Starting phenix.real_space_refine on Sun Sep 13 04:54:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mus_9254/09_2026/6mus_9254_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mus_9254/09_2026/6mus_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 { model { file = "/net/cci-nas-00/data/ceres_data/6mus_9254/09_2026/6mus_9254_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mus_9254/09_2026/6mus_9254_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mus_9254/09_2026/6mus_9254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mus_9254/09_2026/6mus_9254.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 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, 'TRP:plan': 2, 'GLU:plan': 3, 'TYR:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 2, '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: {'TRP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 2, '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: {'ASN:plan1': 6, 'ASP:plan': 11, 'GLU:plan': 8, 'TYR:plan': 7, 'TRP:plan': 2, 'PHE:plan': 6, 'HIS:plan': 2, 'ARG:plan': 10, 'GLN:plan1': 1} 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: 4.61, per 1000 atoms: 0.22 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: 1.68 Conformation dependent library (CDL) restraints added in 901.0 milliseconds 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: 2.14 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: 3.55 Time building geometry restraints manager: 2.28 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' U H 14 " pdb=" N1 U H 14 " ideal model delta sigma weight residual 1.464 1.561 -0.097 1.40e-02 5.10e+03 4.84e+01 bond pdb=" C1' G G 33 " pdb=" N9 G G 33 " ideal model delta sigma weight residual 1.464 1.368 0.096 1.40e-02 5.10e+03 4.71e+01 bond pdb=" C1' G H 17 " pdb=" N9 G H 17 " ideal model delta sigma weight residual 1.483 1.384 0.099 1.50e-02 4.44e+03 4.35e+01 bond pdb=" C1' A H 12 " pdb=" N9 A H 12 " ideal model delta sigma weight residual 1.464 1.382 0.082 1.40e-02 5.10e+03 3.41e+01 bond pdb=" C1' C G 27 " pdb=" N1 C G 27 " ideal model delta sigma weight residual 1.464 1.541 -0.077 1.40e-02 5.10e+03 3.03e+01 ... (remaining 21416 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 27236 2.07 - 4.14: 1723 4.14 - 6.21: 178 6.21 - 8.28: 69 8.28 - 10.35: 13 Bond angle restraints: 29219 Sorted by residual: angle pdb=" N1 C H 28 " pdb=" C2 C H 28 " pdb=" O2 C H 28 " ideal model delta sigma weight residual 118.90 123.82 -4.92 6.00e-01 2.78e+00 6.72e+01 angle pdb=" N1 C G 20 " pdb=" C2 C G 20 " pdb=" O2 C G 20 " ideal model delta sigma weight residual 118.90 123.69 -4.79 6.00e-01 2.78e+00 6.38e+01 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=" O2 C G 20 " pdb=" C2 C G 20 " pdb=" N3 C G 20 " ideal model delta sigma weight residual 121.90 116.80 5.10 7.00e-01 2.04e+00 5.32e+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 ... (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: 2852 0.100 - 0.201: 341 0.201 - 0.301: 32 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 301)) selection = (chain 'D' and (resid 4 through 24 or resid 37 through 301)) selection = (chain 'K' and resid 4 through 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: 1.120 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.260 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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= 0.466 Angle : 1.163 26.849 29233 Z= 0.718 Chirality : 0.065 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 : 10.98 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.014 0.001 ARG F 212 TYR 0.041 0.003 TYR K 49 PHE 0.028 0.004 PHE K 194 TRP 0.030 0.003 TRP C 206 HIS 0.013 0.003 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.45 (21421) covalent geometry : angle 1.12825 / 0.72 (29219) SS BOND : bond 0.00581 / 0.31 ( 1) SS BOND : angle 2.99116 / 1.70 ( 2) hydrogen bonds : bond 0.30409 / 19.91 ( 651) hydrogen bonds : angle 11.07488 / 7.55 ( 1854) metal coordination : bond 0.14083 / 8.93 ( 15) metal coordination : angle 13.97182 / 7.61 ( 12) *********************** 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 : 0.707 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: 0.6999 (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: 0.8043 (t0) REVERT: A 751 LYS cc_start: 0.7696 (ttpm) cc_final: 0.7259 (tttp) REVERT: B 101 MET cc_start: 0.6498 (tpp) cc_final: 0.6131 (tmm) REVERT: B 153 LEU cc_start: 0.6441 (mt) cc_final: 0.6080 (mt) REVERT: C 263 ASP cc_start: 0.7330 (p0) cc_final: 0.6777 (p0) REVERT: D 125 CYS cc_start: 0.7396 (m) cc_final: 0.6795 (m) REVERT: D 172 ASP cc_start: 0.7303 (t0) cc_final: 0.7029 (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: 0.5520 (m100) REVERT: K 259 ILE cc_start: 0.7975 (mp) cc_final: 0.7685 (mp) outliers start: 11 outliers final: 2 residues processed: 576 average time/residue: 0.1902 time to fit residues: 158.2278 Evaluate side-chains 334 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 331 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.0050 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 0.4980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 33 GLN A 102 ASN A 201 HIS A 456 GLN A 598 GLN C 37 ASN C 93 ASN C 111 HIS C 136 ASN D 83 ASN D 136 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN K 136 ASN F 18 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.183146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148233 restraints weight = 31282.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146670 restraints weight = 39237.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148313 restraints weight = 37354.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148478 restraints weight = 24258.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.149308 restraints weight = 21220.747| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21437 Z= 0.158 Angle : 0.743 13.469 29233 Z= 0.382 Chirality : 0.047 0.289 3227 Planarity : 0.006 0.063 3560 Dihedral : 15.547 176.376 3693 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.59 % Favored : 94.37 % Rotamer: Outliers : 2.72 % Allowed : 11.39 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.13), residues: 2485 helix: -2.98 (0.12), residues: 926 sheet: -2.43 (0.24), residues: 332 loop : -2.54 (0.15), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 177 TYR 0.025 0.002 TYR F 111 PHE 0.021 0.002 PHE A 37 TRP 0.014 0.001 TRP C 206 HIS 0.016 0.002 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (21421) covalent geometry : angle 0.73785 / 0.38 (29219) SS BOND : bond 0.00029 / 0.02 ( 1) SS BOND : angle 2.36822 / 1.27 ( 2) hydrogen bonds : bond 0.06686 / 4.43 ( 651) hydrogen bonds : angle 6.63797 / 4.56 ( 1854) metal coordination : bond 0.01377 / 0.93 ( 15) metal coordination : angle 4.08777 / 2.17 ( 12) *********************** 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 443 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 389 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7014 (pm20) REVERT: A 135 ASP cc_start: 0.7174 (OUTLIER) cc_final: 0.6736 (p0) REVERT: A 239 ASP cc_start: 0.8376 (t70) cc_final: 0.8091 (t0) REVERT: A 759 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: B 80 THR cc_start: 0.7148 (p) cc_final: 0.6805 (t) REVERT: B 101 MET cc_start: 0.6485 (tpp) cc_final: 0.6158 (tmm) REVERT: B 106 GLU cc_start: 0.6824 (tp30) cc_final: 0.6398 (tp30) REVERT: B 162 LYS cc_start: 0.5437 (mptt) cc_final: 0.5223 (mtmt) REVERT: C 193 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7138 (pt0) REVERT: C 263 ASP cc_start: 0.7451 (p0) cc_final: 0.7142 (p0) REVERT: D 62 LEU cc_start: 0.9045 (mt) cc_final: 0.8778 (mt) REVERT: K 78 TYR cc_start: 0.7139 (m-80) cc_final: 0.6357 (m-10) REVERT: K 249 ASP cc_start: 0.7461 (t0) cc_final: 0.7238 (t0) REVERT: F 24 ASP cc_start: 0.4196 (OUTLIER) cc_final: 0.3257 (m-30) REVERT: F 105 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7930 (mttp) outliers start: 54 outliers final: 33 residues processed: 428 average time/residue: 0.1694 time to fit residues: 108.1751 Evaluate side-chains 357 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 320 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 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 151 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 269 VAL 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 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 255 ASN Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain K residue 45 THR 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 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 142 optimal weight: 0.5980 chunk 176 optimal weight: 40.0000 chunk 186 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 456 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.182473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.148640 restraints weight = 31597.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147411 restraints weight = 40711.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.148709 restraints weight = 39118.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149156 restraints weight = 24647.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.150325 restraints weight = 21655.324| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21437 Z= 0.139 Angle : 0.654 13.910 29233 Z= 0.334 Chirality : 0.045 0.253 3227 Planarity : 0.005 0.053 3560 Dihedral : 15.229 178.249 3689 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.33 % Allowed : 13.16 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.14), residues: 2485 helix: -2.14 (0.14), residues: 926 sheet: -2.04 (0.25), residues: 327 loop : -2.33 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 252 TYR 0.033 0.002 TYR F 297 PHE 0.018 0.001 PHE D 243 TRP 0.013 0.001 TRP C 152 HIS 0.007 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (21421) covalent geometry : angle 0.64919 / 0.33 (29219) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 1.76795 / 0.95 ( 2) hydrogen bonds : bond 0.05034 / 3.42 ( 651) hydrogen bonds : angle 5.84414 / 4.03 ( 1854) metal coordination : bond 0.00901 / 0.62 ( 15) metal coordination : angle 3.70820 / 1.96 ( 12) *********************** 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 415 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 349 time to evaluate : 0.706 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: A 61 HIS cc_start: 0.6695 (OUTLIER) cc_final: 0.6186 (t-90) REVERT: A 135 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6722 (p0) REVERT: A 239 ASP cc_start: 0.8214 (t70) cc_final: 0.8007 (t0) REVERT: A 759 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6501 (mp10) REVERT: B 80 THR cc_start: 0.6988 (p) cc_final: 0.6608 (t) REVERT: B 101 MET cc_start: 0.6433 (tpp) cc_final: 0.5886 (tmm) REVERT: B 106 GLU cc_start: 0.6775 (tp30) cc_final: 0.6471 (tp30) REVERT: C 193 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: C 263 ASP cc_start: 0.7342 (p0) cc_final: 0.6742 (p0) REVERT: D 62 LEU cc_start: 0.9038 (mt) cc_final: 0.8667 (mt) REVERT: K 78 TYR cc_start: 0.6911 (m-80) cc_final: 0.6154 (m-10) REVERT: K 249 ASP cc_start: 0.7533 (t0) cc_final: 0.7251 (t0) REVERT: F 24 ASP cc_start: 0.3905 (OUTLIER) cc_final: 0.3265 (m-30) REVERT: F 266 TYR cc_start: 0.4436 (t80) cc_final: 0.4092 (t80) outliers start: 66 outliers final: 41 residues processed: 390 average time/residue: 0.1707 time to fit residues: 99.5386 Evaluate side-chains 347 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 61 HIS 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 151 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 420 VAL 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 759 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 193 GLU 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 94 GLN Chi-restraints excluded: chain D residue 181 ARG 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 J residue 127 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 182 THR 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 249 THR Chi-restraints excluded: chain F residue 300 VAL 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 115 optimal weight: 3.9990 chunk 234 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 238 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 134 optimal weight: 0.0000 chunk 229 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 241 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 456 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.180358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145052 restraints weight = 31393.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143158 restraints weight = 42699.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144764 restraints weight = 37347.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145603 restraints weight = 24109.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145962 restraints weight = 22122.370| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21437 Z= 0.163 Angle : 0.648 14.742 29233 Z= 0.329 Chirality : 0.045 0.241 3227 Planarity : 0.005 0.043 3560 Dihedral : 15.106 176.536 3689 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.58 % Allowed : 13.66 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.15), residues: 2485 helix: -1.59 (0.15), residues: 930 sheet: -2.01 (0.25), residues: 333 loop : -2.23 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 252 TYR 0.030 0.002 TYR F 297 PHE 0.018 0.001 PHE A 56 TRP 0.018 0.002 TRP F 239 HIS 0.009 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (21421) covalent geometry : angle 0.64277 / 0.33 (29219) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 1.66858 / 0.90 ( 2) hydrogen bonds : bond 0.04535 / 3.13 ( 651) hydrogen bonds : angle 5.55078 / 3.82 ( 1854) metal coordination : bond 0.00986 / 0.61 ( 15) metal coordination : angle 3.86077 / 2.03 ( 12) *********************** 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 404 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 333 time to evaluate : 0.822 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: 0.7628 (tm-30) cc_final: 0.6914 (tm-30) REVERT: A 59 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6345 (m-10) REVERT: A 61 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.6050 (t-90) REVERT: A 239 ASP cc_start: 0.8271 (t70) cc_final: 0.7948 (t0) REVERT: A 635 ARG cc_start: 0.6690 (tpt170) cc_final: 0.6358 (tpt170) REVERT: A 759 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6538 (mp10) REVERT: B 80 THR cc_start: 0.6788 (p) cc_final: 0.6421 (t) REVERT: C 14 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8288 (mttp) REVERT: C 193 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6969 (pt0) REVERT: C 263 ASP cc_start: 0.7498 (p0) cc_final: 0.6940 (p0) REVERT: D 62 LEU cc_start: 0.9092 (mt) cc_final: 0.8674 (mt) REVERT: J 180 LYS cc_start: 0.6568 (mtmt) cc_final: 0.6339 (tttm) REVERT: K 78 TYR cc_start: 0.6936 (m-80) cc_final: 0.6179 (m-10) REVERT: K 109 TRP cc_start: 0.6646 (m100) cc_final: 0.5866 (m100) REVERT: K 249 ASP cc_start: 0.7576 (t0) cc_final: 0.7290 (t0) REVERT: F 24 ASP cc_start: 0.4157 (OUTLIER) cc_final: 0.3455 (m-30) REVERT: F 266 TYR cc_start: 0.4071 (t80) cc_final: 0.3837 (t80) REVERT: F 389 MET cc_start: 0.2531 (ttp) cc_final: 0.2069 (ptm) outliers start: 71 outliers final: 45 residues processed: 383 average time/residue: 0.1671 time to fit residues: 97.0723 Evaluate side-chains 359 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 59 PHE Chi-restraints excluded: chain A residue 61 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 151 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 420 VAL 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 759 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 116 ILE 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 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 207 ARG 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 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 143 ILE Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 182 THR 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 227 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 122 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 191 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 456 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.178382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142672 restraints weight = 31301.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140476 restraints weight = 42677.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142163 restraints weight = 37091.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142656 restraints weight = 25374.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143026 restraints weight = 23367.389| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21437 Z= 0.192 Angle : 0.669 15.570 29233 Z= 0.338 Chirality : 0.046 0.237 3227 Planarity : 0.005 0.051 3560 Dihedral : 15.000 172.916 3687 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.83 % Allowed : 14.42 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.15), residues: 2485 helix: -1.30 (0.16), residues: 946 sheet: -2.02 (0.25), residues: 333 loop : -2.22 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 252 TYR 0.029 0.002 TYR F 297 PHE 0.014 0.002 PHE E 159 TRP 0.014 0.002 TRP A 162 HIS 0.008 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (21421) covalent geometry : angle 0.66387 / 0.34 (29219) SS BOND : bond 0.00284 / 0.15 ( 1) SS BOND : angle 1.57483 / 0.86 ( 2) hydrogen bonds : bond 0.04346 / 2.97 ( 651) hydrogen bonds : angle 5.42368 / 3.73 ( 1854) metal coordination : bond 0.01120 / 0.65 ( 15) metal coordination : angle 3.96438 / 2.07 ( 12) *********************** 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 405 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 329 time to evaluate : 0.797 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: 0.7528 (tm-30) cc_final: 0.6904 (tm-30) REVERT: A 61 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6077 (t-90) REVERT: A 195 ILE cc_start: 0.8769 (pp) cc_final: 0.8407 (mt) REVERT: A 239 ASP cc_start: 0.8285 (t70) cc_final: 0.7898 (t0) REVERT: A 635 ARG cc_start: 0.6933 (tpt170) cc_final: 0.6594 (tpt170) REVERT: A 759 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: A 777 ARG cc_start: 0.2259 (OUTLIER) cc_final: 0.1536 (ppt-90) REVERT: B 80 THR cc_start: 0.6671 (p) cc_final: 0.6280 (t) REVERT: B 106 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6240 (mm-30) REVERT: C 14 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8352 (mttp) REVERT: C 263 ASP cc_start: 0.7512 (p0) cc_final: 0.6932 (p0) REVERT: J 180 LYS cc_start: 0.6508 (mtmt) cc_final: 0.6104 (tttm) REVERT: K 78 TYR cc_start: 0.7038 (m-80) cc_final: 0.6278 (m-10) REVERT: K 109 TRP cc_start: 0.6723 (m100) cc_final: 0.6049 (m100) REVERT: K 162 ILE cc_start: 0.8040 (tp) cc_final: 0.7757 (tp) REVERT: K 249 ASP cc_start: 0.7690 (t0) cc_final: 0.7397 (t0) REVERT: F 24 ASP cc_start: 0.4232 (OUTLIER) cc_final: 0.3550 (m-30) REVERT: F 266 TYR cc_start: 0.4030 (t80) cc_final: 0.3682 (t80) REVERT: F 301 MET cc_start: 0.2981 (tmm) cc_final: 0.2588 (tmm) REVERT: F 389 MET cc_start: 0.2878 (ttp) cc_final: 0.2437 (ptm) outliers start: 76 outliers final: 57 residues processed: 381 average time/residue: 0.1717 time to fit residues: 98.5605 Evaluate side-chains 372 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 59 PHE Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 64 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 151 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 116 ILE 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 45 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 207 ARG 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 151 GLU 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 44 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 45 THR 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 3 GLU 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 227 VAL Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 243 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 33 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 chunk 57 optimal weight: 0.0980 chunk 93 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.179949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144536 restraints weight = 31161.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142969 restraints weight = 40191.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144996 restraints weight = 35774.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144935 restraints weight = 24945.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146016 restraints weight = 22624.593| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21437 Z= 0.133 Angle : 0.626 15.575 29233 Z= 0.314 Chirality : 0.044 0.221 3227 Planarity : 0.004 0.053 3560 Dihedral : 14.926 171.708 3687 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.48 % Allowed : 15.78 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.16), residues: 2485 helix: -0.92 (0.16), residues: 939 sheet: -1.73 (0.26), residues: 333 loop : -2.14 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 252 TYR 0.030 0.002 TYR F 322 PHE 0.023 0.001 PHE F 288 TRP 0.019 0.001 TRP A 162 HIS 0.006 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (21421) covalent geometry : angle 0.62200 / 0.31 (29219) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 1.27402 / 0.70 ( 2) hydrogen bonds : bond 0.03964 / 2.74 ( 651) hydrogen bonds : angle 5.20843 / 3.59 ( 1854) metal coordination : bond 0.00780 / 0.52 ( 15) metal coordination : angle 3.42524 / 1.76 ( 12) *********************** 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 399 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 330 time to evaluate : 0.770 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: 0.7545 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 61 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.6038 (t-90) REVERT: A 195 ILE cc_start: 0.8746 (pp) cc_final: 0.8391 (mt) REVERT: A 239 ASP cc_start: 0.8208 (t70) cc_final: 0.7865 (t0) REVERT: A 489 ASP cc_start: 0.6533 (p0) cc_final: 0.6120 (p0) REVERT: A 759 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6519 (mp10) REVERT: A 777 ARG cc_start: 0.2209 (OUTLIER) cc_final: 0.1399 (ppt-90) REVERT: B 73 LYS cc_start: 0.1573 (OUTLIER) cc_final: 0.0652 (pttp) REVERT: B 80 THR cc_start: 0.6629 (p) cc_final: 0.6310 (t) REVERT: C 14 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8251 (mttp) REVERT: C 263 ASP cc_start: 0.7454 (p0) cc_final: 0.6799 (p0) REVERT: E 122 ILE cc_start: 0.8113 (tt) cc_final: 0.7902 (pt) REVERT: K 78 TYR cc_start: 0.6915 (m-80) cc_final: 0.6385 (m-80) REVERT: K 109 TRP cc_start: 0.6783 (m100) cc_final: 0.6130 (m100) REVERT: K 162 ILE cc_start: 0.7997 (tp) cc_final: 0.7770 (tp) REVERT: K 249 ASP cc_start: 0.7644 (t0) cc_final: 0.7308 (t0) REVERT: F 24 ASP cc_start: 0.4162 (OUTLIER) cc_final: 0.3475 (m-30) REVERT: F 122 ARG cc_start: 0.5846 (ttt90) cc_final: 0.5580 (mtm180) REVERT: F 132 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: F 266 TYR cc_start: 0.4005 (t80) cc_final: 0.3637 (t80) REVERT: F 301 MET cc_start: 0.3273 (tmm) cc_final: 0.2899 (tmm) REVERT: F 389 MET cc_start: 0.2849 (ttp) cc_final: 0.2426 (ptm) outliers start: 69 outliers final: 50 residues processed: 377 average time/residue: 0.1677 time to fit residues: 95.5776 Evaluate side-chains 367 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 310 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 151 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 759 GLN 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 155 VAL Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 207 ARG 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 151 GLU 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 44 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 182 THR Chi-restraints excluded: chain K residue 236 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 132 GLU 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 249 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 177 optimal weight: 30.0000 chunk 141 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 201 optimal weight: 0.2980 chunk 86 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143557 restraints weight = 31506.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141516 restraints weight = 40391.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142949 restraints weight = 40147.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143589 restraints weight = 26257.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144534 restraints weight = 22847.549| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21437 Z= 0.170 Angle : 0.644 15.656 29233 Z= 0.324 Chirality : 0.045 0.225 3227 Planarity : 0.005 0.057 3560 Dihedral : 14.918 171.243 3687 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.98 % Allowed : 16.08 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2485 helix: -0.74 (0.17), residues: 932 sheet: -1.69 (0.26), residues: 335 loop : -2.09 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 252 TYR 0.024 0.002 TYR B 178 PHE 0.025 0.002 PHE B 171 TRP 0.019 0.001 TRP A 162 HIS 0.005 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (21421) covalent geometry : angle 0.63945 / 0.32 (29219) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 2.32853 / 1.28 ( 2) hydrogen bonds : bond 0.04026 / 2.76 ( 651) hydrogen bonds : angle 5.20487 / 3.57 ( 1854) metal coordination : bond 0.00903 / 0.54 ( 15) metal coordination : angle 3.65776 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 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 396 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7514 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 61 HIS cc_start: 0.6397 (OUTLIER) cc_final: 0.5973 (t-90) REVERT: A 195 ILE cc_start: 0.8777 (pp) cc_final: 0.8423 (mt) REVERT: A 239 ASP cc_start: 0.8205 (t70) cc_final: 0.7851 (t0) REVERT: A 489 ASP cc_start: 0.6596 (p0) cc_final: 0.6221 (p0) REVERT: A 759 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: A 777 ARG cc_start: 0.2275 (OUTLIER) cc_final: 0.1598 (ppt-90) REVERT: B 73 LYS cc_start: 0.1357 (OUTLIER) cc_final: 0.0010 (pttp) REVERT: B 80 THR cc_start: 0.6602 (p) cc_final: 0.6294 (t) REVERT: C 14 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8333 (mttp) REVERT: C 263 ASP cc_start: 0.7500 (p0) cc_final: 0.6967 (p0) REVERT: E 157 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8869 (t) REVERT: K 78 TYR cc_start: 0.7004 (m-80) cc_final: 0.6249 (m-10) REVERT: K 109 TRP cc_start: 0.6692 (m100) cc_final: 0.6111 (m100) REVERT: K 162 ILE cc_start: 0.8084 (tp) cc_final: 0.7859 (tp) REVERT: F 122 ARG cc_start: 0.5860 (ttt90) cc_final: 0.5569 (mtm180) REVERT: F 132 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5773 (pm20) REVERT: F 266 TYR cc_start: 0.3622 (t80) cc_final: 0.3165 (t80) REVERT: F 268 ASN cc_start: 0.7058 (t0) cc_final: 0.6818 (t0) REVERT: F 301 MET cc_start: 0.3236 (tmm) cc_final: 0.2826 (tmm) REVERT: F 389 MET cc_start: 0.3276 (ttp) cc_final: 0.2827 (ptm) outliers start: 79 outliers final: 58 residues processed: 370 average time/residue: 0.1635 time to fit residues: 91.9059 Evaluate side-chains 368 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 HIS 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 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 759 GLN Chi-restraints excluded: chain A residue 761 VAL 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 C residue 14 LYS 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 207 ARG 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 151 GLU 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 44 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 66 LEU 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 24 ASP Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 132 GLU 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 249 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 394 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 72 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 211 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145881 restraints weight = 31120.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144325 restraints weight = 43033.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145587 restraints weight = 42847.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146269 restraints weight = 27239.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146629 restraints weight = 24340.682| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.003 0.046 21437 Z= 0.140 Angle : 0.626 15.621 29233 Z= 0.315 Chirality : 0.044 0.216 3227 Planarity : 0.004 0.059 3560 Dihedral : 14.845 171.344 3687 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.28 % Allowed : 17.14 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2485 helix: -0.55 (0.17), residues: 923 sheet: -1.56 (0.26), residues: 341 loop : -2.04 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 252 TYR 0.030 0.002 TYR F 322 PHE 0.020 0.001 PHE J 171 TRP 0.022 0.001 TRP A 162 HIS 0.005 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21421) covalent geometry : angle 0.62236 / 0.31 (29219) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 1.50845 / 0.82 ( 2) hydrogen bonds : bond 0.03814 / 2.62 ( 651) hydrogen bonds : angle 5.09840 / 3.50 ( 1854) metal coordination : bond 0.00800 / 0.51 ( 15) metal coordination : angle 3.34736 / 1.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 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 386 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 321 time to evaluate : 0.613 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 21 GLN cc_start: 0.7518 (tm-30) cc_final: 0.6875 (tm-30) REVERT: A 61 HIS cc_start: 0.6214 (OUTLIER) cc_final: 0.5873 (t-90) REVERT: A 195 ILE cc_start: 0.8739 (pp) cc_final: 0.8425 (mt) REVERT: A 239 ASP cc_start: 0.8095 (t70) cc_final: 0.7769 (t0) REVERT: A 489 ASP cc_start: 0.6526 (p0) cc_final: 0.6116 (p0) REVERT: A 635 ARG cc_start: 0.6428 (mmp-170) cc_final: 0.5955 (mmm160) REVERT: A 759 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.6593 (mp10) REVERT: A 777 ARG cc_start: 0.2264 (OUTLIER) cc_final: 0.1576 (ppt-90) REVERT: B 73 LYS cc_start: 0.1519 (OUTLIER) cc_final: 0.0503 (pttp) REVERT: B 80 THR cc_start: 0.6581 (p) cc_final: 0.6292 (t) REVERT: C 14 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8261 (mttp) REVERT: C 263 ASP cc_start: 0.7421 (p0) cc_final: 0.6866 (p0) REVERT: D 172 ASP cc_start: 0.7253 (t0) cc_final: 0.6549 (t0) REVERT: E 105 LYS cc_start: 0.8136 (tptp) cc_final: 0.7804 (tptp) REVERT: E 157 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8897 (t) REVERT: K 78 TYR cc_start: 0.6897 (m-80) cc_final: 0.6421 (m-80) REVERT: K 109 TRP cc_start: 0.6655 (m100) cc_final: 0.6229 (m100) REVERT: F 132 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5726 (pm20) REVERT: F 266 TYR cc_start: 0.3777 (t80) cc_final: 0.3261 (t80) REVERT: F 268 ASN cc_start: 0.6976 (t0) cc_final: 0.6718 (t0) REVERT: F 301 MET cc_start: 0.3512 (tmm) cc_final: 0.3134 (tmm) REVERT: F 389 MET cc_start: 0.3371 (ttp) cc_final: 0.3048 (ptm) outliers start: 65 outliers final: 50 residues processed: 364 average time/residue: 0.1631 time to fit residues: 89.8248 Evaluate side-chains 363 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 HIS 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 151 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 759 GLN 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 C residue 14 LYS Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 207 ARG 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 151 GLU 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 44 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain J residue 127 LEU 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 236 VAL Chi-restraints excluded: chain K residue 256 ASP 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 132 GLU 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 249 THR Chi-restraints excluded: chain F residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 58 optimal weight: 3.9990 chunk 235 optimal weight: 0.0010 chunk 253 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN C 44 HIS ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 217 ASN ** J 94 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 = 0.4046 r_free = 0.4046 target = 0.174105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139009 restraints weight = 31276.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136001 restraints weight = 42140.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137574 restraints weight = 38751.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138484 restraints weight = 25625.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138785 restraints weight = 23100.215| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 21437 Z= 0.295 Angle : 0.773 15.735 29233 Z= 0.389 Chirality : 0.050 0.255 3227 Planarity : 0.006 0.086 3560 Dihedral : 15.052 172.343 3687 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.88 % Allowed : 16.94 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.16), residues: 2485 helix: -0.79 (0.17), residues: 935 sheet: -1.86 (0.26), residues: 340 loop : -2.16 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 252 TYR 0.035 0.003 TYR F 297 PHE 0.034 0.003 PHE B 171 TRP 0.021 0.002 TRP A 162 HIS 0.008 0.002 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.29 (21421) covalent geometry : angle 0.76755 / 0.39 (29219) SS BOND : bond 0.00254 / 0.13 ( 1) SS BOND : angle 2.73181 / 1.50 ( 2) hydrogen bonds : bond 0.04549 / 3.08 ( 651) hydrogen bonds : angle 5.45568 / 3.71 ( 1854) metal coordination : bond 0.01997 / 1.09 ( 15) metal coordination : angle 4.53468 / 2.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 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 375 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 298 time to evaluate : 0.526 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 61 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5778 (t-90) REVERT: A 239 ASP cc_start: 0.8234 (t70) cc_final: 0.7844 (t0) REVERT: A 635 ARG cc_start: 0.6635 (mmp-170) cc_final: 0.6270 (mmm160) REVERT: A 759 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6534 (mp10) REVERT: A 777 ARG cc_start: 0.2554 (OUTLIER) cc_final: 0.1863 (ppt-90) REVERT: B 73 LYS cc_start: 0.1174 (OUTLIER) cc_final: -0.0467 (pttp) REVERT: B 80 THR cc_start: 0.6610 (p) cc_final: 0.6207 (t) REVERT: B 106 GLU cc_start: 0.6257 (mm-30) cc_final: 0.6022 (mm-30) REVERT: B 162 LYS cc_start: 0.5752 (mptt) cc_final: 0.5505 (mttp) REVERT: C 263 ASP cc_start: 0.7560 (p0) cc_final: 0.7091 (p0) REVERT: D 172 ASP cc_start: 0.7458 (t0) cc_final: 0.6742 (t0) REVERT: E 157 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.9016 (t) REVERT: K 78 TYR cc_start: 0.7209 (m-80) cc_final: 0.6470 (m-10) REVERT: K 109 TRP cc_start: 0.6553 (m100) cc_final: 0.6123 (m100) REVERT: K 249 ASP cc_start: 0.7899 (t0) cc_final: 0.7518 (t0) REVERT: F 266 TYR cc_start: 0.3661 (t80) cc_final: 0.2979 (t80) REVERT: F 301 MET cc_start: 0.3497 (tmm) cc_final: 0.3061 (tmm) REVERT: F 389 MET cc_start: 0.3523 (ttp) cc_final: 0.3168 (ptm) outliers start: 77 outliers final: 58 residues processed: 353 average time/residue: 0.1660 time to fit residues: 88.0275 Evaluate side-chains 350 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 287 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER 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 721 ASN Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 759 GLN 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 120 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 207 ARG 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 151 GLU 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 35 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain J residue 127 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 66 LEU 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 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 32 ILE 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 249 THR Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 76 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 242 optimal weight: 0.2980 chunk 86 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 456 GLN A 759 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.178699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144422 restraints weight = 31340.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142226 restraints weight = 42018.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144141 restraints weight = 38426.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144373 restraints weight = 25749.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145571 restraints weight = 22861.545| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21437 Z= 0.128 Angle : 0.663 15.793 29233 Z= 0.330 Chirality : 0.044 0.220 3227 Planarity : 0.005 0.059 3560 Dihedral : 14.854 170.771 3687 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.52 % Allowed : 18.25 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2485 helix: -0.50 (0.17), residues: 932 sheet: -1.59 (0.26), residues: 354 loop : -2.06 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 252 TYR 0.034 0.002 TYR F 322 PHE 0.017 0.001 PHE J 171 TRP 0.025 0.002 TRP A 162 HIS 0.005 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (21421) covalent geometry : angle 0.65930 / 0.33 (29219) SS BOND : bond 0.00001 / 0.00 ( 1) SS BOND : angle 1.68999 / 0.92 ( 2) hydrogen bonds : bond 0.03772 / 2.58 ( 651) hydrogen bonds : angle 5.16315 / 3.54 ( 1854) metal coordination : bond 0.00737 / 0.52 ( 15) metal coordination : angle 3.28177 / 1.65 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 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 368 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 0.773 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 61 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.6084 (t-90) REVERT: A 161 LEU cc_start: 0.8430 (tp) cc_final: 0.8204 (tp) REVERT: A 239 ASP cc_start: 0.8151 (t70) cc_final: 0.7771 (t0) REVERT: A 489 ASP cc_start: 0.6457 (p0) cc_final: 0.6058 (p0) REVERT: A 572 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6176 (ppt-90) REVERT: A 635 ARG cc_start: 0.6486 (mmp-170) cc_final: 0.6150 (mmm160) REVERT: A 777 ARG cc_start: 0.2511 (OUTLIER) cc_final: 0.1624 (ppt-90) REVERT: B 73 LYS cc_start: 0.1283 (OUTLIER) cc_final: -0.0152 (pttp) REVERT: B 80 THR cc_start: 0.6525 (p) cc_final: 0.6224 (t) REVERT: B 162 LYS cc_start: 0.5649 (mptt) cc_final: 0.5344 (mtmm) REVERT: C 263 ASP cc_start: 0.7571 (p0) cc_final: 0.7107 (p0) REVERT: E 105 LYS cc_start: 0.8146 (tptp) cc_final: 0.7822 (tptp) REVERT: E 157 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8931 (t) REVERT: K 78 TYR cc_start: 0.7006 (m-80) cc_final: 0.6495 (m-80) REVERT: K 109 TRP cc_start: 0.6587 (m100) cc_final: 0.6061 (m100) REVERT: K 249 ASP cc_start: 0.7729 (t0) cc_final: 0.7369 (t0) REVERT: F 98 MET cc_start: 0.2498 (tpt) cc_final: 0.2147 (tpt) REVERT: F 266 TYR cc_start: 0.3689 (t80) cc_final: 0.3123 (t80) REVERT: F 301 MET cc_start: 0.3680 (tmm) cc_final: 0.3306 (tmm) REVERT: F 389 MET cc_start: 0.3494 (ttp) cc_final: 0.3146 (ptm) outliers start: 50 outliers final: 39 residues processed: 353 average time/residue: 0.1623 time to fit residues: 86.9160 Evaluate side-chains 344 residues out of total 2146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 HIS 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 184 THR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 759 GLN 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 C residue 15 ILE 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 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 44 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL 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 66 LEU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 382 THR Chi-restraints excluded: chain F residue 394 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 16 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 196 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 179 optimal weight: 0.0770 chunk 108 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 456 GLN A 759 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 ASN J 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.179331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146519 restraints weight = 31131.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145076 restraints weight = 42451.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146333 restraints weight = 42920.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146973 restraints weight = 26274.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147916 restraints weight = 22836.794| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21437 Z= 0.125 Angle : 0.647 15.028 29233 Z= 0.325 Chirality : 0.044 0.213 3227 Planarity : 0.004 0.061 3560 Dihedral : 14.760 171.370 3687 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.27 % Allowed : 18.80 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.16), residues: 2485 helix: -0.34 (0.17), residues: 926 sheet: -1.54 (0.27), residues: 346 loop : -1.97 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 252 TYR 0.021 0.002 TYR B 178 PHE 0.036 0.001 PHE B 171 TRP 0.023 0.001 TRP A 162 HIS 0.006 0.001 HIS F 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (21421) covalent geometry : angle 0.64424 / 0.33 (29219) SS BOND : bond 0.00083 / 0.04 ( 1) SS BOND : angle 1.63769 / 0.89 ( 2) hydrogen bonds : bond 0.03673 / 2.53 ( 651) hydrogen bonds : angle 5.08201 / 3.48 ( 1854) metal coordination : bond 0.00640 / 0.44 ( 15) metal coordination : angle 2.99551 / 1.54 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3435.82 seconds wall clock time: 60 minutes 16.30 seconds (3616.30 seconds total)