Starting phenix.real_space_refine on Sat Sep 12 19:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mur_9253/09_2026/6mur_9253_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mur_9253/09_2026/6mur_9253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mur_9253/09_2026/6mur_9253_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mur_9253/09_2026/6mur_9253_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mur_9253/09_2026/6mur_9253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mur_9253/09_2026/6mur_9253.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 3 6.06 5 P 45 5.49 5 S 49 5.16 5 C 11077 2.51 5 N 3100 2.21 5 O 3386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17660 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6150 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1143 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} 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: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3074 SG CYS A 389 52.089 81.889 90.850 1.00 45.72 S ATOM 3094 SG CYS A 392 49.588 78.659 91.791 1.00 45.83 S ATOM 3249 SG CYS A 413 51.023 81.803 93.938 1.00 59.14 S ATOM 3269 SG CYS A 416 52.416 78.520 93.867 1.00 56.75 S ATOM 8120 SG CYS C 113 61.837 95.927 64.287 1.00 35.30 S ATOM 8187 SG CYS C 122 62.149 94.984 60.481 1.00 30.50 S ATOM 8207 SG CYS C 125 59.882 92.574 63.344 1.00 28.05 S ATOM 10404 SG CYS D 113 86.902 72.810 63.408 1.00 41.86 S ATOM 10471 SG CYS D 122 88.371 73.176 59.968 1.00 38.85 S ATOM 10491 SG CYS D 125 84.383 71.335 60.917 1.00 31.93 S Time building chain proxies: 3.38, per 1000 atoms: 0.19 Number of scatterers: 17660 At special positions: 0 Unit cell: (120.879, 113.256, 156.816, 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 3 29.99 S 49 16.00 P 45 15.00 O 3386 8.00 N 3100 7.00 C 11077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 755.0 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 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 31 sheets defined 40.0% alpha, 14.6% beta 12 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.576A 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 44 removed outlier: 3.774A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.890A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.799A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.661A pdb=" N ARG A 82 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 3.947A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.511A pdb=" N TYR A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.698A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 removed outlier: 3.581A pdb=" N ALA A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.908A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 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 325 removed outlier: 4.268A pdb=" N GLU A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.607A pdb=" N LYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.670A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.711A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.682A pdb=" N ARG A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.646A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.523A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 649 removed outlier: 3.516A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.730A 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: 3.842A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.316A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.456A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.634A pdb=" N LYS B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 63 removed outlier: 4.083A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.826A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 88 " --> pdb=" O TYR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 110 removed outlier: 3.931A pdb=" N VAL B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.834A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 156 removed outlier: 4.170A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.556A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.621A pdb=" N LEU C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.697A pdb=" N ARG C 75 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 122 through 129 removed outlier: 3.746A pdb=" N LEU C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.697A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 221 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.775A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 3.626A pdb=" N PHE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'D' and resid 51 through 70 removed outlier: 3.573A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 149 through 158 removed outlier: 3.563A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.923A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.741A 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 'D' and resid 280 through 285 Processing helix chain 'E' and resid 21 through 36 removed outlier: 4.202A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.550A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 99 removed outlier: 3.522A pdb=" N TYR E 90 " --> pdb=" O GLU E 86 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 4.035A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.855A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 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: 3.743A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.702A 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: 3.952A 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: 6.724A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 346 removed outlier: 3.602A pdb=" N GLU A 346 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 349 " --> pdb=" O GLU A 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.805A pdb=" N ARG A 394 " --> pdb=" O CYS A 389 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 402 through 403 removed outlier: 3.777A pdb=" N VAL A 412 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.985A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 450 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.650A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.727A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.800A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.800A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 242 " --> pdb=" O LYS C 12 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS C 14 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE C 240 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS C 16 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE C 238 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.551A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.960A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.960A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 241 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 7.272A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 171 removed outlier: 3.514A pdb=" N ARG D 181 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 170 " --> pdb=" O ASN D 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.518A pdb=" N TYR E 60 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 61 removed outlier: 3.518A pdb=" N TYR E 60 " --> pdb=" O GLY E 156 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=AC5, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.807A pdb=" N TYR E 144 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 252 through 253 removed outlier: 4.578A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 282 " --> pdb=" O TYR E 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.605A pdb=" N LYS E 232 " --> pdb=" O MET E 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC9, first strand: chain 'E' and resid 261 through 263 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: 5.602A 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) 597 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.20 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: 4684 1.33 - 1.45: 3638 1.45 - 1.57: 9636 1.57 - 1.69: 89 1.69 - 1.81: 80 Bond restraints: 18127 Sorted by residual: bond pdb=" N LEU E 219 " pdb=" CA LEU E 219 " ideal model delta sigma weight residual 1.458 1.501 -0.043 7.40e-03 1.83e+04 3.40e+01 bond pdb=" C GLU A 388 " pdb=" O GLU A 388 " ideal model delta sigma weight residual 1.236 1.290 -0.054 1.21e-02 6.83e+03 2.01e+01 bond pdb=" N GLY F 365 " pdb=" CA GLY F 365 " ideal model delta sigma weight residual 1.447 1.486 -0.039 1.09e-02 8.42e+03 1.29e+01 bond pdb=" C LEU A 396 " pdb=" N PRO A 397 " ideal model delta sigma weight residual 1.332 1.288 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N ILE A 16 " pdb=" CA ILE A 16 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.61e+00 ... (remaining 18122 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 23311 2.08 - 4.16: 1196 4.16 - 6.24: 156 6.24 - 8.31: 47 8.31 - 10.39: 16 Bond angle restraints: 24726 Sorted by residual: angle pdb=" C ASN D 179 " pdb=" N PRO D 180 " pdb=" CA PRO D 180 " ideal model delta sigma weight residual 119.76 128.44 -8.68 1.03e+00 9.43e-01 7.09e+01 angle pdb=" N PRO F 61 " pdb=" CA PRO F 61 " pdb=" CB PRO F 61 " ideal model delta sigma weight residual 103.08 110.18 -7.10 9.70e-01 1.06e+00 5.36e+01 angle pdb=" N PRO F 79 " pdb=" CA PRO F 79 " pdb=" CB PRO F 79 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.19e+01 angle pdb=" N PRO F 62 " pdb=" CA PRO F 62 " pdb=" CB PRO F 62 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO F 191 " pdb=" CA PRO F 191 " pdb=" CB PRO F 191 " ideal model delta sigma weight residual 103.25 110.13 -6.88 1.05e+00 9.07e-01 4.30e+01 ... (remaining 24721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 10653 35.18 - 70.36: 216 70.36 - 105.54: 23 105.54 - 140.73: 0 140.73 - 175.91: 2 Dihedral angle restraints: 10894 sinusoidal: 4735 harmonic: 6159 Sorted by residual: 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 47.91 -175.91 1 1.70e+01 3.46e-03 6.64e+01 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 37.13 -165.13 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" C ASP D 28 " pdb=" N ASP D 28 " pdb=" CA ASP D 28 " pdb=" CB ASP D 28 " ideal model delta harmonic sigma weight residual -122.60 -136.69 14.09 0 2.50e+00 1.60e-01 3.18e+01 ... (remaining 10891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2313 0.090 - 0.181: 374 0.181 - 0.271: 38 0.271 - 0.361: 3 0.361 - 0.452: 1 Chirality restraints: 2729 Sorted by residual: chirality pdb=" CA ASP D 28 " pdb=" N ASP D 28 " pdb=" C ASP D 28 " pdb=" CB ASP D 28 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1' C G 14 " pdb=" O4' C G 14 " pdb=" C2' C G 14 " pdb=" N1 C G 14 " both_signs ideal model delta sigma weight residual False 2.44 2.11 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA CYS A 389 " pdb=" N CYS A 389 " pdb=" C CYS A 389 " pdb=" CB CYS A 389 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2726 not shown) Planarity restraints: 3031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 392 " -0.024 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C CYS A 392 " 0.091 2.00e-02 2.50e+03 pdb=" O CYS A 392 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY A 393 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 47 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ALA E 47 " 0.057 2.00e-02 2.50e+03 pdb=" O ALA E 47 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE E 48 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C G 10 " 0.044 2.00e-02 2.50e+03 2.20e-02 1.08e+01 pdb=" N1 C G 10 " -0.045 2.00e-02 2.50e+03 pdb=" C2 C G 10 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C G 10 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C G 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C G 10 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C G 10 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C G 10 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C G 10 " -0.007 2.00e-02 2.50e+03 ... (remaining 3028 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 149 2.57 - 3.15: 13357 3.15 - 3.74: 26803 3.74 - 4.32: 39114 4.32 - 4.90: 64444 Nonbonded interactions: 143867 Sorted by model distance: nonbonded pdb=" N2 G G 13 " pdb=" O2 C H 31 " model vdw 1.989 3.120 nonbonded pdb=" O ARG A 385 " pdb=" N GLU A 398 " model vdw 2.027 3.120 nonbonded pdb=" OH TYR B 125 " pdb=" CG2 THR F 37 " model vdw 2.078 3.460 nonbonded pdb=" O ALA D 130 " pdb=" O PHE D 137 " model vdw 2.120 3.040 nonbonded pdb=" N GLU F 38 " pdb=" OE1 GLU F 38 " model vdw 2.233 3.120 ... (remaining 143862 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 'C' selection = (chain 'D' and (resid 4 through 27 or resid 34 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.009 0.180 18139 Z= 0.448 Angle : 1.133 36.419 24738 Z= 0.662 Chirality : 0.066 0.452 2729 Planarity : 0.008 0.069 3031 Dihedral : 13.727 175.907 6958 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.43 % Favored : 92.43 % Rotamer: Outliers : 0.66 % Allowed : 5.09 % Favored : 94.25 % Cbeta Deviations : 0.05 % 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: -4.96 (0.14), residues: 2127 helix: -4.27 (0.09), residues: 807 sheet: -2.62 (0.28), residues: 282 loop : -2.55 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 212 TYR 0.029 0.003 TYR C 233 PHE 0.032 0.003 PHE D 194 TRP 0.029 0.003 TRP A 320 HIS 0.013 0.002 HIS D 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00845 / 0.44 (18127) covalent geometry : angle 1.06227 / 0.66 (24726) hydrogen bonds : bond 0.28891 / 19.22 ( 613) hydrogen bonds : angle 10.29539 / 7.16 ( 1743) metal coordination : bond 0.11815 / 6.98 ( 12) metal coordination : angle 17.98338 / 8.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 497 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7233 (tt0) cc_final: 0.7027 (tt0) REVERT: A 98 TYR cc_start: 0.6699 (t80) cc_final: 0.6204 (t80) REVERT: A 195 ILE cc_start: 0.8770 (pp) cc_final: 0.8456 (pt) REVERT: A 735 ARG cc_start: 0.7728 (ppp80) cc_final: 0.7509 (ptm160) REVERT: C 90 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6821 (ttp-110) REVERT: D 115 ASP cc_start: 0.6446 (t70) cc_final: 0.6073 (t70) REVERT: D 177 GLN cc_start: 0.8142 (tp40) cc_final: 0.7902 (tp-100) REVERT: D 184 GLU cc_start: 0.7636 (tt0) cc_final: 0.7416 (tt0) REVERT: D 255 LYS cc_start: 0.6865 (mmtm) cc_final: 0.6657 (mmtt) REVERT: E 104 LEU cc_start: 0.8737 (tm) cc_final: 0.8467 (tp) REVERT: F 19 GLU cc_start: 0.7970 (mp0) cc_final: 0.7522 (mp0) REVERT: F 329 SER cc_start: 0.7083 (t) cc_final: 0.6805 (p) outliers start: 11 outliers final: 4 residues processed: 507 average time/residue: 0.1713 time to fit residues: 121.5146 Evaluate side-chains 278 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 274 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain D residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 GLN A 102 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 380 HIS A 692 ASN B 77 ASN C 37 ASN C 136 ASN C 177 GLN C 179 ASN D 83 ASN D 102 ASN D 179 ASN D 183 ASN D 205 HIS E 217 ASN F 107 ASN F 268 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132891 restraints weight = 24305.790| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.18 r_work: 0.3314 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 18139 Z= 0.164 Angle : 0.695 12.370 24738 Z= 0.359 Chirality : 0.047 0.276 2729 Planarity : 0.006 0.051 3031 Dihedral : 14.987 173.955 3109 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.65 % Rotamer: Outliers : 2.75 % Allowed : 10.06 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.58 (0.15), residues: 2127 helix: -2.55 (0.14), residues: 823 sheet: -1.93 (0.28), residues: 292 loop : -2.26 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 755 TYR 0.044 0.002 TYR B 125 PHE 0.027 0.002 PHE A 502 TRP 0.015 0.002 TRP A 596 HIS 0.007 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (18127) covalent geometry : angle 0.68292 / 0.36 (24726) hydrogen bonds : bond 0.06417 / 4.26 ( 613) hydrogen bonds : angle 5.94545 / 4.10 ( 1743) metal coordination : bond 0.00946 / 0.60 ( 12) metal coordination : angle 5.93160 / 3.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7556 (ttm110) REVERT: A 59 PHE cc_start: 0.7651 (m-80) cc_final: 0.7384 (m-10) REVERT: A 98 TYR cc_start: 0.7163 (t80) cc_final: 0.6508 (t80) REVERT: A 146 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.6600 (t) REVERT: A 167 LYS cc_start: 0.8376 (mttt) cc_final: 0.8051 (mttm) REVERT: A 195 ILE cc_start: 0.8801 (pp) cc_final: 0.8517 (pt) REVERT: A 245 ASP cc_start: 0.7745 (p0) cc_final: 0.7391 (p0) REVERT: A 438 ASN cc_start: 0.7546 (p0) cc_final: 0.7343 (p0) REVERT: A 629 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6490 (pt0) REVERT: A 705 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8029 (tt) REVERT: A 735 ARG cc_start: 0.8213 (ppp80) cc_final: 0.7930 (ptm160) REVERT: A 777 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5215 (ttt180) REVERT: B 122 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7735 (tppt) REVERT: B 148 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8341 (mp) REVERT: B 150 ASP cc_start: 0.7946 (m-30) cc_final: 0.7649 (m-30) REVERT: C 284 GLU cc_start: 0.5611 (mt-10) cc_final: 0.5361 (mt-10) REVERT: D 184 GLU cc_start: 0.7989 (tt0) cc_final: 0.7719 (tt0) REVERT: F 19 GLU cc_start: 0.8103 (mp0) cc_final: 0.7587 (mp0) REVERT: F 29 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: F 256 ASP cc_start: 0.7924 (t70) cc_final: 0.7699 (t70) REVERT: F 303 TYR cc_start: 0.7972 (t80) cc_final: 0.7703 (t80) REVERT: F 329 SER cc_start: 0.7081 (t) cc_final: 0.6699 (p) REVERT: F 341 TRP cc_start: 0.8358 (t60) cc_final: 0.8091 (t60) outliers start: 46 outliers final: 21 residues processed: 332 average time/residue: 0.1559 time to fit residues: 74.2487 Evaluate side-chains 275 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 248 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 132 optimal weight: 0.0770 chunk 72 optimal weight: 1.9990 chunk 162 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS F 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.167327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133792 restraints weight = 24618.309| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.18 r_work: 0.3321 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18139 Z= 0.126 Angle : 0.608 12.198 24738 Z= 0.312 Chirality : 0.044 0.236 2729 Planarity : 0.005 0.055 3031 Dihedral : 14.650 174.425 3104 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.63 % Allowed : 11.44 % Favored : 85.93 % 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: -2.73 (0.17), residues: 2127 helix: -1.46 (0.16), residues: 826 sheet: -1.69 (0.28), residues: 311 loop : -2.08 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 36 TYR 0.015 0.001 TYR F 297 PHE 0.024 0.001 PHE F 288 TRP 0.009 0.001 TRP A 320 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (18127) covalent geometry : angle 0.60516 / 0.31 (24726) hydrogen bonds : bond 0.04910 / 3.23 ( 613) hydrogen bonds : angle 5.25922 / 3.61 ( 1743) metal coordination : bond 0.00415 / 0.24 ( 12) metal coordination : angle 2.87026 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7760 (mtp85) REVERT: A 98 TYR cc_start: 0.7178 (t80) cc_final: 0.6499 (t80) REVERT: A 146 VAL cc_start: 0.6743 (OUTLIER) cc_final: 0.6523 (t) REVERT: A 195 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8511 (pt) REVERT: A 245 ASP cc_start: 0.7834 (p0) cc_final: 0.7446 (p0) REVERT: A 438 ASN cc_start: 0.7472 (p0) cc_final: 0.7261 (p0) REVERT: A 629 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6425 (pt0) REVERT: A 735 ARG cc_start: 0.8196 (ppp80) cc_final: 0.7946 (ptm160) REVERT: A 777 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5395 (ttt180) REVERT: B 148 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 150 ASP cc_start: 0.8154 (m-30) cc_final: 0.7745 (m-30) REVERT: C 75 ARG cc_start: 0.7679 (mtm110) cc_final: 0.7349 (mtm110) REVERT: C 284 GLU cc_start: 0.5556 (mt-10) cc_final: 0.5262 (mt-10) REVERT: D 184 GLU cc_start: 0.7913 (tt0) cc_final: 0.7658 (tt0) REVERT: E 96 LEU cc_start: 0.8881 (tp) cc_final: 0.8631 (mt) REVERT: F 19 GLU cc_start: 0.8060 (mp0) cc_final: 0.7522 (mp0) REVERT: F 29 GLU cc_start: 0.6242 (OUTLIER) cc_final: 0.5730 (mp0) REVERT: F 109 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6825 (mtm110) REVERT: F 256 ASP cc_start: 0.7917 (t70) cc_final: 0.7703 (t70) REVERT: F 329 SER cc_start: 0.7048 (t) cc_final: 0.6654 (p) REVERT: F 341 TRP cc_start: 0.8369 (t60) cc_final: 0.8085 (t60) outliers start: 44 outliers final: 24 residues processed: 300 average time/residue: 0.1526 time to fit residues: 65.7817 Evaluate side-chains 271 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN D 199 ASN D 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.166804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132199 restraints weight = 24602.050| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.29 r_work: 0.3309 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18139 Z= 0.132 Angle : 0.576 10.278 24738 Z= 0.296 Chirality : 0.044 0.245 2729 Planarity : 0.004 0.048 3031 Dihedral : 14.564 175.340 3104 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.69 % Allowed : 12.51 % Favored : 84.79 % 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: -2.24 (0.17), residues: 2127 helix: -0.89 (0.17), residues: 829 sheet: -1.49 (0.29), residues: 291 loop : -1.96 (0.18), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 36 TYR 0.025 0.001 TYR B 125 PHE 0.025 0.001 PHE F 288 TRP 0.011 0.001 TRP C 152 HIS 0.004 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (18127) covalent geometry : angle 0.57357 / 0.30 (24726) hydrogen bonds : bond 0.04271 / 2.81 ( 613) hydrogen bonds : angle 4.95312 / 3.39 ( 1743) metal coordination : bond 0.00511 / 0.36 ( 12) metal coordination : angle 2.21750 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7788 (mtm-85) REVERT: A 98 TYR cc_start: 0.7243 (t80) cc_final: 0.6509 (t80) REVERT: A 146 VAL cc_start: 0.6765 (OUTLIER) cc_final: 0.6542 (t) REVERT: A 195 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (pt) REVERT: A 438 ASN cc_start: 0.7559 (p0) cc_final: 0.7326 (p0) REVERT: A 629 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6311 (pt0) REVERT: A 735 ARG cc_start: 0.8131 (ppp80) cc_final: 0.7922 (ptm160) REVERT: A 777 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5349 (ttt180) REVERT: C 139 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8792 (m) REVERT: C 284 GLU cc_start: 0.5634 (mt-10) cc_final: 0.5412 (mt-10) REVERT: D 184 GLU cc_start: 0.7918 (tt0) cc_final: 0.7646 (tt0) REVERT: E 96 LEU cc_start: 0.8879 (tp) cc_final: 0.8660 (mt) REVERT: F 109 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6863 (mtm110) REVERT: F 256 ASP cc_start: 0.7938 (t70) cc_final: 0.7708 (t70) REVERT: F 329 SER cc_start: 0.7216 (t) cc_final: 0.6825 (p) REVERT: F 341 TRP cc_start: 0.8336 (t60) cc_final: 0.8109 (t60) outliers start: 45 outliers final: 31 residues processed: 286 average time/residue: 0.1503 time to fit residues: 62.6601 Evaluate side-chains 272 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.167036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132914 restraints weight = 24360.304| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.25 r_work: 0.3318 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18139 Z= 0.121 Angle : 0.559 11.232 24738 Z= 0.287 Chirality : 0.043 0.237 2729 Planarity : 0.004 0.050 3031 Dihedral : 14.514 175.462 3104 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.75 % Allowed : 13.65 % Favored : 83.59 % 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: -1.88 (0.17), residues: 2127 helix: -0.49 (0.18), residues: 830 sheet: -1.36 (0.29), residues: 284 loop : -1.82 (0.18), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 262 TYR 0.014 0.001 TYR F 297 PHE 0.026 0.001 PHE F 288 TRP 0.016 0.001 TRP D 206 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (18127) covalent geometry : angle 0.55748 / 0.29 (24726) hydrogen bonds : bond 0.03960 / 2.60 ( 613) hydrogen bonds : angle 4.76068 / 3.26 ( 1743) metal coordination : bond 0.00286 / 0.18 ( 12) metal coordination : angle 1.79228 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: A 39 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7711 (mtm-85) REVERT: A 59 PHE cc_start: 0.7509 (m-80) cc_final: 0.7157 (m-80) REVERT: A 65 MET cc_start: 0.5966 (ptm) cc_final: 0.5521 (mtm) REVERT: A 98 TYR cc_start: 0.7199 (t80) cc_final: 0.6415 (t80) REVERT: A 146 VAL cc_start: 0.6770 (OUTLIER) cc_final: 0.6563 (t) REVERT: A 195 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8514 (pt) REVERT: A 297 MET cc_start: 0.9111 (ttm) cc_final: 0.8776 (ttm) REVERT: A 438 ASN cc_start: 0.7504 (p0) cc_final: 0.7253 (p0) REVERT: A 629 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6313 (pt0) REVERT: A 724 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7716 (ttm-80) REVERT: A 735 ARG cc_start: 0.8114 (ppp80) cc_final: 0.7827 (ptm160) REVERT: C 284 GLU cc_start: 0.5646 (mt-10) cc_final: 0.5405 (mt-10) REVERT: D 56 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8149 (tttm) REVERT: E 96 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8649 (mt) REVERT: E 104 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8747 (tt) REVERT: F 19 GLU cc_start: 0.8037 (mp0) cc_final: 0.7540 (mp0) REVERT: F 200 GLU cc_start: 0.7724 (tt0) cc_final: 0.7240 (tt0) REVERT: F 256 ASP cc_start: 0.7908 (t70) cc_final: 0.7683 (t70) REVERT: F 329 SER cc_start: 0.7205 (t) cc_final: 0.6799 (p) outliers start: 46 outliers final: 27 residues processed: 296 average time/residue: 0.1428 time to fit residues: 62.3983 Evaluate side-chains 272 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 197 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 194 ASN C 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129353 restraints weight = 24352.767| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.20 r_work: 0.3255 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 18139 Z= 0.198 Angle : 0.620 11.192 24738 Z= 0.316 Chirality : 0.046 0.263 2729 Planarity : 0.005 0.055 3031 Dihedral : 14.504 175.678 3104 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.17 % Allowed : 14.13 % Favored : 82.69 % 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: -1.81 (0.18), residues: 2127 helix: -0.35 (0.18), residues: 840 sheet: -1.48 (0.28), residues: 311 loop : -1.81 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 60 TYR 0.019 0.002 TYR B 125 PHE 0.028 0.002 PHE F 288 TRP 0.029 0.002 TRP F 341 HIS 0.006 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (18127) covalent geometry : angle 0.61821 / 0.32 (24726) hydrogen bonds : bond 0.04230 / 2.76 ( 613) hydrogen bonds : angle 4.77395 / 3.26 ( 1743) metal coordination : bond 0.01170 / 1.01 ( 12) metal coordination : angle 2.05247 / 1.06 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.8001 (mmm-85) REVERT: A 39 ARG cc_start: 0.8042 (ttm-80) cc_final: 0.7741 (mtm110) REVERT: A 59 PHE cc_start: 0.7392 (m-80) cc_final: 0.6678 (m-80) REVERT: A 65 MET cc_start: 0.6010 (ptm) cc_final: 0.5592 (mtm) REVERT: A 87 MET cc_start: 0.8028 (tpp) cc_final: 0.6896 (mtp) REVERT: A 195 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8602 (pt) REVERT: A 297 MET cc_start: 0.9135 (ttm) cc_final: 0.8722 (ttm) REVERT: A 629 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6423 (pt0) REVERT: A 724 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7742 (ttm-80) REVERT: A 777 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5588 (ttt180) REVERT: B 162 LYS cc_start: 0.6561 (tptt) cc_final: 0.5691 (mppt) REVERT: C 195 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7500 (tp30) REVERT: C 284 GLU cc_start: 0.5829 (mt-10) cc_final: 0.5404 (mt-10) REVERT: D 56 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8073 (tttt) REVERT: E 96 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8673 (mt) REVERT: E 104 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8788 (tt) REVERT: F 40 LEU cc_start: 0.7677 (tm) cc_final: 0.7400 (tp) REVERT: F 256 ASP cc_start: 0.7964 (t70) cc_final: 0.7729 (t70) REVERT: F 329 SER cc_start: 0.7166 (t) cc_final: 0.6758 (p) REVERT: F 341 TRP cc_start: 0.8444 (t60) cc_final: 0.7922 (t60) outliers start: 53 outliers final: 35 residues processed: 288 average time/residue: 0.1413 time to fit residues: 59.4664 Evaluate side-chains 279 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.164161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129303 restraints weight = 24365.921| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.36 r_work: 0.3268 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18139 Z= 0.165 Angle : 0.590 11.079 24738 Z= 0.301 Chirality : 0.045 0.257 2729 Planarity : 0.004 0.046 3031 Dihedral : 14.464 175.230 3104 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.93 % Allowed : 14.49 % Favored : 82.57 % 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: -1.65 (0.18), residues: 2127 helix: -0.18 (0.18), residues: 836 sheet: -1.46 (0.28), residues: 300 loop : -1.74 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 20 TYR 0.018 0.002 TYR D 233 PHE 0.026 0.002 PHE F 288 TRP 0.015 0.001 TRP F 341 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (18127) covalent geometry : angle 0.58841 / 0.30 (24726) hydrogen bonds : bond 0.04029 / 2.63 ( 613) hydrogen bonds : angle 4.66973 / 3.19 ( 1743) metal coordination : bond 0.00792 / 0.68 ( 12) metal coordination : angle 1.86072 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7965 (mmm-85) REVERT: A 39 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7710 (mtm110) REVERT: A 59 PHE cc_start: 0.7394 (m-80) cc_final: 0.6655 (m-80) REVERT: A 65 MET cc_start: 0.6113 (ptm) cc_final: 0.5617 (mtm) REVERT: A 195 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8594 (pt) REVERT: A 297 MET cc_start: 0.9168 (ttm) cc_final: 0.8774 (ttm) REVERT: A 629 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6356 (pt0) REVERT: A 724 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7758 (ttm-80) REVERT: A 777 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5633 (ttt180) REVERT: B 162 LYS cc_start: 0.6582 (tptt) cc_final: 0.5659 (mppt) REVERT: C 195 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: C 284 GLU cc_start: 0.5948 (mt-10) cc_final: 0.5640 (mt-10) REVERT: D 56 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7916 (tttt) REVERT: E 96 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8658 (mt) REVERT: E 104 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8812 (tt) REVERT: F 39 ARG cc_start: 0.5273 (tmt170) cc_final: 0.4876 (tmm160) REVERT: F 40 LEU cc_start: 0.7718 (tm) cc_final: 0.7358 (tp) REVERT: F 256 ASP cc_start: 0.7954 (t70) cc_final: 0.7706 (t70) REVERT: F 329 SER cc_start: 0.7130 (t) cc_final: 0.6716 (p) outliers start: 49 outliers final: 36 residues processed: 279 average time/residue: 0.1381 time to fit residues: 57.2127 Evaluate side-chains 277 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129944 restraints weight = 24147.921| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.28 r_work: 0.3281 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18139 Z= 0.123 Angle : 0.563 10.988 24738 Z= 0.287 Chirality : 0.043 0.247 2729 Planarity : 0.004 0.045 3031 Dihedral : 14.406 175.404 3104 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.63 % Allowed : 14.73 % Favored : 82.63 % 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: -1.45 (0.18), residues: 2127 helix: 0.00 (0.18), residues: 841 sheet: -1.31 (0.29), residues: 285 loop : -1.67 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 75 TYR 0.017 0.001 TYR B 125 PHE 0.025 0.001 PHE F 288 TRP 0.015 0.001 TRP F 341 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (18127) covalent geometry : angle 0.56201 / 0.29 (24726) hydrogen bonds : bond 0.03751 / 2.44 ( 613) hydrogen bonds : angle 4.53101 / 3.10 ( 1743) metal coordination : bond 0.00271 / 0.14 ( 12) metal coordination : angle 1.76870 / 0.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7938 (mmm-85) REVERT: A 39 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7726 (mtm110) REVERT: A 59 PHE cc_start: 0.7390 (m-80) cc_final: 0.6701 (m-80) REVERT: A 65 MET cc_start: 0.6078 (ptm) cc_final: 0.5671 (mtm) REVERT: A 87 MET cc_start: 0.7954 (tpp) cc_final: 0.6659 (mtp) REVERT: A 95 TRP cc_start: 0.7509 (m100) cc_final: 0.7100 (m100) REVERT: A 195 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8533 (pt) REVERT: A 297 MET cc_start: 0.9152 (ttm) cc_final: 0.8843 (ttm) REVERT: A 629 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6235 (pt0) REVERT: A 724 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: A 777 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5562 (ttt180) REVERT: B 74 ARG cc_start: 0.7695 (mtm180) cc_final: 0.7438 (mtm180) REVERT: B 140 TYR cc_start: 0.6300 (m-80) cc_final: 0.5873 (m-80) REVERT: B 162 LYS cc_start: 0.6589 (tptt) cc_final: 0.5662 (mppt) REVERT: C 195 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: C 284 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5759 (mt-10) REVERT: E 96 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8641 (mt) REVERT: F 28 ARG cc_start: 0.5386 (mmt90) cc_final: 0.5121 (mmt90) REVERT: F 39 ARG cc_start: 0.5525 (tmt170) cc_final: 0.5172 (tmm160) REVERT: F 40 LEU cc_start: 0.7597 (tm) cc_final: 0.7319 (tp) REVERT: F 200 GLU cc_start: 0.7704 (tt0) cc_final: 0.7222 (tt0) REVERT: F 256 ASP cc_start: 0.7928 (t70) cc_final: 0.7672 (t70) REVERT: F 329 SER cc_start: 0.6901 (t) cc_final: 0.6581 (p) REVERT: F 341 TRP cc_start: 0.8408 (t60) cc_final: 0.7913 (t60) outliers start: 44 outliers final: 33 residues processed: 292 average time/residue: 0.1425 time to fit residues: 61.9906 Evaluate side-chains 283 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 154 optimal weight: 0.4980 chunk 129 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 215 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 GLN F 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.166762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.131520 restraints weight = 24247.968| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.18 r_work: 0.3316 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18139 Z= 0.108 Angle : 0.550 10.775 24738 Z= 0.280 Chirality : 0.043 0.234 2729 Planarity : 0.004 0.046 3031 Dihedral : 14.332 175.669 3104 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.16 % Allowed : 15.51 % Favored : 82.34 % 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: -1.28 (0.18), residues: 2127 helix: 0.22 (0.18), residues: 836 sheet: -1.28 (0.29), residues: 289 loop : -1.62 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.015 0.001 TYR F 297 PHE 0.023 0.001 PHE F 288 TRP 0.021 0.001 TRP A 162 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (18127) covalent geometry : angle 0.54908 / 0.28 (24726) hydrogen bonds : bond 0.03588 / 2.35 ( 613) hydrogen bonds : angle 4.42692 / 3.03 ( 1743) metal coordination : bond 0.00327 / 0.22 ( 12) metal coordination : angle 1.67628 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.7328 (m-80) cc_final: 0.6699 (m-80) REVERT: A 65 MET cc_start: 0.6051 (ptm) cc_final: 0.5676 (mtm) REVERT: A 87 MET cc_start: 0.8081 (tpp) cc_final: 0.6722 (mtp) REVERT: A 95 TRP cc_start: 0.7477 (m100) cc_final: 0.7042 (m100) REVERT: A 195 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8503 (pt) REVERT: A 245 ASP cc_start: 0.7924 (p0) cc_final: 0.7704 (p0) REVERT: A 297 MET cc_start: 0.9130 (ttm) cc_final: 0.8767 (ttm) REVERT: A 301 GLN cc_start: 0.9192 (pm20) cc_final: 0.8909 (pm20) REVERT: A 629 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6292 (pt0) REVERT: A 724 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: B 140 TYR cc_start: 0.6269 (m-80) cc_final: 0.5851 (m-80) REVERT: B 162 LYS cc_start: 0.6399 (tptt) cc_final: 0.5560 (mppt) REVERT: C 195 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: C 284 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5713 (mt-10) REVERT: D 56 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7952 (tttm) REVERT: E 96 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8545 (mt) REVERT: F 19 GLU cc_start: 0.8063 (mp0) cc_final: 0.7595 (mp0) REVERT: F 28 ARG cc_start: 0.5461 (mmt90) cc_final: 0.5235 (mmt90) REVERT: F 39 ARG cc_start: 0.5376 (tmt170) cc_final: 0.5051 (tmm160) REVERT: F 40 LEU cc_start: 0.7607 (tm) cc_final: 0.7402 (tp) REVERT: F 200 GLU cc_start: 0.7644 (tt0) cc_final: 0.7191 (tt0) REVERT: F 256 ASP cc_start: 0.7913 (t70) cc_final: 0.7674 (t70) REVERT: F 329 SER cc_start: 0.6947 (t) cc_final: 0.6602 (p) REVERT: F 341 TRP cc_start: 0.8401 (t60) cc_final: 0.7937 (t60) outliers start: 36 outliers final: 27 residues processed: 287 average time/residue: 0.1394 time to fit residues: 59.4853 Evaluate side-chains 282 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 15 optimal weight: 5.9990 chunk 145 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 44 optimal weight: 0.0030 chunk 175 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN F 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132520 restraints weight = 24130.172| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.28 r_work: 0.3313 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18139 Z= 0.115 Angle : 0.561 10.753 24738 Z= 0.285 Chirality : 0.043 0.215 2729 Planarity : 0.004 0.046 3031 Dihedral : 14.269 175.771 3104 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.10 % Allowed : 15.69 % Favored : 82.22 % 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: -1.21 (0.18), residues: 2127 helix: 0.25 (0.18), residues: 849 sheet: -1.30 (0.29), residues: 291 loop : -1.56 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 22 TYR 0.037 0.001 TYR A 552 PHE 0.023 0.001 PHE F 288 TRP 0.015 0.001 TRP A 162 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (18127) covalent geometry : angle 0.56045 / 0.28 (24726) hydrogen bonds : bond 0.03582 / 2.35 ( 613) hydrogen bonds : angle 4.39488 / 3.01 ( 1743) metal coordination : bond 0.00254 / 0.13 ( 12) metal coordination : angle 1.63064 / 0.88 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7799 (tp30) cc_final: 0.7541 (tp30) REVERT: A 59 PHE cc_start: 0.7446 (m-80) cc_final: 0.6746 (m-80) REVERT: A 65 MET cc_start: 0.6025 (ptm) cc_final: 0.5674 (mtm) REVERT: A 87 MET cc_start: 0.8066 (tpp) cc_final: 0.6712 (mtp) REVERT: A 95 TRP cc_start: 0.7499 (m100) cc_final: 0.7114 (m100) REVERT: A 131 TRP cc_start: 0.8057 (t60) cc_final: 0.7802 (t60) REVERT: A 195 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8551 (pt) REVERT: A 245 ASP cc_start: 0.7940 (p0) cc_final: 0.7726 (p0) REVERT: A 297 MET cc_start: 0.9151 (ttm) cc_final: 0.8844 (ttm) REVERT: A 301 GLN cc_start: 0.9199 (pm20) cc_final: 0.8911 (pm20) REVERT: A 629 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6189 (pt0) REVERT: A 724 ARG cc_start: 0.7996 (ttm-80) cc_final: 0.7711 (ttm-80) REVERT: B 125 TYR cc_start: 0.7995 (t80) cc_final: 0.7760 (t80) REVERT: B 140 TYR cc_start: 0.6301 (m-80) cc_final: 0.5887 (m-80) REVERT: B 162 LYS cc_start: 0.6431 (tptt) cc_final: 0.5601 (mppt) REVERT: C 195 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: C 284 GLU cc_start: 0.6013 (mt-10) cc_final: 0.5674 (mt-10) REVERT: D 56 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7970 (tttm) REVERT: E 53 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8087 (pmm-80) REVERT: E 96 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8556 (mt) REVERT: F 37 THR cc_start: 0.8442 (p) cc_final: 0.8179 (p) REVERT: F 39 ARG cc_start: 0.5520 (tmt170) cc_final: 0.4958 (tmm160) REVERT: F 200 GLU cc_start: 0.7649 (tt0) cc_final: 0.7200 (tt0) REVERT: F 329 SER cc_start: 0.6923 (t) cc_final: 0.6559 (p) REVERT: F 341 TRP cc_start: 0.8403 (t60) cc_final: 0.7945 (t60) outliers start: 35 outliers final: 27 residues processed: 289 average time/residue: 0.1514 time to fit residues: 64.5333 Evaluate side-chains 285 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 56 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 15 optimal weight: 7.9990 chunk 88 optimal weight: 0.0030 chunk 59 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 56 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 160 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 overall best weight: 0.3728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 380 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.168111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134152 restraints weight = 24259.614| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.18 r_work: 0.3341 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18139 Z= 0.102 Angle : 0.542 10.471 24738 Z= 0.275 Chirality : 0.042 0.165 2729 Planarity : 0.004 0.046 3031 Dihedral : 14.162 175.925 3104 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.04 % Allowed : 15.99 % Favored : 81.98 % 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: -1.03 (0.18), residues: 2127 helix: 0.45 (0.18), residues: 844 sheet: -1.22 (0.29), residues: 284 loop : -1.49 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 20 TYR 0.019 0.001 TYR A 552 PHE 0.022 0.001 PHE F 288 TRP 0.016 0.001 TRP A 162 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (18127) covalent geometry : angle 0.54119 / 0.28 (24726) hydrogen bonds : bond 0.03407 / 2.23 ( 613) hydrogen bonds : angle 4.29776 / 2.95 ( 1743) metal coordination : bond 0.00497 / 0.39 ( 12) metal coordination : angle 1.65483 / 0.90 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4152.01 seconds wall clock time: 71 minutes 43.45 seconds (4303.45 seconds total)