Starting phenix.real_space_refine on Thu Mar 5 01:05:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mur_9253/03_2026/6mur_9253_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mur_9253/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mur_9253/03_2026/6mur_9253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mur_9253/03_2026/6mur_9253.map" model { file = "/net/cci-nas-00/data/ceres_data/6mur_9253/03_2026/6mur_9253_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mur_9253/03_2026/6mur_9253_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.40, 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: 1.47 Conformation dependent library (CDL) restraints added in 843.9 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: 2.25 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: 3.37 Time building geometry restraints manager: 1.84 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: 23384 2.08 - 4.16: 1124 4.16 - 6.24: 155 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: 2352 0.090 - 0.181: 338 0.181 - 0.271: 35 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 2.45 2.11 0.34 2.00e-01 2.50e+01 2.82e+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: 1.500 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.900 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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= 0.420 Angle : 1.122 36.419 24738 Z= 0.621 Chirality : 0.064 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 covalent geometry : bond 0.00844 (18127) covalent geometry : angle 1.05013 (24726) hydrogen bonds : bond 0.28891 ( 613) hydrogen bonds : angle 10.29539 ( 1743) metal coordination : bond 0.11815 ( 12) metal coordination : angle 17.98338 ( 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 : 0.655 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: 0.6817 (ttp-110) REVERT: D 115 ASP cc_start: 0.6446 (t70) cc_final: 0.6071 (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: 0.7415 (tt0) REVERT: D 255 LYS cc_start: 0.6865 (mmtm) cc_final: 0.6656 (mmtt) REVERT: E 104 LEU cc_start: 0.8737 (tm) cc_final: 0.8466 (tp) REVERT: F 19 GLU cc_start: 0.7970 (mp0) cc_final: 0.7521 (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: 0.1760 time to fit residues: 123.6096 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 : 0.646 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 380 HIS A 692 ASN B 77 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.166932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.131291 restraints weight = 24307.575| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.34 r_work: 0.3298 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18139 Z= 0.150 Angle : 0.676 11.465 24738 Z= 0.344 Chirality : 0.045 0.191 2729 Planarity : 0.006 0.050 3031 Dihedral : 14.947 173.223 3109 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.69 % Allowed : 9.82 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.54 (0.15), residues: 2127 helix: -2.50 (0.14), residues: 822 sheet: -1.96 (0.27), residues: 312 loop : -2.24 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 20 TYR 0.042 0.002 TYR B 125 PHE 0.026 0.002 PHE A 502 TRP 0.014 0.001 TRP A 320 HIS 0.008 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00322 (18127) covalent geometry : angle 0.66444 (24726) hydrogen bonds : bond 0.05797 ( 613) hydrogen bonds : angle 5.74934 ( 1743) metal coordination : bond 0.00789 ( 12) metal coordination : angle 5.67446 ( 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 354 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7540 (ttm110) REVERT: A 98 TYR cc_start: 0.7256 (t80) cc_final: 0.6649 (t80) REVERT: A 146 VAL cc_start: 0.6817 (OUTLIER) cc_final: 0.6608 (t) REVERT: A 167 LYS cc_start: 0.8354 (mttt) cc_final: 0.7953 (mttp) REVERT: A 195 ILE cc_start: 0.8808 (pp) cc_final: 0.8517 (pt) REVERT: A 245 ASP cc_start: 0.7797 (p0) cc_final: 0.7437 (p0) REVERT: A 438 ASN cc_start: 0.7554 (p0) cc_final: 0.7349 (p0) REVERT: A 629 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6428 (pt0) REVERT: A 705 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8044 (tt) REVERT: A 735 ARG cc_start: 0.8246 (ppp80) cc_final: 0.7949 (ptm160) REVERT: A 777 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5285 (ttt180) REVERT: B 95 VAL cc_start: 0.6795 (t) cc_final: 0.6585 (t) REVERT: B 122 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7745 (tppt) REVERT: B 148 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8368 (mp) REVERT: B 162 LYS cc_start: 0.6685 (tptt) cc_final: 0.6479 (tptt) REVERT: C 284 GLU cc_start: 0.5612 (mt-10) cc_final: 0.5344 (mt-10) REVERT: D 107 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7960 (mtm-85) REVERT: F 19 GLU cc_start: 0.8127 (mp0) cc_final: 0.7585 (mp0) REVERT: F 29 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.5740 (mp0) REVERT: F 256 ASP cc_start: 0.7950 (t70) cc_final: 0.7729 (t70) REVERT: F 303 TYR cc_start: 0.7909 (t80) cc_final: 0.7655 (t80) REVERT: F 329 SER cc_start: 0.7079 (t) cc_final: 0.6674 (p) REVERT: F 341 TRP cc_start: 0.8383 (t60) cc_final: 0.8121 (t60) outliers start: 45 outliers final: 21 residues processed: 342 average time/residue: 0.1608 time to fit residues: 78.4334 Evaluate side-chains 273 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 246 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 748 ILE 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 176 SER Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 169 VAL 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 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: 0.0470 chunk 72 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 GLN C 37 ASN D 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131476 restraints weight = 24586.299| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.19 r_work: 0.3288 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18139 Z= 0.160 Angle : 0.617 10.676 24738 Z= 0.315 Chirality : 0.044 0.170 2729 Planarity : 0.005 0.052 3031 Dihedral : 14.609 173.821 3104 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.87 % Allowed : 11.50 % Favored : 85.63 % 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: -2.62 (0.17), residues: 2127 helix: -1.33 (0.16), residues: 818 sheet: -1.73 (0.27), residues: 312 loop : -2.03 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 262 TYR 0.017 0.002 TYR A 265 PHE 0.027 0.002 PHE F 288 TRP 0.010 0.001 TRP E 227 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00367 (18127) covalent geometry : angle 0.61474 (24726) hydrogen bonds : bond 0.04381 ( 613) hydrogen bonds : angle 5.07490 ( 1743) metal coordination : bond 0.00772 ( 12) metal coordination : angle 2.45730 ( 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 305 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 39 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7751 (mtp85) REVERT: A 87 MET cc_start: 0.7530 (tmm) cc_final: 0.7138 (tpt) REVERT: A 98 TYR cc_start: 0.7197 (t80) cc_final: 0.6554 (t80) REVERT: A 146 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6532 (t) REVERT: A 195 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8532 (pt) REVERT: A 213 LEU cc_start: 0.8562 (tp) cc_final: 0.8354 (tp) REVERT: A 438 ASN cc_start: 0.7500 (p0) cc_final: 0.7286 (p0) REVERT: A 629 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6315 (pt0) REVERT: A 777 ARG cc_start: 0.5936 (OUTLIER) cc_final: 0.5503 (ttt180) REVERT: B 150 ASP cc_start: 0.8186 (m-30) cc_final: 0.7740 (m-30) REVERT: C 284 GLU cc_start: 0.5661 (mt-10) cc_final: 0.5396 (mt-10) REVERT: D 107 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7788 (mtm-85) REVERT: E 96 LEU cc_start: 0.8924 (tp) cc_final: 0.8665 (mt) REVERT: F 256 ASP cc_start: 0.7941 (t70) cc_final: 0.7704 (t70) REVERT: F 329 SER cc_start: 0.7088 (t) cc_final: 0.6670 (p) REVERT: F 341 TRP cc_start: 0.8349 (t60) cc_final: 0.7996 (t60) outliers start: 48 outliers final: 29 residues processed: 289 average time/residue: 0.1559 time to fit residues: 64.6196 Evaluate side-chains 271 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 777 ARG 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 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 F residue 23 VAL 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 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: 0.5980 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132362 restraints weight = 24588.209| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.23 r_work: 0.3301 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18139 Z= 0.127 Angle : 0.567 10.516 24738 Z= 0.290 Chirality : 0.043 0.160 2729 Planarity : 0.004 0.047 3031 Dihedral : 14.510 173.562 3104 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.57 % Allowed : 12.75 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.17), residues: 2127 helix: -0.75 (0.17), residues: 837 sheet: -1.43 (0.29), residues: 284 loop : -1.92 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 36 TYR 0.016 0.001 TYR B 125 PHE 0.027 0.001 PHE F 288 TRP 0.009 0.001 TRP E 227 HIS 0.004 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00289 (18127) covalent geometry : angle 0.56511 (24726) hydrogen bonds : bond 0.03821 ( 613) hydrogen bonds : angle 4.77688 ( 1743) metal coordination : bond 0.00274 ( 12) metal coordination : angle 2.05260 ( 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 308 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7899 (mmm-85) REVERT: A 39 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7715 (mtm-85) REVERT: A 59 PHE cc_start: 0.7475 (m-80) cc_final: 0.7112 (m-10) REVERT: A 98 TYR cc_start: 0.7265 (t80) cc_final: 0.6581 (t80) REVERT: A 195 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8532 (pt) REVERT: A 213 LEU cc_start: 0.8598 (tp) cc_final: 0.8327 (tp) REVERT: A 297 MET cc_start: 0.9094 (ttm) cc_final: 0.8685 (ttm) REVERT: A 438 ASN cc_start: 0.7497 (p0) cc_final: 0.7224 (p0) REVERT: A 629 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6230 (pt0) REVERT: A 724 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7599 (ttm-80) REVERT: B 150 ASP cc_start: 0.8055 (m-30) cc_final: 0.7837 (m-30) REVERT: B 162 LYS cc_start: 0.6560 (tptt) cc_final: 0.5727 (mppt) REVERT: C 284 GLU cc_start: 0.5846 (mt-10) cc_final: 0.5500 (mt-10) REVERT: E 96 LEU cc_start: 0.8850 (tp) cc_final: 0.8637 (mt) REVERT: E 104 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8796 (tt) REVERT: F 40 LEU cc_start: 0.7743 (tm) cc_final: 0.7308 (tp) REVERT: F 256 ASP cc_start: 0.7928 (t70) cc_final: 0.7686 (t70) REVERT: F 285 PHE cc_start: 0.8375 (t80) cc_final: 0.7997 (t80) REVERT: F 329 SER cc_start: 0.7224 (t) cc_final: 0.6822 (p) REVERT: F 341 TRP cc_start: 0.8350 (t60) cc_final: 0.8050 (t60) outliers start: 43 outliers final: 25 residues processed: 295 average time/residue: 0.1468 time to fit residues: 63.0303 Evaluate side-chains 265 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 107 ARG Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 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 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 E residue 260 MET 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 320 SER 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: 3.9990 chunk 181 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127969 restraints weight = 24392.498| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.33 r_work: 0.3232 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18139 Z= 0.228 Angle : 0.647 11.098 24738 Z= 0.330 Chirality : 0.047 0.179 2729 Planarity : 0.005 0.056 3031 Dihedral : 14.522 174.908 3104 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.53 % Allowed : 13.83 % 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: -1.99 (0.17), residues: 2127 helix: -0.57 (0.18), residues: 849 sheet: -1.53 (0.28), residues: 304 loop : -1.87 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 75 TYR 0.017 0.002 TYR A 265 PHE 0.030 0.002 PHE F 288 TRP 0.019 0.002 TRP A 95 HIS 0.007 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00542 (18127) covalent geometry : angle 0.64517 (24726) hydrogen bonds : bond 0.04262 ( 613) hydrogen bonds : angle 4.85866 ( 1743) metal coordination : bond 0.01638 ( 12) metal coordination : angle 2.29848 ( 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 309 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.7259 (m-80) cc_final: 0.6800 (m-80) REVERT: A 65 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5520 (mtm) REVERT: A 142 VAL cc_start: 0.8942 (t) cc_final: 0.8716 (m) REVERT: A 195 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8628 (pt) REVERT: A 297 MET cc_start: 0.9139 (ttm) cc_final: 0.8801 (ttm) REVERT: A 629 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6320 (pt0) REVERT: A 777 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5617 (ttt180) REVERT: B 162 LYS cc_start: 0.6739 (tptt) cc_final: 0.5857 (mppt) REVERT: C 284 GLU cc_start: 0.5982 (mt-10) cc_final: 0.5645 (mt-10) REVERT: D 56 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7959 (tttt) REVERT: D 160 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 96 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8701 (mt) REVERT: E 104 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8807 (tt) REVERT: F 40 LEU cc_start: 0.7883 (tm) cc_final: 0.7450 (tp) REVERT: F 256 ASP cc_start: 0.8044 (t70) cc_final: 0.7803 (t70) REVERT: F 329 SER cc_start: 0.7197 (t) cc_final: 0.6800 (p) REVERT: F 341 TRP cc_start: 0.8488 (t60) cc_final: 0.8105 (t60) outliers start: 59 outliers final: 36 residues processed: 291 average time/residue: 0.1552 time to fit residues: 65.0928 Evaluate side-chains 272 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 65 MET Chi-restraints excluded: chain A residue 97 VAL 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 748 ILE Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 107 ARG 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 56 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 160 GLU 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 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 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 196 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN C 177 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.128608 restraints weight = 24294.539| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.23 r_work: 0.3256 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18139 Z= 0.185 Angle : 0.608 10.786 24738 Z= 0.309 Chirality : 0.045 0.163 2729 Planarity : 0.004 0.046 3031 Dihedral : 14.440 174.300 3104 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.17 % Allowed : 14.43 % Favored : 82.40 % 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: -1.83 (0.18), residues: 2127 helix: -0.37 (0.18), residues: 845 sheet: -1.54 (0.28), residues: 299 loop : -1.81 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 39 TYR 0.016 0.002 TYR B 125 PHE 0.026 0.002 PHE F 288 TRP 0.014 0.001 TRP A 95 HIS 0.006 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00433 (18127) covalent geometry : angle 0.60684 (24726) hydrogen bonds : bond 0.03981 ( 613) hydrogen bonds : angle 4.74333 ( 1743) metal coordination : bond 0.00856 ( 12) metal coordination : angle 2.00226 ( 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 304 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 251 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7903 (mtm110) cc_final: 0.7562 (mtm110) REVERT: A 59 PHE cc_start: 0.7261 (m-80) cc_final: 0.7009 (m-80) REVERT: A 65 MET cc_start: 0.6244 (ptm) cc_final: 0.5580 (mtm) REVERT: A 142 VAL cc_start: 0.8967 (t) cc_final: 0.8766 (m) REVERT: A 195 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8617 (pt) REVERT: A 297 MET cc_start: 0.9152 (ttm) cc_final: 0.8794 (ttm) REVERT: A 513 ARG cc_start: 0.7387 (ptm160) cc_final: 0.7167 (ptm160) REVERT: A 629 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6118 (pt0) REVERT: A 724 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7785 (ttm-80) REVERT: A 777 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5588 (ttt180) REVERT: B 162 LYS cc_start: 0.6651 (tptt) cc_final: 0.5711 (mppt) REVERT: C 195 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: C 284 GLU cc_start: 0.5969 (mt-10) cc_final: 0.5633 (mt-10) REVERT: D 160 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: E 96 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8724 (mt) REVERT: F 39 ARG cc_start: 0.5372 (tmt170) cc_final: 0.4565 (tmm160) REVERT: F 109 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7109 (ttm170) REVERT: F 256 ASP cc_start: 0.8009 (t70) cc_final: 0.7746 (t70) REVERT: F 329 SER cc_start: 0.7176 (t) cc_final: 0.6758 (p) REVERT: F 341 TRP cc_start: 0.8478 (t60) cc_final: 0.8092 (t60) outliers start: 53 outliers final: 38 residues processed: 288 average time/residue: 0.1576 time to fit residues: 65.6349 Evaluate side-chains 289 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 748 ILE Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 107 ARG 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 160 GLU 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 E residue 23 THR 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 23 VAL 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 243 ILE Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 192 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126056 restraints weight = 24332.346| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.49 r_work: 0.3212 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18139 Z= 0.206 Angle : 0.629 11.072 24738 Z= 0.319 Chirality : 0.046 0.171 2729 Planarity : 0.005 0.045 3031 Dihedral : 14.416 174.619 3104 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.41 % Allowed : 14.91 % Favored : 81.68 % 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: -1.78 (0.18), residues: 2127 helix: -0.29 (0.18), residues: 847 sheet: -1.51 (0.28), residues: 299 loop : -1.82 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 755 TYR 0.015 0.002 TYR F 297 PHE 0.023 0.002 PHE F 288 TRP 0.018 0.002 TRP A 95 HIS 0.007 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00488 (18127) covalent geometry : angle 0.62762 (24726) hydrogen bonds : bond 0.04065 ( 613) hydrogen bonds : angle 4.73837 ( 1743) metal coordination : bond 0.01182 ( 12) metal coordination : angle 2.12795 ( 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 305 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 TRP cc_start: 0.7410 (t-100) cc_final: 0.7206 (t-100) REVERT: A 195 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8667 (pt) REVERT: A 513 ARG cc_start: 0.7563 (ptm160) cc_final: 0.7346 (ptm160) REVERT: A 629 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6350 (pt0) REVERT: A 707 TRP cc_start: 0.7580 (m100) cc_final: 0.7344 (m100) REVERT: A 724 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7829 (ttm-80) REVERT: A 777 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5611 (ttt180) REVERT: B 74 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7290 (mtm180) REVERT: B 162 LYS cc_start: 0.6667 (tptt) cc_final: 0.5694 (mppt) REVERT: C 195 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: C 284 GLU cc_start: 0.6124 (mt-10) cc_final: 0.5728 (mt-10) REVERT: D 160 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: E 96 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8688 (mt) REVERT: F 256 ASP cc_start: 0.8039 (t70) cc_final: 0.7788 (t70) REVERT: F 329 SER cc_start: 0.6962 (t) cc_final: 0.6607 (p) REVERT: F 341 TRP cc_start: 0.8502 (t60) cc_final: 0.8102 (t60) outliers start: 57 outliers final: 44 residues processed: 288 average time/residue: 0.1533 time to fit residues: 64.0572 Evaluate side-chains 285 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 748 ILE 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 152 MET Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 107 ARG 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 160 GLU 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 273 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 23 THR 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 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 243 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 102 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 165 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131403 restraints weight = 24089.456| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.17 r_work: 0.3288 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18139 Z= 0.117 Angle : 0.570 10.316 24738 Z= 0.287 Chirality : 0.043 0.173 2729 Planarity : 0.004 0.045 3031 Dihedral : 14.303 173.764 3104 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.46 % Allowed : 15.69 % Favored : 81.86 % 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: -1.47 (0.18), residues: 2127 helix: -0.04 (0.18), residues: 851 sheet: -1.34 (0.30), residues: 281 loop : -1.66 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.017 0.001 TYR F 297 PHE 0.019 0.001 PHE A 548 TRP 0.019 0.001 TRP A 95 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00269 (18127) covalent geometry : angle 0.56857 (24726) hydrogen bonds : bond 0.03560 ( 613) hydrogen bonds : angle 4.49006 ( 1743) metal coordination : bond 0.00403 ( 12) metal coordination : angle 1.73226 ( 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 306 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8113 (tpp) cc_final: 0.6798 (mtp) REVERT: A 162 TRP cc_start: 0.7379 (t-100) cc_final: 0.7179 (t-100) REVERT: A 195 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8586 (pt) REVERT: A 438 ASN cc_start: 0.7504 (p0) cc_final: 0.7298 (p0) REVERT: A 513 ARG cc_start: 0.7363 (ptm160) cc_final: 0.7123 (ptm160) REVERT: A 629 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6240 (pt0) REVERT: A 707 TRP cc_start: 0.7500 (m100) cc_final: 0.7252 (m100) REVERT: A 724 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: A 777 ARG cc_start: 0.5706 (OUTLIER) cc_final: 0.5470 (ttt180) REVERT: B 74 ARG cc_start: 0.7566 (mtm180) cc_final: 0.7321 (mtm180) REVERT: B 162 LYS cc_start: 0.6414 (tptt) cc_final: 0.5577 (mppt) REVERT: C 284 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5770 (mt-10) REVERT: D 160 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: E 96 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8638 (mt) REVERT: F 39 ARG cc_start: 0.5449 (tmt170) cc_final: 0.4665 (tmm160) REVERT: F 200 GLU cc_start: 0.7661 (tt0) cc_final: 0.7185 (tt0) REVERT: F 256 ASP cc_start: 0.7913 (t70) cc_final: 0.7645 (t70) REVERT: F 329 SER cc_start: 0.6950 (t) cc_final: 0.6570 (p) REVERT: F 341 TRP cc_start: 0.8412 (t60) cc_final: 0.8100 (t60) outliers start: 41 outliers final: 30 residues processed: 289 average time/residue: 0.1559 time to fit residues: 65.5788 Evaluate side-chains 277 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 107 ARG 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 66 LEU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 160 GLU 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 273 LEU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 223 THR 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 229 VAL Chi-restraints excluded: chain F residue 243 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 154 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.164364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130241 restraints weight = 24192.033| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.15 r_work: 0.3269 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18139 Z= 0.144 Angle : 0.594 10.494 24738 Z= 0.298 Chirality : 0.044 0.184 2729 Planarity : 0.004 0.044 3031 Dihedral : 14.267 174.106 3104 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.40 % Allowed : 16.41 % Favored : 81.20 % 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: -1.38 (0.18), residues: 2127 helix: 0.01 (0.18), residues: 860 sheet: -1.23 (0.30), residues: 277 loop : -1.62 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 20 TYR 0.026 0.001 TYR A 552 PHE 0.021 0.001 PHE B 145 TRP 0.030 0.001 TRP A 95 HIS 0.006 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00336 (18127) covalent geometry : angle 0.59274 (24726) hydrogen bonds : bond 0.03672 ( 613) hydrogen bonds : angle 4.50894 ( 1743) metal coordination : bond 0.00498 ( 12) metal coordination : angle 1.73435 ( 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 287 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7651 (mtm110) REVERT: A 59 PHE cc_start: 0.7154 (m-80) cc_final: 0.6807 (m-80) REVERT: A 87 MET cc_start: 0.8168 (tpp) cc_final: 0.6798 (mtp) REVERT: A 195 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8596 (pt) REVERT: A 297 MET cc_start: 0.9161 (ttm) cc_final: 0.8818 (ttm) REVERT: A 513 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7099 (ptm160) REVERT: A 629 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6375 (pt0) REVERT: A 707 TRP cc_start: 0.7514 (m100) cc_final: 0.7281 (m100) REVERT: A 724 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7776 (ttm-80) REVERT: A 777 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5473 (ttt180) REVERT: B 74 ARG cc_start: 0.7552 (mtm180) cc_final: 0.7297 (mtm180) REVERT: B 140 TYR cc_start: 0.6184 (m-80) cc_final: 0.5800 (m-80) REVERT: B 162 LYS cc_start: 0.6432 (tptt) cc_final: 0.6059 (mmtt) REVERT: C 195 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: C 284 GLU cc_start: 0.6086 (mt-10) cc_final: 0.5728 (mt-10) REVERT: D 160 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: E 96 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8625 (mt) REVERT: F 39 ARG cc_start: 0.5394 (tmt170) cc_final: 0.4371 (tmm160) REVERT: F 200 GLU cc_start: 0.7693 (tt0) cc_final: 0.7219 (tt0) REVERT: F 256 ASP cc_start: 0.7978 (t70) cc_final: 0.7729 (t70) REVERT: F 270 LEU cc_start: 0.8597 (tp) cc_final: 0.8356 (tp) REVERT: F 329 SER cc_start: 0.6881 (t) cc_final: 0.6494 (p) REVERT: F 341 TRP cc_start: 0.8430 (t60) cc_final: 0.8067 (t60) outliers start: 40 outliers final: 29 residues processed: 271 average time/residue: 0.1538 time to fit residues: 60.3299 Evaluate side-chains 276 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 705 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 169 VAL 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 160 GLU 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 23 THR 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 223 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 265 ASP 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: 0.9990 chunk 145 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.130721 restraints weight = 24049.505| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.17 r_work: 0.3278 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18139 Z= 0.135 Angle : 0.587 10.573 24738 Z= 0.295 Chirality : 0.043 0.172 2729 Planarity : 0.004 0.045 3031 Dihedral : 14.218 174.039 3102 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.34 % Allowed : 16.23 % Favored : 81.44 % 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: -1.27 (0.18), residues: 2127 helix: 0.14 (0.18), residues: 858 sheet: -1.19 (0.30), residues: 284 loop : -1.59 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 20 TYR 0.021 0.001 TYR A 552 PHE 0.021 0.001 PHE F 288 TRP 0.012 0.001 TRP A 162 HIS 0.006 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00313 (18127) covalent geometry : angle 0.58588 (24726) hydrogen bonds : bond 0.03572 ( 613) hydrogen bonds : angle 4.47039 ( 1743) metal coordination : bond 0.00341 ( 12) metal coordination : angle 1.69688 ( 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 288 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 249 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.7196 (m-80) cc_final: 0.6881 (m-80) REVERT: A 195 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8541 (pt) REVERT: A 297 MET cc_start: 0.9149 (ttm) cc_final: 0.8798 (ttm) REVERT: A 629 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6506 (pt0) REVERT: A 707 TRP cc_start: 0.7493 (m100) cc_final: 0.7264 (m100) REVERT: A 724 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7781 (ttm-80) REVERT: A 777 ARG cc_start: 0.5744 (OUTLIER) cc_final: 0.5522 (ttt180) REVERT: B 74 ARG cc_start: 0.7551 (mtm180) cc_final: 0.7338 (mtm180) REVERT: B 140 TYR cc_start: 0.6180 (m-80) cc_final: 0.5796 (m-80) REVERT: B 162 LYS cc_start: 0.6393 (tptt) cc_final: 0.6023 (mmtt) REVERT: C 195 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: C 284 GLU cc_start: 0.6077 (mt-10) cc_final: 0.5723 (mt-10) REVERT: D 160 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 249 ASP cc_start: 0.7909 (t0) cc_final: 0.7681 (m-30) REVERT: E 96 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8632 (mt) REVERT: E 202 MET cc_start: 0.8292 (tpp) cc_final: 0.8044 (mmm) REVERT: F 39 ARG cc_start: 0.5264 (tmt170) cc_final: 0.4243 (tmm160) REVERT: F 200 GLU cc_start: 0.7657 (tt0) cc_final: 0.7204 (tt0) REVERT: F 256 ASP cc_start: 0.7980 (t70) cc_final: 0.7734 (t70) REVERT: F 270 LEU cc_start: 0.8624 (tp) cc_final: 0.8403 (tp) REVERT: F 329 SER cc_start: 0.6871 (t) cc_final: 0.6522 (p) REVERT: F 341 TRP cc_start: 0.8437 (t60) cc_final: 0.8084 (t60) outliers start: 39 outliers final: 31 residues processed: 272 average time/residue: 0.1510 time to fit residues: 60.0769 Evaluate side-chains 274 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET 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 A residue 705 LEU Chi-restraints excluded: chain A residue 777 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 169 VAL 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 160 GLU 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 23 THR 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 223 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 265 ASP Chi-restraints excluded: chain F residue 268 ASN 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: 6.9990 chunk 88 optimal weight: 0.2980 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 168 optimal weight: 0.0570 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.166317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132013 restraints weight = 24231.941| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.20 r_work: 0.3312 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18139 Z= 0.112 Angle : 0.569 10.244 24738 Z= 0.285 Chirality : 0.043 0.178 2729 Planarity : 0.004 0.044 3031 Dihedral : 14.173 173.804 3102 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.10 % Allowed : 16.83 % Favored : 81.08 % 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: -1.12 (0.18), residues: 2127 helix: 0.30 (0.18), residues: 858 sheet: -1.15 (0.30), residues: 277 loop : -1.53 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 20 TYR 0.020 0.001 TYR B 125 PHE 0.020 0.001 PHE F 288 TRP 0.020 0.001 TRP A 162 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00252 (18127) covalent geometry : angle 0.56845 (24726) hydrogen bonds : bond 0.03383 ( 613) hydrogen bonds : angle 4.37080 ( 1743) metal coordination : bond 0.00381 ( 12) metal coordination : angle 1.63421 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4190.03 seconds wall clock time: 72 minutes 22.03 seconds (4342.03 seconds total)