Starting phenix.real_space_refine on Wed Jun 18 08:02:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mus_9254/06_2025/6mus_9254_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mus_9254/06_2025/6mus_9254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mus_9254/06_2025/6mus_9254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mus_9254/06_2025/6mus_9254.map" model { file = "/net/cci-nas-00/data/ceres_data/6mus_9254/06_2025/6mus_9254_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mus_9254/06_2025/6mus_9254_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 4 6.06 5 P 57 5.49 5 S 60 5.16 5 C 13078 2.51 5 N 3660 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20864 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6155 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 736} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1040 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2210 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 1 Chain: "D" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2284 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain: "E" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 20, 'TRANS': 258} Chain breaks: 1 Chain: "G" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 717 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 14, 'rna3p': 18} Chain: "H" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 524 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 9, 'rna3p_pyr': 9} Link IDs: {'rna2p': 7, 'rna3p': 17} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 907 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "K" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2198 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Chain: "F" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2618 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 10, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 8, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 250 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3079 SG CYS A 389 50.580 101.923 109.831 1.00 21.59 S ATOM 3099 SG CYS A 392 48.262 99.410 111.223 1.00 20.72 S ATOM 3254 SG CYS A 413 48.314 102.813 112.592 1.00 33.89 S ATOM 3274 SG CYS A 416 51.311 99.451 113.181 1.00 33.92 S ATOM 8018 SG CYS C 113 57.794 115.203 82.619 1.00 13.78 S ATOM 8085 SG CYS C 122 58.910 115.019 78.959 1.00 16.94 S ATOM 8105 SG CYS C 125 56.661 111.895 81.823 1.00 15.49 S ATOM 10302 SG CYS D 113 85.087 94.589 82.825 1.00 13.94 S ATOM 10369 SG CYS D 122 86.658 94.770 79.353 1.00 12.33 S ATOM 10389 SG CYS D 125 82.761 92.357 80.065 1.00 13.29 S ATOM 16855 SG CYS K 113 98.775 62.859 79.710 1.00 36.26 S ATOM 16922 SG CYS K 122 100.775 63.756 76.873 1.00 33.39 S ATOM 16942 SG CYS K 125 97.010 63.489 76.132 1.00 27.88 S Time building chain proxies: 11.70, per 1000 atoms: 0.56 Number of scatterers: 20864 At special positions: 0 Unit cell: (129.591, 132.858, 179.685, 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 4 29.99 S 60 16.00 P 57 15.00 O 4005 8.00 N 3660 7.00 C 13078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 89 " - pdb=" SG CYS D 97 " distance=2.03 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: 4.57 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 111 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 122 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 113 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 125 " Number of angles added : 12 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 31 sheets defined 39.5% alpha, 13.0% beta 11 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.934A pdb=" N THR A 7 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 29 through 40 removed outlier: 3.506A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.774A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 4.018A pdb=" N SER A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 4.191A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.631A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 4.095A pdb=" N GLU A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 3.867A pdb=" N LEU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.518A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.635A pdb=" N THR A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.953A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 removed outlier: 3.757A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.825A pdb=" N VAL A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.745A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.622A pdb=" N GLU A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.688A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.626A pdb=" N SER A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.625A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.876A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 598 through 614 removed outlier: 4.115A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.610A pdb=" N ASP A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.554A pdb=" N GLU A 679 " --> pdb=" O ASN A 675 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 680 " --> pdb=" O HIS A 676 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.986A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TRP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.530A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.594A pdb=" N VAL A 746 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.568A pdb=" N GLU A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 775 removed outlier: 4.187A pdb=" N VAL A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 62 removed outlier: 3.606A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix removed outlier: 4.936A pdb=" N ASN B 58 " --> pdb=" O PRO B 54 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 59 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.806A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 105 removed outlier: 3.904A pdb=" N THR B 105 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.615A pdb=" N LYS B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 134 removed outlier: 3.624A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 159 removed outlier: 3.852A pdb=" N TYR B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA B 144 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.930A pdb=" N GLU B 154 " --> pdb=" O ASP B 150 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.733A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 70 removed outlier: 3.999A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 removed outlier: 4.450A pdb=" N GLU C 76 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 207 through 223 removed outlier: 3.715A pdb=" N ALA C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.612A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.855A pdb=" N GLU C 284 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 285' Processing helix chain 'D' and resid 52 through 70 removed outlier: 3.947A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.812A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 removed outlier: 4.245A pdb=" N ASN D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.913A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 removed outlier: 3.504A pdb=" N ASP D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.879A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 51 removed outlier: 4.000A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.739A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 179 removed outlier: 3.633A pdb=" N GLY E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Proline residue: E 174 - end of helix removed outlier: 3.864A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 61 removed outlier: 3.680A pdb=" N VAL J 59 " --> pdb=" O TYR J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 82 removed outlier: 3.623A pdb=" N THR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 94 removed outlier: 3.664A pdb=" N GLN J 94 " --> pdb=" O LYS J 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 91 through 94' Processing helix chain 'J' and resid 95 through 108 removed outlier: 4.669A pdb=" N MET J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS J 108 " --> pdb=" O THR J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 134 removed outlier: 3.696A pdb=" N VAL J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS J 122 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU J 127 " --> pdb=" O MET J 123 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL J 131 " --> pdb=" O LEU J 127 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA J 134 " --> pdb=" O THR J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 150 removed outlier: 3.746A pdb=" N LEU J 149 " --> pdb=" O PHE J 145 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP J 150 " --> pdb=" O HIS J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'J' and resid 165 through 183 removed outlier: 3.699A pdb=" N GLN J 173 " --> pdb=" O TYR J 169 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 62 removed outlier: 4.169A pdb=" N ARG K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER K 61 " --> pdb=" O GLY K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 70 removed outlier: 3.705A pdb=" N SER K 69 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG K 70 " --> pdb=" O LEU K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 152 through 158 removed outlier: 4.108A pdb=" N TRP K 156 " --> pdb=" O TRP K 152 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG K 157 " --> pdb=" O GLU K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 223 removed outlier: 3.831A pdb=" N THR K 215 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA K 216 " --> pdb=" O ASN K 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP K 222 " --> pdb=" O ALA K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 254 Processing helix chain 'K' and resid 268 through 273 removed outlier: 3.539A pdb=" N ILE K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU K 273 " --> pdb=" O VAL K 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 268 through 273' Processing helix chain 'K' and resid 275 through 280 removed outlier: 3.756A pdb=" N LEU K 279 " --> pdb=" O GLY K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 51 through 60 removed outlier: 4.014A pdb=" N LEU F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.547A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 123 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.701A pdb=" N ARG F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 148 through 156 removed outlier: 3.690A pdb=" N ARG F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 168 removed outlier: 4.483A pdb=" N SER F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 168 " --> pdb=" O TYR F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.559A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.538A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 304 removed outlier: 3.953A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 326 removed outlier: 3.749A pdb=" N SER F 324 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 326 " --> pdb=" O TYR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.951A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 3.559A pdb=" N ASN F 359 " --> pdb=" O TYR F 355 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.742A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 445 removed outlier: 4.150A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 580 through 585 removed outlier: 4.667A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 519 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA7, first strand: chain 'A' and resid 689 through 691 removed outlier: 3.559A pdb=" N ALA A 690 " --> pdb=" O ARG A 694 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 143 through 148 removed outlier: 5.657A pdb=" N VAL C 143 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE C 197 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP C 145 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU C 195 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 190 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 5.137A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB2, first strand: chain 'C' and resid 163 through 171 Processing sheet with id=AB3, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.551A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 141 through 143 removed outlier: 4.018A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LYS D 14 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE D 240 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS D 16 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE D 238 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 88 removed outlier: 4.502A pdb=" N SER D 85 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE D 101 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLY D 87 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB7, first strand: chain 'D' and resid 163 through 171 Processing sheet with id=AB8, first strand: chain 'E' and resid 101 through 103 removed outlier: 3.648A pdb=" N THR E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 131 Processing sheet with id=AC2, first strand: chain 'E' and resid 252 through 254 removed outlier: 4.481A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.504A pdb=" N LYS E 232 " --> pdb=" O MET E 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC5, first strand: chain 'E' and resid 261 through 263 removed outlier: 3.776A pdb=" N GLU E 261 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 271 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.716A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL K 10 " --> pdb=" O PHE K 243 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE K 243 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS K 12 " --> pdb=" O ASP K 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 241 " --> pdb=" O LYS K 12 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE K 243 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 85 through 88 removed outlier: 7.398A pdb=" N SER K 85 " --> pdb=" O PHE K 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AC9, first strand: chain 'K' and resid 166 through 168 removed outlier: 3.598A pdb=" N ARG K 181 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 250 through 251 removed outlier: 3.652A pdb=" N VAL F 251 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.601A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AD4, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.631A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.82 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5136 1.33 - 1.45: 5032 1.45 - 1.58: 11043 1.58 - 1.70: 113 1.70 - 1.82: 97 Bond restraints: 21421 Sorted by residual: bond pdb=" C1' G G 33 " pdb=" N9 G G 33 " ideal model delta sigma weight residual 1.465 1.368 0.097 1.50e-02 4.44e+03 4.19e+01 bond pdb=" C1' U H 14 " pdb=" N1 U H 14 " ideal model delta sigma weight residual 1.470 1.561 -0.091 1.50e-02 4.44e+03 3.71e+01 bond pdb=" C1' G H 17 " pdb=" N9 G H 17 " ideal model delta sigma weight residual 1.475 1.384 0.091 1.50e-02 4.44e+03 3.68e+01 bond pdb=" C1' A H 12 " pdb=" N9 A H 12 " ideal model delta sigma weight residual 1.465 1.382 0.083 1.50e-02 4.44e+03 3.04e+01 bond pdb=" C1' U G 32 " pdb=" N1 U G 32 " ideal model delta sigma weight residual 1.480 1.561 -0.081 1.50e-02 4.44e+03 2.95e+01 ... (remaining 21416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 27335 2.07 - 4.14: 1624 4.14 - 6.21: 179 6.21 - 8.28: 67 8.28 - 10.35: 14 Bond angle restraints: 29219 Sorted by residual: angle pdb=" N PRO F 61 " pdb=" CA PRO F 61 " pdb=" CB PRO F 61 " ideal model delta sigma weight residual 103.08 110.19 -7.11 9.70e-01 1.06e+00 5.37e+01 angle pdb=" N PRO F 79 " pdb=" CA PRO F 79 " pdb=" CB PRO F 79 " ideal model delta sigma weight residual 103.25 110.85 -7.60 1.05e+00 9.07e-01 5.23e+01 angle pdb=" N PRO B 54 " pdb=" CA PRO B 54 " pdb=" CB PRO B 54 " ideal model delta sigma weight residual 103.20 109.92 -6.72 9.50e-01 1.11e+00 5.00e+01 angle pdb=" N PRO B 71 " pdb=" CA PRO B 71 " pdb=" CB PRO B 71 " ideal model delta sigma weight residual 103.25 110.65 -7.40 1.05e+00 9.07e-01 4.97e+01 angle pdb=" N PRO F 62 " pdb=" CA PRO F 62 " pdb=" CB PRO F 62 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 ... (remaining 29214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 12582 34.34 - 68.67: 277 68.67 - 103.01: 28 103.01 - 137.34: 2 137.34 - 171.67: 2 Dihedral angle restraints: 12891 sinusoidal: 5666 harmonic: 7225 Sorted by residual: dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 43.67 -171.67 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 20 " pdb=" C1' C G 20 " pdb=" N1 C G 20 " pdb=" C2 C G 20 " ideal model delta sinusoidal sigma weight residual -128.00 31.60 -159.60 1 1.70e+01 3.46e-03 6.44e+01 dihedral pdb=" CA SER D 228 " pdb=" C SER D 228 " pdb=" N GLY D 229 " pdb=" CA GLY D 229 " ideal model delta harmonic sigma weight residual 180.00 150.15 29.85 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 12888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 2902 0.100 - 0.201: 289 0.201 - 0.301: 34 0.301 - 0.402: 1 0.402 - 0.502: 1 Chirality restraints: 3227 Sorted by residual: chirality pdb=" CB VAL D 236 " pdb=" CA VAL D 236 " pdb=" CG1 VAL D 236 " pdb=" CG2 VAL D 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" CA ASP A 135 " pdb=" N ASP A 135 " pdb=" C ASP A 135 " pdb=" CB ASP A 135 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ILE D 29 " pdb=" N ILE D 29 " pdb=" C ILE D 29 " pdb=" CB ILE D 29 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3224 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 271 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ASP C 271 " -0.065 2.00e-02 2.50e+03 pdb=" O ASP C 271 " 0.025 2.00e-02 2.50e+03 pdb=" N ILE C 272 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 17 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C GLY A 17 " -0.059 2.00e-02 2.50e+03 pdb=" O GLY A 17 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 18 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 146 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.50e+00 pdb=" C ALA C 146 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA C 146 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE C 147 " -0.017 2.00e-02 2.50e+03 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 135 2.50 - 3.10: 13913 3.10 - 3.70: 31990 3.70 - 4.30: 46154 4.30 - 4.90: 76652 Nonbonded interactions: 168844 Sorted by model distance: nonbonded pdb=" O SER C 25 " pdb=" CG GLN C 26 " model vdw 1.904 3.440 nonbonded pdb=" O SER C 25 " pdb=" CD GLN C 26 " model vdw 2.014 3.270 nonbonded pdb=" O SER C 25 " pdb=" NE2 GLN C 26 " model vdw 2.059 3.120 nonbonded pdb=" N4 C H 11 " pdb=" N6 A H 12 " model vdw 2.113 3.200 nonbonded pdb=" O2' C G 27 " pdb=" C8 G G 28 " model vdw 2.142 3.260 ... (remaining 168839 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 49 through 83 or resid 91 through 108 or resid 116 through \ 183)) selection = chain 'J' } ncs_group { reference = (chain 'C' and (resid 4 through 24 or resid 37 through 287 or resid 301)) selection = (chain 'D' and (resid 4 through 24 or resid 37 through 287 or resid 301)) selection = (chain 'K' and (resid 4 through 287 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 52.590 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 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 0.316 21437 Z= 0.437 Angle : 1.151 26.849 29233 Z= 0.665 Chirality : 0.063 0.502 3227 Planarity : 0.008 0.070 3560 Dihedral : 14.036 171.675 8264 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 0.55 % Allowed : 5.34 % Favored : 94.10 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.22 (0.12), residues: 2485 helix: -4.32 (0.09), residues: 887 sheet: -2.89 (0.23), residues: 363 loop : -2.90 (0.14), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 206 HIS 0.013 0.003 HIS C 111 PHE 0.028 0.004 PHE K 194 TYR 0.041 0.003 TYR K 49 ARG 0.014 0.001 ARG F 212 Details of bonding type rmsd hydrogen bonds : bond 0.30409 ( 651) hydrogen bonds : angle 11.07488 ( 1854) metal coordination : bond 0.14083 ( 15) metal coordination : angle 13.97182 ( 12) SS BOND : bond 0.00581 ( 1) SS BOND : angle 2.99116 ( 2) covalent geometry : bond 0.00879 (21421) covalent geometry : angle 1.11594 (29219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 569 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7000 (pm20) REVERT: A 135 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6747 (p0) REVERT: A 239 ASP cc_start: 0.8357 (t70) cc_final: 0.8044 (t0) REVERT: A 751 LYS cc_start: 0.7696 (ttpm) cc_final: 0.7258 (tttp) REVERT: B 101 MET cc_start: 0.6498 (tpp) cc_final: 0.6129 (tmm) REVERT: B 153 LEU cc_start: 0.6441 (mt) cc_final: 0.6082 (mt) REVERT: C 263 ASP cc_start: 0.7330 (p0) cc_final: 0.6779 (p0) REVERT: D 125 CYS cc_start: 0.7396 (m) cc_final: 0.6794 (m) REVERT: D 172 ASP cc_start: 0.7303 (t0) cc_final: 0.7027 (t0) REVERT: E 17 ASP cc_start: 0.8303 (t0) cc_final: 0.8061 (t0) REVERT: K 109 TRP cc_start: 0.6738 (m100) cc_final: 0.5521 (m100) REVERT: K 259 ILE cc_start: 0.7975 (mp) cc_final: 0.7686 (mp) outliers start: 11 outliers final: 2 residues processed: 576 average time/residue: 0.4056 time to fit residues: 331.6682 Evaluate side-chains 335 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 332 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain D residue 236 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 214 optimal weight: 6.9990 chunk 192 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 129 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 230 optimal weight: 50.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN A 598 GLN A 675 ASN C 44 HIS C 111 HIS C 136 ASN D 83 ASN D 136 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 ASN E 139 GLN K 83 ASN K 136 ASN F 18 ASN F 99 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.141383 restraints weight = 31413.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138539 restraints weight = 39930.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140657 restraints weight = 38095.011| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 21437 Z= 0.283 Angle : 0.811 15.346 29233 Z= 0.410 Chirality : 0.050 0.282 3227 Planarity : 0.007 0.077 3560 Dihedral : 15.475 171.997 3693 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.68 % Allowed : 11.39 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.14), residues: 2485 helix: -2.89 (0.13), residues: 912 sheet: -2.45 (0.24), residues: 340 loop : -2.52 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 131 HIS 0.013 0.002 HIS F 331 PHE 0.022 0.002 PHE A 37 TYR 0.045 0.003 TYR D 233 ARG 0.009 0.001 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.05364 ( 651) hydrogen bonds : angle 6.27697 ( 1854) metal coordination : bond 0.01929 ( 15) metal coordination : angle 5.44735 ( 12) SS BOND : bond 0.00308 ( 1) SS BOND : angle 2.56134 ( 2) covalent geometry : bond 0.00654 (21421) covalent geometry : angle 0.80319 (29219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6322 (mm-30) REVERT: A 61 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6063 (t-90) REVERT: A 239 ASP cc_start: 0.8394 (t70) cc_final: 0.8145 (t0) REVERT: A 514 ARG cc_start: 0.7173 (tpp80) cc_final: 0.6962 (mmt90) REVERT: A 635 ARG cc_start: 0.6682 (mmm160) cc_final: 0.6400 (tpt170) REVERT: B 80 THR cc_start: 0.7062 (p) cc_final: 0.6656 (t) REVERT: B 122 LYS cc_start: 0.8218 (mttt) cc_final: 0.7998 (mmtt) REVERT: B 162 LYS cc_start: 0.5640 (mptt) cc_final: 0.5421 (mtmt) REVERT: C 193 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7266 (pt0) REVERT: C 263 ASP cc_start: 0.7714 (p0) cc_final: 0.7203 (p0) REVERT: D 62 LEU cc_start: 0.9081 (mt) cc_final: 0.8777 (mt) REVERT: D 181 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5946 (ptp90) REVERT: E 95 ARG cc_start: 0.7913 (ptp-110) cc_final: 0.7635 (ptm-80) REVERT: K 2 ASP cc_start: 0.6644 (t70) cc_final: 0.6443 (t70) REVERT: K 78 TYR cc_start: 0.7114 (m-80) cc_final: 0.6425 (m-10) REVERT: K 162 ILE cc_start: 0.8190 (tp) cc_final: 0.7781 (mp) REVERT: K 249 ASP cc_start: 0.7771 (t0) cc_final: 0.7447 (t0) REVERT: F 24 ASP cc_start: 0.4117 (OUTLIER) cc_final: 0.3373 (m-30) REVERT: F 105 LYS cc_start: 0.8427 (mtmm) cc_final: 0.8152 (mttp) REVERT: F 389 MET cc_start: 0.2298 (tmm) cc_final: 0.1210 (ttp) REVERT: F 391 MET cc_start: 0.5258 (mtp) cc_final: 0.4535 (mtp) outliers start: 73 outliers final: 50 residues processed: 412 average time/residue: 0.3794 time to fit residues: 228.9280 Evaluate side-chains 366 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 246 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 chunk 219 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 181 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 154 optimal weight: 4.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN C 37 ASN D 26 GLN D 83 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN ** F 99 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 = 0.4076 r_free = 0.4076 target = 0.176663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142819 restraints weight = 31346.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140332 restraints weight = 47309.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141903 restraints weight = 41113.908| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21437 Z= 0.208 Angle : 0.704 14.753 29233 Z= 0.354 Chirality : 0.046 0.287 3227 Planarity : 0.005 0.050 3560 Dihedral : 15.178 164.511 3689 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.93 % Allowed : 14.36 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.15), residues: 2485 helix: -2.06 (0.15), residues: 927 sheet: -2.26 (0.25), residues: 340 loop : -2.37 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 152 HIS 0.008 0.001 HIS F 331 PHE 0.022 0.002 PHE F 288 TYR 0.025 0.002 TYR D 233 ARG 0.008 0.001 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 651) hydrogen bonds : angle 5.72291 ( 1854) metal coordination : bond 0.01445 ( 15) metal coordination : angle 4.10940 ( 12) SS BOND : bond 0.00286 ( 1) SS BOND : angle 1.89983 ( 2) covalent geometry : bond 0.00482 (21421) covalent geometry : angle 0.69910 (29219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 334 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7494 (tm130) cc_final: 0.6833 (tm-30) REVERT: A 87 MET cc_start: 0.7195 (tpp) cc_final: 0.6956 (tpt) REVERT: A 239 ASP cc_start: 0.8355 (t70) cc_final: 0.8077 (t0) REVERT: A 322 TYR cc_start: 0.7510 (t80) cc_final: 0.7277 (t80) REVERT: B 80 THR cc_start: 0.6990 (p) cc_final: 0.6472 (t) REVERT: B 106 GLU cc_start: 0.6929 (tp30) cc_final: 0.6428 (tp30) REVERT: B 147 ARG cc_start: 0.7310 (ptp90) cc_final: 0.6977 (ptm-80) REVERT: C 133 LYS cc_start: 0.7580 (mttm) cc_final: 0.7366 (mtpm) REVERT: C 240 PHE cc_start: 0.8456 (m-80) cc_final: 0.8249 (m-80) REVERT: C 263 ASP cc_start: 0.7613 (p0) cc_final: 0.7036 (p0) REVERT: K 78 TYR cc_start: 0.6880 (m-80) cc_final: 0.6292 (m-10) REVERT: K 109 TRP cc_start: 0.6750 (m100) cc_final: 0.6091 (m100) REVERT: K 162 ILE cc_start: 0.8192 (tp) cc_final: 0.7839 (mp) REVERT: K 249 ASP cc_start: 0.7680 (t0) cc_final: 0.7394 (t0) REVERT: F 24 ASP cc_start: 0.4160 (OUTLIER) cc_final: 0.3371 (m-30) REVERT: F 109 ARG cc_start: 0.5922 (ttp-110) cc_final: 0.5471 (mtm180) REVERT: F 268 ASN cc_start: 0.7133 (t0) cc_final: 0.6923 (t0) REVERT: F 301 MET cc_start: 0.3338 (tmm) cc_final: 0.2965 (tmm) outliers start: 78 outliers final: 58 residues processed: 380 average time/residue: 0.3650 time to fit residues: 206.8685 Evaluate side-chains 357 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 298 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 233 TYR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 224 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 0.0000 chunk 186 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 240 optimal weight: 6.9990 chunk 37 optimal weight: 0.0050 chunk 22 optimal weight: 6.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 456 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN K 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144553 restraints weight = 31494.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139938 restraints weight = 33623.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141410 restraints weight = 32263.291| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21437 Z= 0.136 Angle : 0.616 14.197 29233 Z= 0.311 Chirality : 0.044 0.296 3227 Planarity : 0.004 0.041 3560 Dihedral : 14.891 162.221 3687 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.03 % Allowed : 14.67 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.15), residues: 2485 helix: -1.43 (0.16), residues: 934 sheet: -1.95 (0.25), residues: 343 loop : -2.24 (0.16), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 162 HIS 0.010 0.001 HIS F 331 PHE 0.015 0.001 PHE A 59 TYR 0.029 0.002 TYR F 322 ARG 0.009 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 651) hydrogen bonds : angle 5.22360 ( 1854) metal coordination : bond 0.00857 ( 15) metal coordination : angle 3.30724 ( 12) SS BOND : bond 0.00190 ( 1) SS BOND : angle 1.44383 ( 2) covalent geometry : bond 0.00306 (21421) covalent geometry : angle 0.61279 (29219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 336 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7587 (tm130) cc_final: 0.6991 (tm-30) REVERT: A 61 HIS cc_start: 0.6651 (OUTLIER) cc_final: 0.6094 (t-90) REVERT: A 121 SER cc_start: 0.8841 (t) cc_final: 0.8545 (p) REVERT: A 239 ASP cc_start: 0.8302 (t70) cc_final: 0.8052 (t0) REVERT: A 322 TYR cc_start: 0.7513 (t80) cc_final: 0.7255 (t80) REVERT: A 572 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6439 (ppt-90) REVERT: A 759 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6761 (mp10) REVERT: A 768 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 777 ARG cc_start: 0.2532 (OUTLIER) cc_final: 0.1921 (ppt-90) REVERT: B 80 THR cc_start: 0.6410 (p) cc_final: 0.6156 (t) REVERT: B 147 ARG cc_start: 0.7329 (ptp90) cc_final: 0.7006 (ptm-80) REVERT: C 224 TYR cc_start: 0.8669 (p90) cc_final: 0.8364 (p90) REVERT: C 263 ASP cc_start: 0.7709 (p0) cc_final: 0.7071 (p0) REVERT: E 139 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: E 252 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8627 (mp) REVERT: J 169 TYR cc_start: 0.6476 (t80) cc_final: 0.6236 (t80) REVERT: J 180 LYS cc_start: 0.7552 (tttm) cc_final: 0.7344 (tttm) REVERT: K 78 TYR cc_start: 0.7031 (m-80) cc_final: 0.6247 (m-10) REVERT: K 109 TRP cc_start: 0.6623 (m100) cc_final: 0.5956 (m100) REVERT: F 24 ASP cc_start: 0.4214 (OUTLIER) cc_final: 0.3906 (m-30) REVERT: F 109 ARG cc_start: 0.6129 (ttp-110) cc_final: 0.5526 (mtm180) REVERT: F 266 TYR cc_start: 0.3248 (t80) cc_final: 0.2837 (t80) REVERT: F 268 ASN cc_start: 0.7055 (t0) cc_final: 0.6837 (t0) REVERT: F 301 MET cc_start: 0.3586 (tmm) cc_final: 0.3213 (tmm) REVERT: F 389 MET cc_start: 0.1100 (OUTLIER) cc_final: 0.0520 (ptm) outliers start: 80 outliers final: 50 residues processed: 393 average time/residue: 0.3631 time to fit residues: 212.7889 Evaluate side-chains 352 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 389 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 186 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN D 205 HIS E 139 GLN E 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.177744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143288 restraints weight = 31565.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141488 restraints weight = 41915.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143455 restraints weight = 37068.015| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21437 Z= 0.160 Angle : 0.628 12.982 29233 Z= 0.316 Chirality : 0.044 0.295 3227 Planarity : 0.004 0.041 3560 Dihedral : 14.792 162.691 3687 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.69 % Allowed : 15.12 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2485 helix: -0.99 (0.17), residues: 929 sheet: -1.94 (0.25), residues: 361 loop : -2.18 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 162 HIS 0.007 0.001 HIS F 331 PHE 0.015 0.001 PHE J 171 TYR 0.026 0.002 TYR B 125 ARG 0.010 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 651) hydrogen bonds : angle 5.14267 ( 1854) metal coordination : bond 0.00958 ( 15) metal coordination : angle 3.43048 ( 12) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.47002 ( 2) covalent geometry : bond 0.00368 (21421) covalent geometry : angle 0.62437 (29219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 316 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7536 (tm130) cc_final: 0.6976 (tm-30) REVERT: A 61 HIS cc_start: 0.6486 (OUTLIER) cc_final: 0.5936 (t-90) REVERT: A 239 ASP cc_start: 0.8328 (t70) cc_final: 0.7990 (t0) REVERT: A 322 TYR cc_start: 0.7593 (t80) cc_final: 0.7334 (t80) REVERT: A 572 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6501 (ppt-90) REVERT: A 759 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6662 (mp10) REVERT: A 768 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 777 ARG cc_start: 0.2567 (OUTLIER) cc_final: 0.1945 (ppt-90) REVERT: B 73 LYS cc_start: 0.1545 (OUTLIER) cc_final: 0.1018 (pttp) REVERT: B 80 THR cc_start: 0.6642 (p) cc_final: 0.6328 (t) REVERT: B 106 GLU cc_start: 0.6519 (mm-30) cc_final: 0.6262 (mm-30) REVERT: B 147 ARG cc_start: 0.7208 (ptp90) cc_final: 0.6953 (ptm-80) REVERT: C 224 TYR cc_start: 0.8670 (p90) cc_final: 0.8334 (p90) REVERT: C 263 ASP cc_start: 0.7625 (p0) cc_final: 0.7014 (p0) REVERT: E 252 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8723 (mp) REVERT: K 78 TYR cc_start: 0.6996 (m-80) cc_final: 0.6267 (m-10) REVERT: K 109 TRP cc_start: 0.6686 (m100) cc_final: 0.6071 (m100) REVERT: F 24 ASP cc_start: 0.4352 (OUTLIER) cc_final: 0.3611 (m-30) REVERT: F 266 TYR cc_start: 0.3572 (t80) cc_final: 0.3060 (t80) REVERT: F 322 TYR cc_start: 0.2886 (m-80) cc_final: 0.2674 (m-80) outliers start: 93 outliers final: 67 residues processed: 381 average time/residue: 0.3533 time to fit residues: 200.4947 Evaluate side-chains 370 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 382 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 167 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 187 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 456 GLN ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.176951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143267 restraints weight = 31246.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.142581 restraints weight = 38818.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143327 restraints weight = 42263.692| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21437 Z= 0.172 Angle : 0.634 13.072 29233 Z= 0.320 Chirality : 0.044 0.300 3227 Planarity : 0.004 0.040 3560 Dihedral : 14.758 163.076 3687 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.84 % Allowed : 15.68 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2485 helix: -0.79 (0.17), residues: 939 sheet: -1.76 (0.26), residues: 353 loop : -2.19 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 162 HIS 0.006 0.001 HIS F 331 PHE 0.014 0.001 PHE D 243 TYR 0.025 0.002 TYR B 125 ARG 0.012 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 651) hydrogen bonds : angle 5.08318 ( 1854) metal coordination : bond 0.01019 ( 15) metal coordination : angle 3.43911 ( 12) SS BOND : bond 0.00239 ( 1) SS BOND : angle 1.43157 ( 2) covalent geometry : bond 0.00400 (21421) covalent geometry : angle 0.62979 (29219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 305 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7492 (tm130) cc_final: 0.6932 (tm-30) REVERT: A 61 HIS cc_start: 0.6395 (OUTLIER) cc_final: 0.5858 (t-90) REVERT: A 239 ASP cc_start: 0.8277 (t70) cc_final: 0.7978 (t0) REVERT: A 322 TYR cc_start: 0.7623 (t80) cc_final: 0.7347 (t80) REVERT: A 572 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6484 (ppt-90) REVERT: A 759 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6557 (mp10) REVERT: A 777 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.1889 (ppt-90) REVERT: B 73 LYS cc_start: 0.1311 (OUTLIER) cc_final: 0.0221 (pttp) REVERT: B 80 THR cc_start: 0.6651 (p) cc_final: 0.6337 (t) REVERT: B 147 ARG cc_start: 0.7233 (ptp90) cc_final: 0.6980 (ptm-80) REVERT: C 14 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8327 (mttp) REVERT: C 224 TYR cc_start: 0.8732 (p90) cc_final: 0.8384 (p90) REVERT: C 263 ASP cc_start: 0.7588 (p0) cc_final: 0.7048 (p0) REVERT: D 96 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7956 (m-40) REVERT: D 99 LYS cc_start: 0.6747 (mmtt) cc_final: 0.6542 (mtmm) REVERT: E 139 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: E 252 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8719 (mp) REVERT: J 105 THR cc_start: 0.6339 (p) cc_final: 0.6062 (p) REVERT: J 120 LEU cc_start: 0.5395 (mp) cc_final: 0.5166 (mp) REVERT: K 78 TYR cc_start: 0.7043 (m-80) cc_final: 0.6283 (m-10) REVERT: K 109 TRP cc_start: 0.6644 (m100) cc_final: 0.6054 (m100) REVERT: K 249 ASP cc_start: 0.7922 (t0) cc_final: 0.7563 (t0) REVERT: F 24 ASP cc_start: 0.4221 (OUTLIER) cc_final: 0.3486 (m-30) REVERT: F 266 TYR cc_start: 0.3397 (t80) cc_final: 0.2884 (t80) REVERT: F 301 MET cc_start: 0.3440 (tmm) cc_final: 0.3008 (tmm) outliers start: 96 outliers final: 72 residues processed: 370 average time/residue: 0.3560 time to fit residues: 198.2599 Evaluate side-chains 372 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 290 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain J residue 92 THR Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 256 ASP Chi-restraints excluded: chain K residue 273 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 382 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2532 > 50: distance: 82 - 87: 8.925 distance: 87 - 88: 19.713 distance: 88 - 89: 14.982 distance: 88 - 91: 16.155 distance: 89 - 90: 13.741 distance: 91 - 92: 9.742 distance: 92 - 93: 10.049 distance: 93 - 94: 11.445 distance: 94 - 95: 4.003 distance: 95 - 96: 6.229 distance: 95 - 97: 7.101 distance: 98 - 99: 12.658 distance: 99 - 100: 12.985 distance: 99 - 102: 8.249 distance: 100 - 101: 6.112 distance: 100 - 103: 7.942 distance: 103 - 104: 11.561 distance: 104 - 105: 7.966 distance: 104 - 107: 9.626 distance: 105 - 106: 6.463 distance: 105 - 111: 4.141 distance: 107 - 108: 8.707 distance: 108 - 109: 10.335 distance: 108 - 110: 8.556 distance: 111 - 112: 9.057 distance: 112 - 113: 13.843 distance: 112 - 115: 3.611 distance: 113 - 114: 11.960 distance: 113 - 118: 13.371 distance: 115 - 116: 5.721 distance: 115 - 117: 9.075 distance: 118 - 119: 6.739 distance: 118 - 174: 7.113 distance: 119 - 120: 16.081 distance: 119 - 122: 15.619 distance: 120 - 121: 15.731 distance: 120 - 125: 8.971 distance: 122 - 123: 16.874 distance: 122 - 124: 13.485 distance: 125 - 126: 5.485 distance: 126 - 127: 12.540 distance: 127 - 128: 10.565 distance: 127 - 136: 6.847 distance: 129 - 130: 4.267 distance: 130 - 131: 4.205 distance: 130 - 132: 3.050 distance: 131 - 133: 6.505 distance: 132 - 134: 4.972 distance: 133 - 135: 4.332 distance: 134 - 135: 5.629 distance: 136 - 137: 7.023 distance: 137 - 138: 8.399 distance: 137 - 140: 6.484 distance: 138 - 139: 13.839 distance: 138 - 144: 6.590 distance: 140 - 141: 4.001 distance: 141 - 142: 3.365 distance: 141 - 143: 5.408 distance: 144 - 145: 10.274 distance: 145 - 146: 18.647 distance: 145 - 148: 9.492 distance: 146 - 147: 22.856 distance: 146 - 149: 10.907 distance: 149 - 150: 16.475 distance: 150 - 151: 18.023 distance: 151 - 152: 34.386 distance: 151 - 153: 28.792 distance: 153 - 154: 11.168 distance: 154 - 155: 13.535 distance: 155 - 156: 20.386 distance: 155 - 157: 24.618