Starting phenix.real_space_refine on Sat Sep 12 17:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mut_9255/09_2026/6mut_9255_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mut_9255/09_2026/6mut_9255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mut_9255/09_2026/6mut_9255_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mut_9255/09_2026/6mut_9255_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mut_9255/09_2026/6mut_9255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mut_9255/09_2026/6mut_9255.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 38 5.49 5 S 50 5.16 5 C 10800 2.51 5 N 2991 2.21 5 O 3269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17151 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5958 Classifications: {'peptide': 747} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 713} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 25 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: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2202 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2138 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 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: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 440 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 1} Link IDs: {'rna2p': 9, 'rna3p': 10} Chain: "H" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 388 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 14} Link IDs: {'rna2p': 2, 'rna3p': 16} 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 3111 SG CYS A 389 47.005 69.717 95.875 1.00 49.83 S ATOM 3131 SG CYS A 392 45.001 66.558 95.210 1.00 47.28 S ATOM 3286 SG CYS A 413 45.413 68.202 98.783 1.00 48.96 S ATOM 3306 SG CYS A 416 47.913 65.828 97.907 1.00 46.14 S ATOM 7916 SG CYS C 113 55.739 95.945 78.587 1.00 47.08 S ATOM 7983 SG CYS C 122 57.365 96.835 75.093 1.00 42.26 S ATOM 8003 SG CYS C 125 55.610 92.889 76.569 1.00 36.60 S ATOM 10134 SG CYS D 113 86.479 81.027 78.348 1.00 64.42 S ATOM 10201 SG CYS D 122 88.282 82.794 75.313 1.00 61.95 S ATOM 10221 SG CYS D 125 85.158 80.035 74.681 1.00 56.51 S Time building chain proxies: 3.75, per 1000 atoms: 0.22 Number of scatterers: 17151 At special positions: 0 Unit cell: (137.214, 118.701, 142.659, 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 50 16.00 P 38 15.00 O 3269 8.00 N 2991 7.00 C 10800 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: 1.52 Conformation dependent library (CDL) restraints added in 750.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 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 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 38.3% alpha, 13.5% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.755A pdb=" N LEU A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 24 removed outlier: 3.870A pdb=" N ARG A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 removed outlier: 5.060A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.563A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.529A pdb=" N VAL A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 171 through 183 Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.627A pdb=" N LEU A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.634A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 324 removed outlier: 3.857A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 369 removed outlier: 3.974A pdb=" N LEU A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 369 " --> pdb=" O VAL A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.847A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 removed outlier: 3.641A pdb=" N SER A 506 " --> pdb=" O PHE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.784A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.712A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 removed outlier: 3.640A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.635A pdb=" N ALA A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.641A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 717 removed outlier: 3.750A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.751A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.681A pdb=" N VAL A 746 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'A' and resid 764 through 775 removed outlier: 3.503A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 4.039A pdb=" N ALA B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.548A pdb=" N ASP B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 85 removed outlier: 3.777A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 removed outlier: 4.390A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.561A pdb=" N GLU B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.939A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.563A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 4.220A pdb=" N GLN B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.820A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 248 through 254 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.615A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.715A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 3.587A pdb=" N ALA D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 206 through 221 removed outlier: 3.539A pdb=" N LEU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.761A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.515A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.601A pdb=" N LEU D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.530A pdb=" N PHE E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.674A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 removed outlier: 4.530A pdb=" N ALA E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 99 removed outlier: 4.014A pdb=" N ARG E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.596A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.614A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 3.955A pdb=" N GLY E 180 " --> pdb=" O MET E 176 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 51 through 60 removed outlier: 4.014A pdb=" N LEU F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 71 Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.547A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.703A 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: 3.560A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.538A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 304 removed outlier: 3.953A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR F 298 " --> pdb=" O ASP F 294 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.657A 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 292 removed outlier: 5.946A pdb=" N VAL A 288 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 299 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 290 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 295 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.906A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.798A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA A 585 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.986A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 15 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS C 8 " --> pdb=" O PHE C 245 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE C 245 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 259 " --> pdb=" O PHE C 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.888A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB1, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.886A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 50 removed outlier: 4.083A pdb=" N SER D 242 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS D 14 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N PHE D 240 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS D 16 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE D 238 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 163 through 167 removed outlier: 3.533A pdb=" N LYS D 166 " --> pdb=" O ASN D 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.659A pdb=" N THR E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LEU E 160 " --> pdb=" O SER E 55 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA E 57 " --> pdb=" O TYR E 158 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR E 158 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY E 156 " --> pdb=" O PRO E 59 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.552A pdb=" N VAL E 133 " --> pdb=" O SER E 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AB7, first strand: chain 'E' and resid 252 through 253 Processing sheet with id=AB8, first strand: chain 'E' and resid 229 through 232 Processing sheet with id=AB9, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC1, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC2, 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=AC3, 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=AC4, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AC5, 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: 3.655A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3400 1.32 - 1.45: 4540 1.45 - 1.57: 9496 1.57 - 1.69: 73 1.69 - 1.82: 82 Bond restraints: 17591 Sorted by residual: bond pdb=" C5 G G 12 " pdb=" C4 G G 12 " ideal model delta sigma weight residual 1.379 1.347 0.032 7.00e-03 2.04e+04 2.08e+01 bond pdb=" C5 G G 11 " pdb=" C4 G G 11 " ideal model delta sigma weight residual 1.379 1.347 0.032 7.00e-03 2.04e+04 2.08e+01 bond pdb=" N GLY A 111 " pdb=" CA GLY A 111 " ideal model delta sigma weight residual 1.444 1.483 -0.038 9.60e-03 1.09e+04 1.58e+01 bond pdb=" N9 G G 12 " pdb=" C4 G G 12 " ideal model delta sigma weight residual 1.375 1.344 0.031 8.00e-03 1.56e+04 1.54e+01 bond pdb=" N ILE A 195 " pdb=" CA ILE A 195 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.46e+01 ... (remaining 17586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 22047 2.27 - 4.54: 1652 4.54 - 6.81: 199 6.81 - 9.08: 50 9.08 - 11.35: 10 Bond angle restraints: 23958 Sorted by residual: angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 102.65 110.00 -7.35 6.80e-01 2.16e+00 1.17e+02 angle pdb=" C ASN C 179 " pdb=" N PRO C 180 " pdb=" CA PRO C 180 " ideal model delta sigma weight residual 119.85 129.71 -9.86 1.01e+00 9.80e-01 9.53e+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=" C LEU E 219 " pdb=" N PRO E 220 " pdb=" CA PRO E 220 " ideal model delta sigma weight residual 119.76 127.26 -7.50 1.03e+00 9.43e-01 5.30e+01 angle pdb=" N PRO F 79 " pdb=" CA PRO F 79 " pdb=" CB PRO F 79 " ideal model delta sigma weight residual 103.25 110.81 -7.56 1.05e+00 9.07e-01 5.19e+01 ... (remaining 23953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 10315 33.87 - 67.74: 210 67.74 - 101.61: 23 101.61 - 135.48: 1 135.48 - 169.35: 2 Dihedral angle restraints: 10551 sinusoidal: 4519 harmonic: 6032 Sorted by residual: dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 41.35 -169.35 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O4' C G 20 " pdb=" C1' C G 20 " pdb=" N1 C G 20 " pdb=" C2 C G 20 " ideal model delta sinusoidal sigma weight residual 232.00 69.54 162.46 1 1.70e+01 3.46e-03 6.49e+01 dihedral pdb=" C5' C G 20 " pdb=" C4' C G 20 " pdb=" C3' C G 20 " pdb=" O3' C G 20 " ideal model delta sinusoidal sigma weight residual 147.00 107.36 39.64 1 8.00e+00 1.56e-02 3.45e+01 ... (remaining 10548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2152 0.098 - 0.195: 415 0.195 - 0.293: 70 0.293 - 0.390: 6 0.390 - 0.488: 1 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE D 40 " pdb=" CA ILE D 40 " pdb=" CG1 ILE D 40 " pdb=" CG2 ILE D 40 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB VAL E 157 " pdb=" CA VAL E 157 " pdb=" CG1 VAL E 157 " pdb=" CG2 VAL E 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C2' G G 9 " pdb=" C3' G G 9 " pdb=" O2' G G 9 " pdb=" C1' G G 9 " both_signs ideal model delta sigma weight residual False -2.60 -2.25 -0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 2641 not shown) Planarity restraints: 2951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 229 " -0.020 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C LEU E 229 " 0.073 2.00e-02 2.50e+03 pdb=" O LEU E 229 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU E 230 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 89 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C CYS C 89 " 0.064 2.00e-02 2.50e+03 pdb=" O CYS C 89 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG C 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 192 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C ALA E 192 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA E 192 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY E 193 " 0.020 2.00e-02 2.50e+03 ... (remaining 2948 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 56 2.44 - 3.06: 10063 3.06 - 3.67: 25484 3.67 - 4.29: 38693 4.29 - 4.90: 64526 Nonbonded interactions: 138822 Sorted by model distance: nonbonded pdb=" O2' G G 16 " pdb=" O5' A G 17 " model vdw 1.830 3.040 nonbonded pdb=" O6 G G 16 " pdb=" O4 U H 29 " model vdw 1.969 2.432 nonbonded pdb=" O ASN A 102 " pdb=" CA GLY A 106 " model vdw 2.004 3.440 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.191 3.040 nonbonded pdb=" O2' G G 16 " pdb=" C8 A G 17 " model vdw 2.202 3.260 ... (remaining 138817 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' and (resid 3 through 168 or resid 180 through 301)) selection = (chain 'D' and resid 3 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.740 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 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 : 0.013 0.161 17603 Z= 0.651 Angle : 1.333 34.808 23970 Z= 0.813 Chirality : 0.080 0.488 2644 Planarity : 0.009 0.076 2951 Dihedral : 14.222 169.354 6691 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.48 % Favored : 92.32 % Rotamer: Outliers : 1.23 % Allowed : 6.07 % Favored : 92.71 % Cbeta Deviations : 0.10 % 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: -4.80 (0.15), residues: 2071 helix: -4.17 (0.10), residues: 779 sheet: -1.54 (0.29), residues: 298 loop : -2.81 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 203 TYR 0.042 0.004 TYR D 49 PHE 0.038 0.004 PHE A 343 TRP 0.034 0.004 TRP E 227 HIS 0.017 0.003 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.01300 / 0.65 (17591) covalent geometry : angle 1.29236 / 0.81 (23958) hydrogen bonds : bond 0.29070 / 19.44 ( 579) hydrogen bonds : angle 10.69692 / 7.51 ( 1637) metal coordination : bond 0.10271 / 7.03 ( 12) metal coordination : angle 14.58550 / 8.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 319 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 HIS cc_start: 0.7623 (m-70) cc_final: 0.7296 (m-70) REVERT: A 82 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7435 (mmm160) REVERT: A 267 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 297 MET cc_start: 0.8838 (ttt) cc_final: 0.8611 (ttm) REVERT: A 380 HIS cc_start: 0.6171 (p-80) cc_final: 0.5501 (p-80) REVERT: A 406 SER cc_start: 0.8373 (t) cc_final: 0.7986 (p) REVERT: A 491 PHE cc_start: 0.8571 (p90) cc_final: 0.8311 (p90) REVERT: A 507 MET cc_start: 0.7581 (mmm) cc_final: 0.7327 (mpp) REVERT: D 115 ASP cc_start: 0.8161 (t70) cc_final: 0.7648 (t70) REVERT: D 162 ILE cc_start: 0.7970 (tp) cc_final: 0.7697 (mt) REVERT: E 104 LEU cc_start: 0.9268 (tm) cc_final: 0.8890 (tt) REVERT: E 228 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7398 (ttm-80) outliers start: 20 outliers final: 13 residues processed: 333 average time/residue: 0.1731 time to fit residues: 80.6035 Evaluate side-chains 202 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 243 PHE Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 217 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 676 HIS B 94 GLN C 37 ASN C 177 GLN D 44 HIS D 199 ASN E 106 ASN E 139 GLN E 200 HIS ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.194627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145301 restraints weight = 24053.021| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.96 r_work: 0.3225 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17603 Z= 0.180 Angle : 0.735 11.132 23970 Z= 0.385 Chirality : 0.048 0.259 2644 Planarity : 0.006 0.051 2951 Dihedral : 14.730 176.109 2957 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 2.14 % Allowed : 10.11 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.15), residues: 2071 helix: -2.88 (0.14), residues: 819 sheet: -1.24 (0.29), residues: 273 loop : -2.62 (0.17), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 107 TYR 0.021 0.002 TYR A 182 PHE 0.018 0.002 PHE A 549 TRP 0.016 0.002 TRP A 131 HIS 0.006 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (17591) covalent geometry : angle 0.72923 / 0.38 (23958) hydrogen bonds : bond 0.06595 / 4.63 ( 579) hydrogen bonds : angle 6.23830 / 4.28 ( 1637) metal coordination : bond 0.01297 / 0.82 ( 12) metal coordination : angle 4.14911 / 2.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8281 (pt0) cc_final: 0.8054 (pt0) REVERT: A 64 HIS cc_start: 0.7483 (m-70) cc_final: 0.7157 (m-70) REVERT: A 65 MET cc_start: 0.7545 (ttm) cc_final: 0.6953 (ttt) REVERT: A 82 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7489 (mmm160) REVERT: A 297 MET cc_start: 0.8931 (ttt) cc_final: 0.8709 (ttm) REVERT: A 406 SER cc_start: 0.8194 (t) cc_final: 0.7882 (p) REVERT: A 491 PHE cc_start: 0.8863 (p90) cc_final: 0.8593 (p90) REVERT: A 507 MET cc_start: 0.7933 (mmm) cc_final: 0.7567 (mpp) REVERT: C 115 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: C 172 ASP cc_start: 0.8298 (t0) cc_final: 0.8031 (t0) REVERT: E 104 LEU cc_start: 0.9385 (tm) cc_final: 0.9029 (tt) REVERT: E 228 ARG cc_start: 0.8534 (ttp-110) cc_final: 0.8261 (ttm-80) outliers start: 35 outliers final: 17 residues processed: 231 average time/residue: 0.1607 time to fit residues: 53.6337 Evaluate side-chains 191 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain F residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 204 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 chunk 136 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN D 199 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.194846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145836 restraints weight = 24246.409| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.50 r_work: 0.3211 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17603 Z= 0.148 Angle : 0.615 10.737 23970 Z= 0.323 Chirality : 0.045 0.170 2644 Planarity : 0.005 0.044 2951 Dihedral : 14.494 175.807 2941 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.70 % Allowed : 11.46 % Favored : 85.85 % 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: -3.17 (0.16), residues: 2071 helix: -2.09 (0.16), residues: 818 sheet: -1.22 (0.28), residues: 274 loop : -2.32 (0.17), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 713 TYR 0.019 0.001 TYR A 265 PHE 0.013 0.001 PHE E 159 TRP 0.015 0.001 TRP D 109 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (17591) covalent geometry : angle 0.61231 / 0.32 (23958) hydrogen bonds : bond 0.05339 / 3.71 ( 579) hydrogen bonds : angle 5.50086 / 3.80 ( 1637) metal coordination : bond 0.00652 / 0.51 ( 12) metal coordination : angle 2.80502 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 HIS cc_start: 0.7513 (m-70) cc_final: 0.7221 (m-70) REVERT: A 65 MET cc_start: 0.7602 (ttm) cc_final: 0.7083 (ttt) REVERT: A 184 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.9011 (m) REVERT: A 297 MET cc_start: 0.8915 (ttt) cc_final: 0.8672 (ttm) REVERT: A 406 SER cc_start: 0.8121 (t) cc_final: 0.7859 (p) REVERT: A 418 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.8044 (mmt-90) REVERT: A 496 LYS cc_start: 0.7249 (mmmt) cc_final: 0.6830 (tppp) REVERT: A 507 MET cc_start: 0.7852 (mmm) cc_final: 0.7289 (mpp) REVERT: D 248 LEU cc_start: 0.8963 (tt) cc_final: 0.8754 (tt) REVERT: E 46 ASP cc_start: 0.8779 (m-30) cc_final: 0.8469 (m-30) REVERT: E 104 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9034 (tt) REVERT: E 228 ARG cc_start: 0.8612 (ttp-110) cc_final: 0.8247 (ttm-80) outliers start: 44 outliers final: 24 residues processed: 224 average time/residue: 0.1540 time to fit residues: 50.4562 Evaluate side-chains 196 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 131 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 190 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 217 ASN ** 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 = 0.4269 r_free = 0.4269 target = 0.196662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146133 restraints weight = 23933.873| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.32 r_work: 0.3238 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17603 Z= 0.122 Angle : 0.579 10.375 23970 Z= 0.299 Chirality : 0.044 0.223 2644 Planarity : 0.004 0.040 2951 Dihedral : 14.359 176.318 2941 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.57 % Allowed : 12.62 % Favored : 84.80 % 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: -2.71 (0.17), residues: 2071 helix: -1.60 (0.17), residues: 819 sheet: -1.27 (0.27), residues: 286 loop : -2.06 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 82 TYR 0.015 0.001 TYR A 265 PHE 0.012 0.001 PHE D 100 TRP 0.014 0.001 TRP D 152 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (17591) covalent geometry : angle 0.57724 / 0.30 (23958) hydrogen bonds : bond 0.04611 / 3.20 ( 579) hydrogen bonds : angle 5.11801 / 3.54 ( 1637) metal coordination : bond 0.00533 / 0.41 ( 12) metal coordination : angle 2.31243 / 1.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9086 (m) REVERT: A 406 SER cc_start: 0.8087 (t) cc_final: 0.7821 (p) REVERT: A 418 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8057 (mmt-90) REVERT: A 470 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8211 (p) REVERT: A 507 MET cc_start: 0.7859 (mmm) cc_final: 0.7389 (mpp) REVERT: A 572 ARG cc_start: 0.8106 (tmm160) cc_final: 0.7850 (ptt90) REVERT: D 248 LEU cc_start: 0.8923 (tt) cc_final: 0.8640 (tt) REVERT: E 3 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8498 (tppt) REVERT: E 104 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9020 (tt) REVERT: E 147 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: E 228 ARG cc_start: 0.8615 (ttp-110) cc_final: 0.8296 (ttm-80) outliers start: 42 outliers final: 25 residues processed: 216 average time/residue: 0.1561 time to fit residues: 49.5856 Evaluate side-chains 205 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 19 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 chunk 148 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN D 199 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.196047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144693 restraints weight = 23731.274| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.21 r_work: 0.3205 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17603 Z= 0.143 Angle : 0.576 9.385 23970 Z= 0.297 Chirality : 0.044 0.206 2644 Planarity : 0.004 0.038 2951 Dihedral : 14.305 176.929 2941 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.88 % Allowed : 13.30 % Favored : 83.82 % 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: -2.36 (0.17), residues: 2071 helix: -1.24 (0.17), residues: 812 sheet: -1.15 (0.28), residues: 285 loop : -1.92 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 82 TYR 0.018 0.001 TYR C 224 PHE 0.013 0.001 PHE E 159 TRP 0.013 0.001 TRP C 152 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17591) covalent geometry : angle 0.57415 / 0.30 (23958) hydrogen bonds : bond 0.04372 / 3.02 ( 579) hydrogen bonds : angle 4.93753 / 3.43 ( 1637) metal coordination : bond 0.00689 / 0.50 ( 12) metal coordination : angle 2.33062 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 THR cc_start: 0.9363 (OUTLIER) cc_final: 0.9133 (m) REVERT: A 229 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8085 (mtmm) REVERT: A 297 MET cc_start: 0.8944 (ttm) cc_final: 0.8669 (ttm) REVERT: A 354 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 406 SER cc_start: 0.8139 (t) cc_final: 0.7865 (p) REVERT: A 418 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.8151 (mmt-90) REVERT: A 507 MET cc_start: 0.7780 (mmm) cc_final: 0.7245 (mpp) REVERT: A 572 ARG cc_start: 0.8138 (tmm160) cc_final: 0.7892 (ptt90) REVERT: C 95 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6370 (tm-30) REVERT: C 102 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8565 (p0) REVERT: C 224 TYR cc_start: 0.9083 (p90) cc_final: 0.8757 (p90) REVERT: D 75 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.7370 (ttm110) REVERT: D 248 LEU cc_start: 0.8940 (tt) cc_final: 0.8688 (tt) REVERT: E 3 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8422 (tppt) REVERT: E 104 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9030 (tt) REVERT: E 228 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8306 (ttm-80) REVERT: F 301 MET cc_start: -0.4002 (ttm) cc_final: -0.4404 (ttm) outliers start: 47 outliers final: 27 residues processed: 210 average time/residue: 0.1551 time to fit residues: 47.9284 Evaluate side-chains 209 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 171 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 151 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 217 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.195247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143835 restraints weight = 23780.548| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.88 r_work: 0.3207 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17603 Z= 0.162 Angle : 0.579 9.738 23970 Z= 0.298 Chirality : 0.044 0.204 2644 Planarity : 0.004 0.038 2951 Dihedral : 14.190 177.542 2937 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 2.76 % Allowed : 13.91 % Favored : 83.33 % 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: -2.18 (0.17), residues: 2071 helix: -1.00 (0.18), residues: 810 sheet: -1.19 (0.27), residues: 285 loop : -1.85 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 103 TYR 0.016 0.001 TYR A 265 PHE 0.014 0.001 PHE A 136 TRP 0.014 0.001 TRP C 152 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (17591) covalent geometry : angle 0.57628 / 0.30 (23958) hydrogen bonds : bond 0.04274 / 2.93 ( 579) hydrogen bonds : angle 4.84539 / 3.37 ( 1637) metal coordination : bond 0.00940 / 0.66 ( 12) metal coordination : angle 2.42257 / 1.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8147 (mtmm) REVERT: A 297 MET cc_start: 0.8947 (ttm) cc_final: 0.8666 (ttm) REVERT: A 354 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: A 406 SER cc_start: 0.8095 (t) cc_final: 0.7844 (p) REVERT: A 418 ARG cc_start: 0.8409 (mmt-90) cc_final: 0.8204 (mmt-90) REVERT: A 507 MET cc_start: 0.7945 (mmm) cc_final: 0.7497 (mpp) REVERT: D 75 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7349 (ttm110) REVERT: D 248 LEU cc_start: 0.8962 (tt) cc_final: 0.8753 (tt) REVERT: E 3 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8383 (tppt) REVERT: E 104 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9035 (tt) REVERT: E 228 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8260 (ttm-80) outliers start: 45 outliers final: 29 residues processed: 205 average time/residue: 0.1584 time to fit residues: 47.8990 Evaluate side-chains 201 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 124 optimal weight: 0.0770 chunk 195 optimal weight: 40.0000 chunk 122 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 95 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN ** E 217 ASN ** 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 = 0.4271 r_free = 0.4271 target = 0.196886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146164 restraints weight = 23671.995| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.07 r_work: 0.3234 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17603 Z= 0.106 Angle : 0.545 9.739 23970 Z= 0.280 Chirality : 0.043 0.209 2644 Planarity : 0.004 0.036 2951 Dihedral : 14.112 177.424 2937 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 2.33 % Allowed : 14.58 % Favored : 83.09 % 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: -1.98 (0.17), residues: 2071 helix: -0.73 (0.18), residues: 816 sheet: -1.25 (0.28), residues: 278 loop : -1.78 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 181 TYR 0.015 0.001 TYR A 731 PHE 0.010 0.001 PHE A 136 TRP 0.013 0.001 TRP C 152 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (17591) covalent geometry : angle 0.54355 / 0.28 (23958) hydrogen bonds : bond 0.03942 / 2.69 ( 579) hydrogen bonds : angle 4.65049 / 3.24 ( 1637) metal coordination : bond 0.00606 / 0.49 ( 12) metal coordination : angle 2.10849 / 1.14 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: A 418 ARG cc_start: 0.8328 (mmt-90) cc_final: 0.8123 (mmt-90) REVERT: A 507 MET cc_start: 0.7906 (mmm) cc_final: 0.7557 (mpp) REVERT: A 572 ARG cc_start: 0.8100 (tmm160) cc_final: 0.7787 (ptt90) REVERT: A 763 TRP cc_start: 0.7011 (m100) cc_final: 0.6385 (m100) REVERT: C 95 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6369 (tm-30) REVERT: D 75 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7354 (ttm110) REVERT: D 134 GLU cc_start: 0.7758 (mp0) cc_final: 0.7509 (mp0) REVERT: D 152 TRP cc_start: 0.7729 (m100) cc_final: 0.7348 (m100) REVERT: E 3 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8224 (tppt) REVERT: E 104 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9027 (tt) REVERT: E 147 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: E 228 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8237 (ttm-80) REVERT: F 301 MET cc_start: -0.4063 (ttm) cc_final: -0.4432 (ttm) outliers start: 38 outliers final: 24 residues processed: 216 average time/residue: 0.1594 time to fit residues: 50.4998 Evaluate side-chains 205 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 88 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 82 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN D 199 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145936 restraints weight = 23834.553| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.77 r_work: 0.3230 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17603 Z= 0.117 Angle : 0.551 9.776 23970 Z= 0.281 Chirality : 0.043 0.206 2644 Planarity : 0.004 0.036 2951 Dihedral : 14.056 177.988 2937 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 2.45 % Allowed : 15.01 % Favored : 82.54 % 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: -1.71 (0.18), residues: 2071 helix: -0.44 (0.18), residues: 811 sheet: -1.11 (0.28), residues: 288 loop : -1.71 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.013 0.001 TYR A 265 PHE 0.010 0.001 PHE A 548 TRP 0.014 0.001 TRP A 596 HIS 0.003 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (17591) covalent geometry : angle 0.54950 / 0.28 (23958) hydrogen bonds : bond 0.03827 / 2.62 ( 579) hydrogen bonds : angle 4.51824 / 3.15 ( 1637) metal coordination : bond 0.00589 / 0.42 ( 12) metal coordination : angle 2.02298 / 1.11 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: A 507 MET cc_start: 0.7924 (mmm) cc_final: 0.7567 (mpp) REVERT: A 572 ARG cc_start: 0.8100 (tmm160) cc_final: 0.7787 (ptt90) REVERT: A 763 TRP cc_start: 0.7069 (m100) cc_final: 0.6438 (m100) REVERT: C 95 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6446 (tm-30) REVERT: C 167 ILE cc_start: 0.8782 (mm) cc_final: 0.8574 (tp) REVERT: C 168 GLU cc_start: 0.8385 (mp0) cc_final: 0.8073 (mp0) REVERT: D 75 ARG cc_start: 0.7603 (ttp-170) cc_final: 0.7356 (ttm110) REVERT: D 152 TRP cc_start: 0.7744 (m100) cc_final: 0.7345 (m100) REVERT: D 199 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8496 (m110) REVERT: E 3 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8193 (tppt) REVERT: E 104 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9041 (tt) REVERT: E 228 ARG cc_start: 0.8589 (ttp-110) cc_final: 0.8251 (ttm-80) outliers start: 40 outliers final: 28 residues processed: 210 average time/residue: 0.1580 time to fit residues: 48.9210 Evaluate side-chains 206 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 11 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 210 optimal weight: 40.0000 chunk 136 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN D 199 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.195920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145229 restraints weight = 23714.077| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.90 r_work: 0.3217 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17603 Z= 0.143 Angle : 0.561 9.754 23970 Z= 0.286 Chirality : 0.044 0.207 2644 Planarity : 0.004 0.035 2951 Dihedral : 14.041 178.398 2937 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.83 % Favored : 95.12 % Rotamer: Outliers : 2.33 % Allowed : 15.26 % Favored : 82.41 % 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: -1.68 (0.18), residues: 2071 helix: -0.40 (0.18), residues: 820 sheet: -1.14 (0.28), residues: 291 loop : -1.69 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 181 TYR 0.016 0.001 TYR D 198 PHE 0.016 0.001 PHE C 276 TRP 0.013 0.001 TRP A 596 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17591) covalent geometry : angle 0.55955 / 0.29 (23958) hydrogen bonds : bond 0.03848 / 2.63 ( 579) hydrogen bonds : angle 4.51716 / 3.15 ( 1637) metal coordination : bond 0.00858 / 0.64 ( 12) metal coordination : angle 2.07677 / 1.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: A 507 MET cc_start: 0.7929 (mmm) cc_final: 0.7574 (mpp) REVERT: A 572 ARG cc_start: 0.8099 (tmm160) cc_final: 0.7789 (ptt90) REVERT: C 95 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6988 (mt-10) REVERT: C 167 ILE cc_start: 0.8740 (mm) cc_final: 0.8527 (tp) REVERT: C 168 GLU cc_start: 0.8410 (mp0) cc_final: 0.8092 (mp0) REVERT: D 134 GLU cc_start: 0.7756 (mp0) cc_final: 0.7494 (mp0) REVERT: D 152 TRP cc_start: 0.7826 (m100) cc_final: 0.7454 (m100) REVERT: D 220 LEU cc_start: 0.9036 (tp) cc_final: 0.8671 (tp) REVERT: E 3 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8170 (tppt) REVERT: E 104 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9040 (tt) REVERT: E 228 ARG cc_start: 0.8593 (ttp-110) cc_final: 0.8261 (ttm-80) REVERT: F 301 MET cc_start: -0.4624 (ttm) cc_final: -0.4827 (ttm) outliers start: 38 outliers final: 29 residues processed: 203 average time/residue: 0.1564 time to fit residues: 47.1550 Evaluate side-chains 202 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 154 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 195 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 160 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.196402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145805 restraints weight = 23741.181| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.86 r_work: 0.3229 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17603 Z= 0.121 Angle : 0.565 13.337 23970 Z= 0.286 Chirality : 0.043 0.207 2644 Planarity : 0.004 0.035 2951 Dihedral : 14.016 178.525 2937 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 2.14 % Allowed : 15.69 % Favored : 82.17 % 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: -1.58 (0.18), residues: 2071 helix: -0.29 (0.18), residues: 820 sheet: -1.12 (0.28), residues: 291 loop : -1.65 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 4 TYR 0.013 0.001 TYR A 265 PHE 0.011 0.001 PHE E 159 TRP 0.019 0.001 TRP A 596 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17591) covalent geometry : angle 0.56340 / 0.29 (23958) hydrogen bonds : bond 0.03753 / 2.56 ( 579) hydrogen bonds : angle 4.46174 / 3.11 ( 1637) metal coordination : bond 0.00710 / 0.55 ( 12) metal coordination : angle 2.00764 / 1.08 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4142 Ramachandran restraints generated. 2071 Oldfield, 0 Emsley, 2071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: A 418 ARG cc_start: 0.8413 (mmt-90) cc_final: 0.8041 (mmt-90) REVERT: A 507 MET cc_start: 0.7952 (mmm) cc_final: 0.7617 (mpp) REVERT: A 572 ARG cc_start: 0.8076 (tmm160) cc_final: 0.7818 (ptt90) REVERT: A 629 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6595 (mt-10) REVERT: C 95 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6962 (mt-10) REVERT: C 167 ILE cc_start: 0.8726 (mm) cc_final: 0.8525 (tp) REVERT: C 168 GLU cc_start: 0.8370 (mp0) cc_final: 0.8070 (mp0) REVERT: D 134 GLU cc_start: 0.7781 (mp0) cc_final: 0.7512 (mp0) REVERT: D 152 TRP cc_start: 0.7840 (m100) cc_final: 0.7397 (m100) REVERT: D 220 LEU cc_start: 0.9033 (tp) cc_final: 0.8650 (tp) REVERT: E 3 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8146 (tppt) REVERT: E 104 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9042 (tt) REVERT: E 228 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8249 (ttm-80) outliers start: 35 outliers final: 30 residues processed: 200 average time/residue: 0.1579 time to fit residues: 46.3801 Evaluate side-chains 207 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 25 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 GLN C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.196581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146667 restraints weight = 23894.091| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.92 r_work: 0.3233 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17603 Z= 0.114 Angle : 0.549 11.301 23970 Z= 0.278 Chirality : 0.043 0.202 2644 Planarity : 0.004 0.036 2951 Dihedral : 13.975 178.771 2937 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 2.14 % Allowed : 15.75 % Favored : 82.11 % 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: -1.44 (0.18), residues: 2071 helix: -0.15 (0.18), residues: 822 sheet: -1.08 (0.28), residues: 290 loop : -1.58 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 4 TYR 0.012 0.001 TYR A 265 PHE 0.010 0.001 PHE E 159 TRP 0.027 0.001 TRP A 596 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17591) covalent geometry : angle 0.54767 / 0.28 (23958) hydrogen bonds : bond 0.03641 / 2.49 ( 579) hydrogen bonds : angle 4.39039 / 3.07 ( 1637) metal coordination : bond 0.00686 / 0.54 ( 12) metal coordination : angle 1.92652 / 1.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5075.65 seconds wall clock time: 87 minutes 26.79 seconds (5246.79 seconds total)