21896 Z= 0.193 Angle : 0.821 15.194 30001 Z= 0.411 Chirality : 0.052 0.340 3465 Planarity : 0.005 0.067 3626 Dihedral : 12.105 145.964 3708 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.29 % Favored : 92.40 % Rotamer: Outliers : 8.94 % Allowed : 28.69 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.15), residues: 2551 helix: -1.23 (0.16), residues: 957 sheet: -1.71 (0.27), residues: 308 loop : -2.94 (0.15), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 21 TYR 0.022 0.001 TYR B 71 PHE 0.027 0.002 PHE F 225 TRP 0.017 0.002 TRP B 182 HIS 0.010 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (21866) covalent geometry : angle 0.81293 / 0.41 (29980) hydrogen bonds : bond 0.05492 / 3.62 ( 775) hydrogen bonds : angle 5.17600 / 3.56 ( 2129) metal coordination : bond 0.01679 / 0.89 ( 30) metal coordination : angle 4.28553 / 2.68 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 142 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8812 (mmm) cc_final: 0.8165 (mmm) REVERT: A 167 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: A 183 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7261 (ttp-110) REVERT: A 197 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8046 (ttm-80) REVERT: A 266 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8795 (mt) REVERT: A 372 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8913 (mp) REVERT: A 758 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8680 (tt) REVERT: A 798 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8574 (mtmm) REVERT: A 818 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8033 (ptm) REVERT: B 62 MET cc_start: 0.6537 (pp-130) cc_final: 0.6309 (ppp) REVERT: B 77 GLU cc_start: 0.9151 (tt0) cc_final: 0.8679 (tm-30) REVERT: B 82 LYS cc_start: 0.8756 (tptt) cc_final: 0.8536 (ttpt) REVERT: C 50 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: D 32 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: D 69 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8274 (tm-30) REVERT: D 73 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8451 (tm-30) REVERT: D 129 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8628 (mtm) REVERT: F 30 CYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8545 (m) REVERT: F 139 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7591 (tptp) REVERT: E 116 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7777 (p0) REVERT: E 136 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: E 192 LYS cc_start: 0.5629 (OUTLIER) cc_final: 0.4427 (mptp) REVERT: E 210 VAL cc_start: 0.8035 (m) cc_final: 0.7789 (m) REVERT: E 243 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7347 (tp40) REVERT: E 329 LYS cc_start: 0.2212 (OUTLIER) cc_final: 0.1997 (tmtt) REVERT: E 361 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7816 (p0) REVERT: E 458 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7585 (p0) outliers start: 197 outliers final: 75 residues processed: 325 average time/residue: 0.5196 time to fit residues: 195.9040 Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 123 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 229 SER Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 575 ILE Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 116 ASN Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 493 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [1, 182, 144, 105, 82, 10, 94, 155, 135, 81, 213] chunk 1 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 534 ASN A 734 ASN A 790 ASN A 909 ASN B 19 GLN B 108 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 HIS ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.125439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.069364 restraints weight = 47029.396| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.62 r_work: 0.2986 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21896 Z= 0.196 Angle : 0.754 14.789 30001 Z= 0.379 Chirality : 0.049 0.285 3465 Planarity : 0.004 0.057 3626 Dihedral : 10.785 144.865 3559 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.43 % Favored : 91.42 % Rotamer: Outliers : 8.03 % Allowed : 28.87 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.15), residues: 2551 helix: -0.87 (0.17), residues: 970 sheet: -1.53 (0.28), residues: 297 loop : -2.65 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 579 TYR 0.020 0.001 TYR F 224 PHE 0.020 0.002 PHE F 357 TRP 0.018 0.002 TRP B 182 HIS 0.006 0.001 HIS F 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (21866) covalent geometry : angle 0.74718 / 0.38 (29980) hydrogen bonds : bond 0.05250 / 3.46 ( 775) hydrogen bonds : angle 4.90081 / 3.37 ( 2129) metal coordination : bond 0.01662 / 0.87 ( 30) metal coordination : angle 3.78713 / 2.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 133 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8824 (m-30) REVERT: A 110 MET cc_start: 0.8959 (mmm) cc_final: 0.8310 (mmm) REVERT: A 183 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7289 (ttp-110) REVERT: A 197 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8115 (ttm-80) REVERT: A 266 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8835 (mt) REVERT: A 411 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8774 (mtpt) REVERT: A 758 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8748 (tt) REVERT: A 818 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8162 (ptm) REVERT: A 855 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8304 (mmt) REVERT: B 77 GLU cc_start: 0.9114 (tt0) cc_final: 0.8682 (tm-30) REVERT: C 50 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: C 69 ASN cc_start: 0.9354 (t0) cc_final: 0.9149 (t0) REVERT: D 69 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8352 (tm-30) REVERT: D 73 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8493 (tm-30) REVERT: F 30 CYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8636 (m) REVERT: F 139 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7546 (tptp) REVERT: F 337 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.5792 (mmp-170) REVERT: E 136 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: E 192 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.4534 (mttp) REVERT: E 243 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7395 (tp40) REVERT: E 343 PHE cc_start: 0.1331 (p90) cc_final: 0.0914 (p90) REVERT: E 394 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8072 (tptp) REVERT: E 411 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8341 (tm) outliers start: 177 outliers final: 72 residues processed: 294 average time/residue: 0.5219 time to fit residues: 178.8372 Evaluate side-chains 213 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 124 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 394 LYS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [125, 206, 162, 21, 3, 144, 205, 239, 31, 234, 182] chunk 125 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 234 optimal weight: 10.0000 chunk 182 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN A 886 GLN A 909 ASN B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.127356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.071692 restraints weight = 46946.148| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.56 r_work: 0.3037 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21896 Z= 0.128 Angle : 0.695 14.764 30001 Z= 0.345 Chirality : 0.047 0.275 3465 Planarity : 0.004 0.042 3626 Dihedral : 10.177 142.693 3535 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.78 % Favored : 93.06 % Rotamer: Outliers : 6.67 % Allowed : 29.64 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2551 helix: -0.52 (0.17), residues: 978 sheet: -1.31 (0.28), residues: 297 loop : -2.44 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 21 TYR 0.020 0.001 TYR B 71 PHE 0.015 0.001 PHE A 77 TRP 0.019 0.001 TRP B 182 HIS 0.005 0.001 HIS F 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21866) covalent geometry : angle 0.68987 / 0.34 (29980) hydrogen bonds : bond 0.04283 / 2.79 ( 775) hydrogen bonds : angle 4.56591 / 3.15 ( 2129) metal coordination : bond 0.01576 / 0.82 ( 30) metal coordination : angle 3.29229 / 2.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 140 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.9048 (mmm) cc_final: 0.8277 (mmm) REVERT: A 197 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8016 (ttm-80) REVERT: A 553 ARG cc_start: 0.8704 (mtm110) cc_final: 0.8500 (ttp-110) REVERT: A 665 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 758 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8718 (tt) REVERT: B 55 MET cc_start: 0.8517 (tpp) cc_final: 0.8276 (tpp) REVERT: B 71 TYR cc_start: 0.7489 (m-80) cc_final: 0.7281 (m-80) REVERT: B 77 GLU cc_start: 0.9051 (tt0) cc_final: 0.8607 (tm-30) REVERT: B 82 LYS cc_start: 0.8791 (tptt) cc_final: 0.8541 (ttpp) REVERT: B 97 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9091 (mtmt) REVERT: C 50 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: C 67 ASP cc_start: 0.9120 (t70) cc_final: 0.8905 (t0) REVERT: D 56 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6914 (pp30) REVERT: D 69 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8309 (tm-30) REVERT: D 73 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8460 (tm-30) REVERT: D 166 ILE cc_start: 0.8938 (mm) cc_final: 0.8664 (tp) REVERT: F 260 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7312 (t70) REVERT: F 337 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.5796 (mmp-170) REVERT: F 347 LYS cc_start: 0.6762 (OUTLIER) cc_final: 0.6557 (pmtt) REVERT: F 429 MET cc_start: 0.2972 (ptt) cc_final: 0.2615 (tmm) REVERT: E 136 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: E 192 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.4653 (mptp) REVERT: E 243 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7415 (tp40) REVERT: E 317 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7030 (tp) REVERT: E 343 PHE cc_start: 0.1082 (p90) cc_final: 0.0711 (p90) REVERT: E 411 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8330 (tm) REVERT: E 458 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7750 (p0) REVERT: E 460 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8266 (mtmm) outliers start: 147 outliers final: 61 residues processed: 272 average time/residue: 0.5789 time to fit residues: 181.0411 Evaluate side-chains 205 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 128 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [153, 200, 116, 93, 255, 32, 152, 69, 40, 132, 245] chunk 153 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 chunk 93 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 overall best weight: 2.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN A 909 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.125201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068847 restraints weight = 47042.086| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.59 r_work: 0.2976 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21896 Z= 0.230 Angle : 0.728 14.603 30001 Z= 0.364 Chirality : 0.049 0.284 3465 Planarity : 0.004 0.042 3626 Dihedral : 9.976 144.282 3522 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.92 % Favored : 91.92 % Rotamer: Outliers : 6.63 % Allowed : 29.60 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.16), residues: 2551 helix: -0.54 (0.17), residues: 979 sheet: -1.28 (0.28), residues: 297 loop : -2.34 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.021 0.002 TYR A 788 PHE 0.022 0.002 PHE F 357 TRP 0.015 0.002 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (21866) covalent geometry : angle 0.72233 / 0.36 (29980) hydrogen bonds : bond 0.05240 / 3.50 ( 775) hydrogen bonds : angle 4.65859 / 3.20 ( 2129) metal coordination : bond 0.01557 / 0.82 ( 30) metal coordination : angle 3.39755 / 2.07 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 126 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9063 (ptpp) REVERT: A 105 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8485 (ptm-80) REVERT: A 110 MET cc_start: 0.9021 (mmm) cc_final: 0.8292 (mmm) REVERT: A 197 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8226 (ttm-80) REVERT: A 411 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8762 (mtpt) REVERT: A 758 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8738 (tt) REVERT: A 790 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8608 (t0) REVERT: A 818 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8174 (ptm) REVERT: A 855 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8441 (mmt) REVERT: B 55 MET cc_start: 0.8721 (tpp) cc_final: 0.8383 (tpp) REVERT: B 71 TYR cc_start: 0.7550 (m-80) cc_final: 0.7312 (m-80) REVERT: B 77 GLU cc_start: 0.9103 (tt0) cc_final: 0.8679 (tm-30) REVERT: B 82 LYS cc_start: 0.8813 (tptt) cc_final: 0.8539 (ttpp) REVERT: B 97 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9072 (mtmt) REVERT: C 50 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: D 56 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6982 (pp30) REVERT: D 73 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8580 (tm-30) REVERT: F 260 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7370 (t70) REVERT: F 337 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.5801 (mmp-170) REVERT: F 587 PHE cc_start: 0.4537 (OUTLIER) cc_final: 0.4105 (m-80) REVERT: E 136 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: E 243 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7432 (tp40) REVERT: E 317 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7090 (tp) REVERT: E 343 PHE cc_start: 0.1097 (p90) cc_final: 0.0638 (p90) REVERT: E 411 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8291 (tm) REVERT: E 458 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7806 (p0) REVERT: E 460 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8425 (mtmm) outliers start: 146 outliers final: 71 residues processed: 256 average time/residue: 0.5716 time to fit residues: 168.6530 Evaluate side-chains 215 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 124 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 503 ASN Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 587 PHE Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 574 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [234, 197, 18, 254, 130, 52, 202, 124, 217, 147, 250] chunk 234 optimal weight: 2.9990 chunk 197 optimal weight: 30.0000 chunk 18 optimal weight: 0.4980 chunk 254 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN A 790 ASN A 909 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.126650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.070705 restraints weight = 46859.774| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.57 r_work: 0.3016 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21896 Z= 0.153 Angle : 0.686 14.635 30001 Z= 0.340 Chirality : 0.047 0.274 3465 Planarity : 0.004 0.042 3626 Dihedral : 9.810 142.146 3519 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.79 % Rotamer: Outliers : 6.17 % Allowed : 29.78 % Favored : 64.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.16), residues: 2551 helix: -0.38 (0.17), residues: 981 sheet: -1.14 (0.29), residues: 299 loop : -2.25 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 21 TYR 0.025 0.001 TYR F 582 PHE 0.024 0.001 PHE A 77 TRP 0.018 0.001 TRP B 182 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (21866) covalent geometry : angle 0.68106 / 0.34 (29980) hydrogen bonds : bond 0.04454 / 2.92 ( 775) hydrogen bonds : angle 4.48198 / 3.08 ( 2129) metal coordination : bond 0.01461 / 0.75 ( 30) metal coordination : angle 3.25103 / 2.02 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 133 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9068 (ptpp) REVERT: A 105 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7819 (ttm-80) REVERT: A 110 MET cc_start: 0.9051 (mmm) cc_final: 0.8319 (mmm) REVERT: A 197 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8137 (ttm-80) REVERT: A 411 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8732 (mtpt) REVERT: A 553 ARG cc_start: 0.8688 (mtm110) cc_final: 0.8485 (ttp-110) REVERT: A 665 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8255 (pt0) REVERT: A 666 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: A 758 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 55 MET cc_start: 0.8567 (tpp) cc_final: 0.8359 (tpp) REVERT: B 71 TYR cc_start: 0.7563 (m-80) cc_final: 0.7340 (m-80) REVERT: B 77 GLU cc_start: 0.9009 (tt0) cc_final: 0.8583 (tm-30) REVERT: B 82 LYS cc_start: 0.8802 (tptt) cc_final: 0.8534 (ttpp) REVERT: B 97 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9098 (mtmt) REVERT: B 155 GLU cc_start: 0.8002 (pp20) cc_final: 0.7585 (pp20) REVERT: C 50 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: C 67 ASP cc_start: 0.9093 (t70) cc_final: 0.8870 (t0) REVERT: D 56 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6934 (pp30) REVERT: D 73 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8538 (tm-30) REVERT: F 139 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7516 (tptp) REVERT: F 260 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7546 (t70) REVERT: F 337 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5724 (mmp-170) REVERT: F 341 GLU cc_start: 0.6125 (tp30) cc_final: 0.4696 (pm20) REVERT: F 391 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7351 (tm) REVERT: F 429 MET cc_start: 0.5102 (tmm) cc_final: 0.3434 (ptt) REVERT: F 437 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.5298 (t80) REVERT: E 136 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: E 192 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.4780 (mtmm) REVERT: E 243 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7403 (tp40) REVERT: E 317 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7143 (tp) REVERT: E 343 PHE cc_start: 0.0980 (p90) cc_final: 0.0543 (p90) REVERT: E 411 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8274 (tm) REVERT: E 458 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7730 (p0) REVERT: E 460 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8489 (mtmm) outliers start: 136 outliers final: 66 residues processed: 258 average time/residue: 0.5469 time to fit residues: 163.0327 Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 129 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [8, 22, 158, 211, 194, 24, 120, 227, 3, 35, 88] chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 158 optimal weight: 20.0000 chunk 211 optimal weight: 4.9990 chunk 194 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN F 388 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.126027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.069820 restraints weight = 46771.308| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.62 r_work: 0.2998 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21896 Z= 0.176 Angle : 0.691 14.606 30001 Z= 0.345 Chirality : 0.047 0.277 3465 Planarity : 0.004 0.041 3626 Dihedral : 9.700 142.749 3519 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.00 % Favored : 91.89 % Rotamer: Outliers : 5.99 % Allowed : 29.87 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.16), residues: 2551 helix: -0.33 (0.17), residues: 976 sheet: -1.14 (0.29), residues: 298 loop : -2.13 (0.16), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 21 TYR 0.047 0.001 TYR F 582 PHE 0.029 0.002 PHE F 357 TRP 0.016 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (21866) covalent geometry : angle 0.68624 / 0.34 (29980) hydrogen bonds : bond 0.04677 / 3.10 ( 775) hydrogen bonds : angle 4.48703 / 3.08 ( 2129) metal coordination : bond 0.01440 / 0.73 ( 30) metal coordination : angle 3.14549 / 1.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 131 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8429 (ptm-80) REVERT: A 110 MET cc_start: 0.9051 (mmm) cc_final: 0.8321 (mmm) REVERT: A 197 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8196 (ttm-80) REVERT: A 411 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: A 758 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 855 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8338 (mmt) REVERT: B 62 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6145 (ppp) REVERT: B 71 TYR cc_start: 0.7564 (m-80) cc_final: 0.7337 (m-80) REVERT: B 77 GLU cc_start: 0.8994 (tt0) cc_final: 0.8581 (tm-30) REVERT: B 82 LYS cc_start: 0.8821 (tptt) cc_final: 0.8533 (ttpp) REVERT: B 97 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9102 (mtmt) REVERT: B 155 GLU cc_start: 0.8031 (pp20) cc_final: 0.7624 (pp20) REVERT: C 50 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: C 67 ASP cc_start: 0.9096 (t70) cc_final: 0.8868 (t0) REVERT: D 39 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.6094 (mtmm) REVERT: D 56 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6959 (pp30) REVERT: D 73 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8552 (tm-30) REVERT: F 139 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7517 (tptp) REVERT: F 189 LYS cc_start: 0.4064 (tptp) cc_final: 0.2497 (ptpp) REVERT: F 274 MET cc_start: 0.6471 (mmm) cc_final: 0.6161 (mmp) REVERT: F 337 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5568 (mmp-170) REVERT: F 341 GLU cc_start: 0.5911 (tp30) cc_final: 0.4549 (pm20) REVERT: F 391 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7414 (tm) REVERT: F 429 MET cc_start: 0.4991 (tmm) cc_final: 0.3362 (ptt) REVERT: F 437 PHE cc_start: 0.5665 (OUTLIER) cc_final: 0.5267 (t80) REVERT: F 438 LEU cc_start: -0.2625 (OUTLIER) cc_final: -0.3186 (pt) REVERT: F 587 PHE cc_start: 0.4507 (OUTLIER) cc_final: 0.4281 (m-10) REVERT: E 96 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8446 (p) REVERT: E 136 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: E 192 LYS cc_start: 0.5906 (OUTLIER) cc_final: 0.4735 (mtmm) REVERT: E 243 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7450 (tp40) REVERT: E 317 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7174 (tp) REVERT: E 343 PHE cc_start: 0.0857 (p90) cc_final: 0.0412 (p90) REVERT: E 411 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8276 (tm) REVERT: E 460 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8518 (mtmm) outliers start: 132 outliers final: 66 residues processed: 250 average time/residue: 0.5190 time to fit residues: 150.4747 Evaluate side-chains 216 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 127 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 587 PHE Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 429 MET Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 574 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [140, 94, 120, 30, 74, 101, 36, 102, 5, 171, 84] chunk 140 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 734 ASN A 790 ASN B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 537 GLN ** F 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.128012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072494 restraints weight = 46951.726| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.58 r_work: 0.3055 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21896 Z= 0.118 Angle : 0.661 14.670 30001 Z= 0.327 Chirality : 0.046 0.267 3465 Planarity : 0.004 0.042 3626 Dihedral : 9.446 140.594 3515 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.98 % Favored : 92.87 % Rotamer: Outliers : 4.58 % Allowed : 31.09 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.16), residues: 2551 helix: -0.11 (0.17), residues: 971 sheet: -1.01 (0.29), residues: 300 loop : -2.01 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.046 0.001 TYR F 582 PHE 0.019 0.001 PHE F 357 TRP 0.020 0.001 TRP B 182 HIS 0.003 0.001 HIS F 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (21866) covalent geometry : angle 0.65694 / 0.33 (29980) hydrogen bonds : bond 0.03905 / 2.54 ( 775) hydrogen bonds : angle 4.30424 / 2.97 ( 2129) metal coordination : bond 0.01433 / 0.74 ( 30) metal coordination : angle 2.98499 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 134 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.9110 (mmm) cc_final: 0.8428 (mmm) REVERT: A 197 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8025 (ttm-80) REVERT: A 411 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8675 (mtpt) REVERT: A 553 ARG cc_start: 0.8553 (ttp-110) cc_final: 0.8176 (ttp80) REVERT: A 758 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8620 (tt) REVERT: B 71 TYR cc_start: 0.7498 (m-80) cc_final: 0.7253 (m-80) REVERT: B 77 GLU cc_start: 0.8969 (tt0) cc_final: 0.8561 (tm-30) REVERT: B 139 LYS cc_start: 0.9356 (ttmm) cc_final: 0.9109 (ptpp) REVERT: B 155 GLU cc_start: 0.7958 (pp20) cc_final: 0.7522 (pp20) REVERT: C 50 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8227 (mm-30) REVERT: C 67 ASP cc_start: 0.9079 (t70) cc_final: 0.8837 (t0) REVERT: D 56 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6884 (pp30) REVERT: D 73 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8528 (tm-30) REVERT: F 139 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7545 (tptp) REVERT: F 189 LYS cc_start: 0.4222 (tptp) cc_final: 0.2568 (mtmm) REVERT: F 274 MET cc_start: 0.6470 (mmm) cc_final: 0.6136 (mmp) REVERT: F 337 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.5601 (mmp-170) REVERT: F 341 GLU cc_start: 0.5768 (tp30) cc_final: 0.4459 (pm20) REVERT: F 391 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7481 (tm) REVERT: F 437 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5330 (t80) REVERT: F 438 LEU cc_start: -0.2992 (OUTLIER) cc_final: -0.3473 (pt) REVERT: F 537 GLN cc_start: 0.0801 (OUTLIER) cc_final: 0.0475 (pt0) REVERT: E 96 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8375 (p) REVERT: E 192 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.4751 (mtmm) REVERT: E 317 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7143 (tp) REVERT: E 343 PHE cc_start: 0.0731 (p90) cc_final: 0.0307 (p90) REVERT: E 460 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8525 (mtmm) REVERT: E 582 TYR cc_start: 0.5696 (OUTLIER) cc_final: 0.5354 (p90) outliers start: 101 outliers final: 48 residues processed: 224 average time/residue: 0.6016 time to fit residues: 153.7944 Evaluate side-chains 195 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 131 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 460 LYS Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 560 ARG Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 582 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [77, 103, 135, 152, 247, 42, 144, 68, 121, 138, 186] chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.0470 chunk 135 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 247 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 537 GLN ** F 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.126173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.070104 restraints weight = 46500.381| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.54 r_work: 0.3000 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21896 Z= 0.193 Angle : 0.701 15.536 30001 Z= 0.349 Chirality : 0.047 0.276 3465 Planarity : 0.004 0.042 3626 Dihedral : 9.326 141.941 3506 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.76 % Favored : 92.12 % Rotamer: Outliers : 3.95 % Allowed : 32.18 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2551 helix: -0.16 (0.17), residues: 970 sheet: -1.04 (0.29), residues: 298 loop : -2.00 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 21 TYR 0.044 0.001 TYR F 582 PHE 0.019 0.002 PHE E 587 TRP 0.014 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 (21866) covalent geometry : angle 0.69694 / 0.35 (29980) hydrogen bonds : bond 0.04708 / 3.13 ( 775) hydrogen bonds : angle 4.44081 / 3.06 ( 2129) metal coordination : bond 0.01483 / 0.76 ( 30) metal coordination : angle 3.04189 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 130 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8407 (ptm-80) REVERT: A 110 MET cc_start: 0.9064 (mmm) cc_final: 0.8362 (mmm) REVERT: A 197 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8208 (ttm-80) REVERT: A 411 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8719 (mtpt) REVERT: A 665 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: A 758 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8625 (tt) REVERT: B 71 TYR cc_start: 0.7519 (m-80) cc_final: 0.7285 (m-80) REVERT: B 77 GLU cc_start: 0.9018 (tt0) cc_final: 0.8611 (tm-30) REVERT: B 82 LYS cc_start: 0.8758 (tptt) cc_final: 0.8496 (ttpt) REVERT: B 155 GLU cc_start: 0.8029 (pp20) cc_final: 0.7603 (pp20) REVERT: C 50 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: D 56 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6860 (pp30) REVERT: D 73 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8553 (tm-30) REVERT: F 139 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7514 (tptp) REVERT: F 189 LYS cc_start: 0.4347 (tptp) cc_final: 0.2727 (mtmm) REVERT: F 274 MET cc_start: 0.6431 (mmm) cc_final: 0.6136 (mmp) REVERT: F 341 GLU cc_start: 0.5567 (tp30) cc_final: 0.4229 (pt0) REVERT: F 391 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7407 (tm) REVERT: F 437 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5484 (t80) REVERT: F 438 LEU cc_start: -0.3061 (OUTLIER) cc_final: -0.3628 (pt) REVERT: E 96 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8452 (p) REVERT: E 192 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.4579 (mttp) REVERT: E 317 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7154 (tp) REVERT: E 343 PHE cc_start: 0.0854 (p90) cc_final: 0.0240 (p90) outliers start: 87 outliers final: 53 residues processed: 215 average time/residue: 0.6065 time to fit residues: 149.6652 Evaluate side-chains 193 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 533 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 589 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [247, 10, 181, 79, 162, 26, 211, 246, 206, 109, 173] chunk 247 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 162 optimal weight: 30.0000 chunk 26 optimal weight: 0.0470 chunk 211 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 chunk 109 optimal weight: 0.0270 chunk 173 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN F 388 ASN F 537 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.129530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072353 restraints weight = 48075.780| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.78 r_work: 0.3023 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21896 Z= 0.120 Angle : 0.668 15.510 30001 Z= 0.331 Chirality : 0.045 0.263 3465 Planarity : 0.004 0.042 3626 Dihedral : 9.247 139.365 3505 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.62 % Favored : 93.26 % Rotamer: Outliers : 3.04 % Allowed : 33.14 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.17), residues: 2551 helix: 0.03 (0.17), residues: 969 sheet: -0.87 (0.29), residues: 300 loop : -1.86 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.035 0.001 TYR F 582 PHE 0.018 0.001 PHE E 587 TRP 0.021 0.001 TRP B 182 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (21866) covalent geometry : angle 0.66387 / 0.33 (29980) hydrogen bonds : bond 0.03794 / 2.45 ( 775) hydrogen bonds : angle 4.29003 / 2.98 ( 2129) metal coordination : bond 0.01523 / 0.78 ( 30) metal coordination : angle 2.95373 / 1.86 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 130 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.9100 (mmm) cc_final: 0.8376 (mmm) REVERT: A 197 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7980 (ttm-80) REVERT: A 665 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: A 758 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8559 (tt) REVERT: B 77 GLU cc_start: 0.8955 (tt0) cc_final: 0.8534 (tm-30) REVERT: B 82 LYS cc_start: 0.8745 (tptt) cc_final: 0.8483 (ttpt) REVERT: B 155 GLU cc_start: 0.7944 (pp20) cc_final: 0.7541 (pp20) REVERT: C 50 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: D 73 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8478 (tm-30) REVERT: F 139 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7532 (tptp) REVERT: F 274 MET cc_start: 0.6432 (mmm) cc_final: 0.6117 (mmp) REVERT: F 341 GLU cc_start: 0.5456 (tp30) cc_final: 0.4196 (pt0) REVERT: F 391 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7512 (tm) REVERT: F 437 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.5537 (t80) REVERT: E 96 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8324 (p) REVERT: E 192 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.4827 (mtmm) REVERT: E 317 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7093 (tp) REVERT: E 343 PHE cc_start: 0.0920 (p90) cc_final: 0.0441 (p90) REVERT: E 489 ASN cc_start: 0.6720 (OUTLIER) cc_final: 0.6478 (t0) REVERT: E 576 MET cc_start: 0.5151 (tpt) cc_final: 0.4938 (tmt) outliers start: 67 outliers final: 42 residues processed: 194 average time/residue: 0.6085 time to fit residues: 135.5297 Evaluate side-chains 178 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 125 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 139 LYS Chi-restraints excluded: chain F residue 205 TYR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain E residue 70 TYR Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 489 ASN Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [107, 22, 183, 88, 74, 249, 192, 142, 204, 193, 141] chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 249 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 909 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 ASN F 388 ASN F 537 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.127250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.071190 restraints weight = 46982.637| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.62 r_work: 0.3026 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21896 Z= 0.164 Angle : 0.684 14.619 30001 Z= 0.340 Chirality : 0.046 0.269 3465 Planarity : 0.004 0.044 3626 Dihedral : 9.159 140.380 3500 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.72 % Favored : 92.16 % Rotamer: Outliers : 3.18 % Allowed : 33.27 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.17), residues: 2551 helix: 0.01 (0.17), residues: 970 sheet: -0.89 (0.29), residues: 300 loop : -1.84 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 21 TYR 0.037 0.001 TYR F 582 PHE 0.020 0.001 PHE F 225 TRP 0.015 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (21866) covalent geometry : angle 0.67965 / 0.34 (29980) hydrogen bonds : bond 0.04286 / 2.81 ( 775) hydrogen bonds : angle 4.33869 / 3.00 ( 2129) metal coordination : bond 0.01502 / 0.76 ( 30) metal coordination : angle 2.87301 / 1.79 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12044.73 seconds wall clock time: 204 minutes 40.57 seconds (12280.57 seconds total)