Starting phenix.real_space_refine on Wed Mar 4 23:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mut_9255/03_2026/6mut_9255_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mut_9255/03_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_9255/03_2026/6mut_9255_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mut_9255/03_2026/6mut_9255_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mut_9255/03_2026/6mut_9255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mut_9255/03_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-dev-5986/lib/python3.9/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: 4.04, per 1000 atoms: 0.24 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: 1.49 Conformation dependent library (CDL) restraints added in 741.9 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: 1.98 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: 2.56 Time building geometry restraints manager: 2.01 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=" 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=" 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 bond pdb=" N ARG A 117 " pdb=" CA ARG A 117 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N GLY F 365 " pdb=" CA GLY F 365 " ideal model delta sigma weight residual 1.447 1.486 -0.040 1.09e-02 8.42e+03 1.32e+01 bond pdb=" N VAL E 127 " pdb=" CA VAL E 127 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.06e+01 ... (remaining 17586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 21932 2.18 - 4.37: 1742 4.37 - 6.55: 210 6.55 - 8.74: 62 8.74 - 10.92: 12 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: 2168 0.098 - 0.195: 399 0.195 - 0.293: 71 0.293 - 0.390: 5 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 16 " pdb=" C3' G G 16 " pdb=" O2' G G 16 " pdb=" C1' G G 16 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.73e+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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 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= 0.622 Angle : 1.326 34.808 23970 Z= 0.788 Chirality : 0.079 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 covalent geometry : bond 0.01300 (17591) covalent geometry : angle 1.28587 (23958) hydrogen bonds : bond 0.29070 ( 579) hydrogen bonds : angle 10.69692 ( 1637) metal coordination : bond 0.10271 ( 12) metal coordination : angle 14.58550 ( 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 : 0.649 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: 0.1790 time to fit residues: 82.5083 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 : 0.626 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 676 HIS B 94 GLN C 37 ASN C 83 ASN D 44 HIS D 136 ASN D 199 ASN E 106 ASN E 139 GLN E 200 HIS ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 99 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.195804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143963 restraints weight = 23907.922| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.88 r_work: 0.3228 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17603 Z= 0.163 Angle : 0.668 8.795 23970 Z= 0.348 Chirality : 0.045 0.169 2644 Planarity : 0.006 0.056 2951 Dihedral : 14.592 174.071 2957 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.02 % Allowed : 10.36 % Favored : 87.62 % 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: -3.67 (0.15), residues: 2071 helix: -2.70 (0.14), residues: 817 sheet: -1.30 (0.29), residues: 266 loop : -2.45 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 262 TYR 0.018 0.002 TYR A 182 PHE 0.015 0.001 PHE D 100 TRP 0.017 0.001 TRP A 131 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00364 (17591) covalent geometry : angle 0.66575 (23958) hydrogen bonds : bond 0.05322 ( 579) hydrogen bonds : angle 5.73241 ( 1637) metal coordination : bond 0.00672 ( 12) metal coordination : angle 2.65341 ( 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 260 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 HIS cc_start: 0.7527 (m-70) cc_final: 0.7237 (m-70) REVERT: A 82 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7507 (mmm160) REVERT: A 297 MET cc_start: 0.8943 (ttt) cc_final: 0.8732 (ttm) REVERT: A 373 GLU cc_start: 0.8762 (pm20) cc_final: 0.8539 (pm20) REVERT: A 406 SER cc_start: 0.8174 (t) cc_final: 0.7849 (p) REVERT: A 418 ARG cc_start: 0.8574 (mmt90) cc_final: 0.8038 (mmt-90) REVERT: A 496 LYS cc_start: 0.7289 (mmmt) cc_final: 0.6853 (tppp) REVERT: A 596 TRP cc_start: 0.7222 (p-90) cc_final: 0.6977 (p-90) REVERT: A 773 MET cc_start: 0.6294 (mtp) cc_final: 0.6090 (mtp) REVERT: C 172 ASP cc_start: 0.8155 (t0) cc_final: 0.7896 (t0) REVERT: E 104 LEU cc_start: 0.9397 (tm) cc_final: 0.9027 (tt) REVERT: E 228 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8293 (ttm-80) outliers start: 33 outliers final: 17 residues processed: 251 average time/residue: 0.1519 time to fit residues: 54.8789 Evaluate side-chains 198 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 227 CYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 365 VAL 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 179 ASN Chi-restraints excluded: chain D residue 40 ILE 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 139 GLN Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 204 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN C 102 ASN C 177 GLN C 179 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.195717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146376 restraints weight = 24091.663| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 4.30 r_work: 0.3246 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17603 Z= 0.132 Angle : 0.586 9.861 23970 Z= 0.301 Chirality : 0.044 0.197 2644 Planarity : 0.005 0.044 2951 Dihedral : 14.272 176.009 2938 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.57 % Allowed : 12.38 % Favored : 85.05 % 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: -2.86 (0.16), residues: 2071 helix: -1.78 (0.16), residues: 814 sheet: -1.30 (0.28), residues: 276 loop : -2.10 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 713 TYR 0.017 0.001 TYR A 265 PHE 0.011 0.001 PHE E 159 TRP 0.015 0.001 TRP D 152 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00294 (17591) covalent geometry : angle 0.58312 (23958) hydrogen bonds : bond 0.04371 ( 579) hydrogen bonds : angle 5.02852 ( 1637) metal coordination : bond 0.00678 ( 12) metal coordination : angle 2.57456 ( 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 243 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7596 (tmt170) REVERT: A 229 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8020 (mtmm) REVERT: A 406 SER cc_start: 0.8225 (t) cc_final: 0.7939 (p) REVERT: A 418 ARG cc_start: 0.8540 (mmt90) cc_final: 0.7977 (mmt-90) REVERT: A 507 MET cc_start: 0.7983 (mmm) cc_final: 0.7582 (mmt) REVERT: C 104 LYS cc_start: 0.8813 (ttpt) cc_final: 0.8611 (ptmm) REVERT: C 177 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: C 201 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7883 (mt-10) REVERT: E 104 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9052 (tt) REVERT: E 147 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: E 228 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8354 (ttm-80) outliers start: 42 outliers final: 19 residues processed: 230 average time/residue: 0.1503 time to fit residues: 50.4970 Evaluate side-chains 205 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 227 CYS Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 461 VAL 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 177 GLN 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 256 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 132 VAL 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 221 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 131 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 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 = 0.4256 r_free = 0.4256 target = 0.195527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144653 restraints weight = 23936.166| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.79 r_work: 0.3219 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3322 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= 0.150 Angle : 0.579 9.074 23970 Z= 0.295 Chirality : 0.044 0.203 2644 Planarity : 0.004 0.042 2951 Dihedral : 14.190 176.847 2938 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.31 % Allowed : 12.19 % Favored : 84.50 % 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: -2.46 (0.17), residues: 2071 helix: -1.32 (0.17), residues: 819 sheet: -1.16 (0.28), residues: 284 loop : -2.00 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 181 TYR 0.019 0.001 TYR A 265 PHE 0.013 0.001 PHE E 159 TRP 0.013 0.001 TRP D 152 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00342 (17591) covalent geometry : angle 0.57606 (23958) hydrogen bonds : bond 0.04126 ( 579) hydrogen bonds : angle 4.77125 ( 1637) metal coordination : bond 0.00884 ( 12) metal coordination : angle 2.55885 ( 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 251 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7859 (mtp180) cc_final: 0.7599 (tmt170) REVERT: A 406 SER cc_start: 0.8180 (t) cc_final: 0.7887 (p) REVERT: A 418 ARG cc_start: 0.8584 (mmt90) cc_final: 0.7891 (mmt-90) REVERT: A 763 TRP cc_start: 0.7051 (m100) cc_final: 0.6435 (m100) REVERT: C 179 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8120 (m-40) REVERT: C 201 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7826 (mt-10) REVERT: D 75 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7208 (ttm110) REVERT: D 134 GLU cc_start: 0.7821 (mp0) cc_final: 0.7557 (mp0) REVERT: E 3 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8219 (tppt) REVERT: E 104 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9056 (tt) REVERT: E 228 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8289 (ttm-80) outliers start: 54 outliers final: 28 residues processed: 233 average time/residue: 0.1446 time to fit residues: 49.7936 Evaluate side-chains 218 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain C residue 171 ILE 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 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 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 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 19 optimal weight: 0.5980 chunk 181 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 48 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** E 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.194683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144990 restraints weight = 23798.931| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.57 r_work: 0.3208 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3576 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= 0.143 Angle : 0.569 11.035 23970 Z= 0.288 Chirality : 0.044 0.211 2644 Planarity : 0.004 0.042 2951 Dihedral : 14.120 177.939 2937 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.94 % Allowed : 13.30 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.17), residues: 2071 helix: -0.91 (0.17), residues: 821 sheet: -1.19 (0.27), residues: 287 loop : -1.81 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 572 TYR 0.016 0.001 TYR A 265 PHE 0.014 0.001 PHE E 159 TRP 0.016 0.001 TRP F 290 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00328 (17591) covalent geometry : angle 0.56609 (23958) hydrogen bonds : bond 0.03845 ( 579) hydrogen bonds : angle 4.62152 ( 1637) metal coordination : bond 0.00780 ( 12) metal coordination : angle 2.59468 ( 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 244 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7586 (tmt170) REVERT: A 418 ARG cc_start: 0.8579 (mmt90) cc_final: 0.8067 (mmt-90) REVERT: A 507 MET cc_start: 0.7905 (mmm) cc_final: 0.7448 (mmt) REVERT: A 572 ARG cc_start: 0.7979 (ptt90) cc_final: 0.7717 (tmm160) REVERT: A 597 ASP cc_start: 0.8021 (t0) cc_final: 0.7794 (t0) REVERT: C 201 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7830 (mt-10) REVERT: C 283 VAL cc_start: 0.8473 (t) cc_final: 0.8270 (p) REVERT: D 75 ARG cc_start: 0.7596 (ttp-110) cc_final: 0.7210 (ttm110) REVERT: E 3 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8255 (tppt) REVERT: E 228 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8322 (ttm-80) outliers start: 48 outliers final: 30 residues processed: 227 average time/residue: 0.1485 time to fit residues: 49.3111 Evaluate side-chains 209 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain A residue 227 CYS Chi-restraints excluded: chain A residue 461 VAL 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 593 VAL Chi-restraints excluded: chain A residue 636 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 655 VAL 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 241 ASP 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 139 GLN Chi-restraints excluded: chain E residue 147 GLU 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 280 LEU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 171 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 151 optimal weight: 0.0970 chunk 163 optimal weight: 0.0000 chunk 98 optimal weight: 0.0870 chunk 130 optimal weight: 0.9980 chunk 162 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.3360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 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 = 0.4282 r_free = 0.4282 target = 0.198044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.148842 restraints weight = 23857.049| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.25 r_work: 0.3282 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17603 Z= 0.092 Angle : 0.527 10.056 23970 Z= 0.266 Chirality : 0.042 0.205 2644 Planarity : 0.004 0.037 2951 Dihedral : 13.938 177.840 2937 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.65 % Allowed : 15.69 % Favored : 82.66 % 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: -1.70 (0.18), residues: 2071 helix: -0.46 (0.18), residues: 829 sheet: -1.23 (0.28), residues: 280 loop : -1.64 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.011 0.001 TYR F 297 PHE 0.008 0.001 PHE A 548 TRP 0.017 0.001 TRP D 152 HIS 0.005 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00197 (17591) covalent geometry : angle 0.52503 (23958) hydrogen bonds : bond 0.03358 ( 579) hydrogen bonds : angle 4.27514 ( 1637) metal coordination : bond 0.00761 ( 12) metal coordination : angle 2.04761 ( 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 228 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 SER cc_start: 0.8875 (m) cc_final: 0.8629 (p) REVERT: A 82 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7495 (tmt170) REVERT: A 354 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: A 418 ARG cc_start: 0.8473 (mmt90) cc_final: 0.8015 (mtp85) REVERT: A 507 MET cc_start: 0.7747 (mmm) cc_final: 0.7387 (mmt) REVERT: A 572 ARG cc_start: 0.7890 (ptt90) cc_final: 0.7587 (ptt90) REVERT: C 102 ASN cc_start: 0.8811 (p0) cc_final: 0.8504 (p0) REVERT: C 103 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7986 (tpp80) REVERT: C 201 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7737 (mt-10) REVERT: C 224 TYR cc_start: 0.8733 (p90) cc_final: 0.8248 (p90) REVERT: C 267 LYS cc_start: 0.8192 (mttp) cc_final: 0.7983 (pttm) REVERT: D 75 ARG cc_start: 0.7523 (ttp-110) cc_final: 0.7166 (ttm110) REVERT: E 147 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8256 (mt-10) REVERT: E 228 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8202 (ttm-80) REVERT: E 260 MET cc_start: 0.8918 (mtt) cc_final: 0.8614 (mtt) outliers start: 27 outliers final: 15 residues processed: 218 average time/residue: 0.1471 time to fit residues: 47.0866 Evaluate side-chains 188 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain C residue 133 LYS 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 267 LYS 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 213 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 124 optimal weight: 4.9990 chunk 195 optimal weight: 30.0000 chunk 122 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 chunk 162 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 163 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4268 r_free = 0.4268 target = 0.196735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145716 restraints weight = 23711.957| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.82 r_work: 0.3245 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17603 Z= 0.110 Angle : 0.533 11.401 23970 Z= 0.267 Chirality : 0.042 0.197 2644 Planarity : 0.004 0.038 2951 Dihedral : 13.850 178.614 2935 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.08 % Allowed : 15.75 % 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: -1.51 (0.18), residues: 2071 helix: -0.21 (0.18), residues: 826 sheet: -1.24 (0.28), residues: 285 loop : -1.58 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.012 0.001 TYR A 265 PHE 0.011 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 covalent geometry : bond 0.00248 (17591) covalent geometry : angle 0.53089 (23958) hydrogen bonds : bond 0.03410 ( 579) hydrogen bonds : angle 4.22435 ( 1637) metal coordination : bond 0.00632 ( 12) metal coordination : angle 2.13743 ( 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 213 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8872 (m) cc_final: 0.8662 (p) REVERT: A 82 ARG cc_start: 0.7862 (mtp180) cc_final: 0.7499 (tmt170) REVERT: A 354 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: A 418 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8055 (mtp85) REVERT: A 507 MET cc_start: 0.7808 (mmm) cc_final: 0.7451 (mmt) REVERT: A 572 ARG cc_start: 0.7924 (ptt90) cc_final: 0.7672 (ptt90) REVERT: A 658 VAL cc_start: 0.8365 (t) cc_final: 0.8093 (m) REVERT: A 763 TRP cc_start: 0.7065 (m100) cc_final: 0.6659 (m100) REVERT: C 103 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8042 (tpp80) REVERT: D 75 ARG cc_start: 0.7486 (ttp-110) cc_final: 0.7167 (ttm110) REVERT: E 3 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8260 (tppt) REVERT: E 228 ARG cc_start: 0.8595 (ttp-110) cc_final: 0.8285 (ttm-80) outliers start: 34 outliers final: 22 residues processed: 201 average time/residue: 0.1360 time to fit residues: 40.3533 Evaluate side-chains 199 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 354 GLU 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 655 VAL Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 241 ASP 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 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 F residue 23 VAL 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: 6.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 133 optimal weight: 9.9990 chunk 163 optimal weight: 0.0370 chunk 180 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN 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 = 0.4254 r_free = 0.4254 target = 0.195418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144169 restraints weight = 23762.030| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 3.88 r_work: 0.3228 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17603 Z= 0.134 Angle : 0.552 9.559 23970 Z= 0.278 Chirality : 0.043 0.203 2644 Planarity : 0.004 0.038 2951 Dihedral : 13.859 179.384 2935 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.39 % Allowed : 15.81 % Favored : 81.80 % 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: -1.39 (0.18), residues: 2071 helix: -0.12 (0.18), residues: 828 sheet: -1.12 (0.29), residues: 280 loop : -1.52 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 735 TYR 0.015 0.001 TYR A 265 PHE 0.014 0.001 PHE E 159 TRP 0.035 0.001 TRP A 596 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00309 (17591) covalent geometry : angle 0.55043 (23958) hydrogen bonds : bond 0.03512 ( 579) hydrogen bonds : angle 4.27070 ( 1637) metal coordination : bond 0.00753 ( 12) metal coordination : angle 2.13617 ( 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 212 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 31 SER cc_start: 0.8911 (m) cc_final: 0.8700 (p) REVERT: A 82 ARG cc_start: 0.7789 (mtp180) cc_final: 0.7439 (tmt170) REVERT: A 354 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: A 418 ARG cc_start: 0.8493 (mmt90) cc_final: 0.7976 (mmt-90) REVERT: A 507 MET cc_start: 0.7844 (mmm) cc_final: 0.7501 (mmt) REVERT: A 658 VAL cc_start: 0.8395 (t) cc_final: 0.8148 (m) REVERT: C 103 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.8037 (tpp80) REVERT: C 267 LYS cc_start: 0.8238 (pttm) cc_final: 0.7623 (ptpp) REVERT: D 75 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.7177 (ttm110) REVERT: E 3 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8234 (tppt) REVERT: E 228 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8300 (ttm-80) outliers start: 39 outliers final: 27 residues processed: 197 average time/residue: 0.1485 time to fit residues: 42.9031 Evaluate side-chains 196 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 A residue 724 ARG Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 241 ASP 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 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 F residue 23 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 391 MET 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: 0.9980 chunk 129 optimal weight: 0.9980 chunk 154 optimal weight: 0.1980 chunk 160 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 178 optimal weight: 30.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 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 = 0.4261 r_free = 0.4261 target = 0.196124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145250 restraints weight = 23667.661| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.96 r_work: 0.3224 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17603 Z= 0.112 Angle : 0.535 9.699 23970 Z= 0.268 Chirality : 0.042 0.205 2644 Planarity : 0.004 0.038 2951 Dihedral : 13.812 179.462 2935 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 1.90 % Allowed : 16.48 % Favored : 81.62 % 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: -1.25 (0.18), residues: 2071 helix: 0.06 (0.18), residues: 828 sheet: -1.11 (0.29), residues: 280 loop : -1.49 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.013 0.001 TYR A 265 PHE 0.011 0.001 PHE E 159 TRP 0.025 0.001 TRP A 596 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00254 (17591) covalent geometry : angle 0.53295 (23958) hydrogen bonds : bond 0.03365 ( 579) hydrogen bonds : angle 4.20716 ( 1637) metal coordination : bond 0.00634 ( 12) metal coordination : angle 2.02324 ( 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 202 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7442 (tmt170) REVERT: A 354 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 418 ARG cc_start: 0.8470 (mmt90) cc_final: 0.7985 (mmt-90) REVERT: A 507 MET cc_start: 0.7849 (mmm) cc_final: 0.7507 (mmt) REVERT: A 658 VAL cc_start: 0.8258 (t) cc_final: 0.8054 (m) REVERT: C 103 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.8046 (tpp80) REVERT: C 267 LYS cc_start: 0.8247 (pttm) cc_final: 0.7637 (ptpp) REVERT: D 75 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.7214 (ttm110) REVERT: D 248 LEU cc_start: 0.8907 (tt) cc_final: 0.8688 (tt) REVERT: E 147 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: E 228 ARG cc_start: 0.8621 (ttp-110) cc_final: 0.8300 (ttm-80) outliers start: 31 outliers final: 23 residues processed: 189 average time/residue: 0.1526 time to fit residues: 42.1837 Evaluate side-chains 194 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 354 GLU 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 A residue 724 ARG Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain E residue 22 ASP 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 213 VAL Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 391 MET 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: 0.0870 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 195 optimal weight: 50.0000 chunk 35 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 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 = 0.4261 r_free = 0.4261 target = 0.196198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146312 restraints weight = 23735.591| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.54 r_work: 0.3240 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17603 Z= 0.111 Angle : 0.536 9.568 23970 Z= 0.268 Chirality : 0.042 0.205 2644 Planarity : 0.004 0.037 2951 Dihedral : 13.785 179.788 2935 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % Favored : 81.62 % 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: -1.16 (0.18), residues: 2071 helix: 0.19 (0.18), residues: 831 sheet: -1.08 (0.29), residues: 279 loop : -1.50 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 459 TYR 0.014 0.001 TYR A 265 PHE 0.012 0.001 PHE E 159 TRP 0.028 0.001 TRP A 596 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00252 (17591) covalent geometry : angle 0.53470 (23958) hydrogen bonds : bond 0.03317 ( 579) hydrogen bonds : angle 4.17662 ( 1637) metal coordination : bond 0.00641 ( 12) metal coordination : angle 1.87326 ( 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 202 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 82 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7425 (tmt170) REVERT: A 354 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: A 418 ARG cc_start: 0.8446 (mmt90) cc_final: 0.7985 (mmt-90) REVERT: A 514 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7129 (mtt180) REVERT: C 103 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8028 (tpp80) REVERT: C 153 GLU cc_start: 0.8025 (tt0) cc_final: 0.7603 (tp30) REVERT: C 267 LYS cc_start: 0.8246 (pttm) cc_final: 0.7641 (ptpp) REVERT: E 147 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8250 (mt-10) REVERT: E 228 ARG cc_start: 0.8602 (ttp-110) cc_final: 0.8293 (ttm-80) outliers start: 28 outliers final: 24 residues processed: 188 average time/residue: 0.1541 time to fit residues: 42.2745 Evaluate side-chains 197 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 354 GLU 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 A residue 724 ARG Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain E residue 22 ASP 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 202 MET 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 F residue 23 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 391 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 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 = 0.4244 r_free = 0.4244 target = 0.194612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144726 restraints weight = 23792.184| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 4.04 r_work: 0.3221 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4250 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= 0.139 Angle : 0.556 10.297 23970 Z= 0.279 Chirality : 0.043 0.194 2644 Planarity : 0.004 0.038 2951 Dihedral : 13.787 179.632 2935 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 1.90 % Allowed : 16.79 % Favored : 81.31 % 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: -1.16 (0.18), residues: 2071 helix: 0.24 (0.18), residues: 827 sheet: -0.96 (0.29), residues: 292 loop : -1.59 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 459 TYR 0.016 0.001 TYR A 265 PHE 0.016 0.001 PHE E 159 TRP 0.019 0.001 TRP A 596 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00322 (17591) covalent geometry : angle 0.55440 (23958) hydrogen bonds : bond 0.03457 ( 579) hydrogen bonds : angle 4.25538 ( 1637) metal coordination : bond 0.00795 ( 12) metal coordination : angle 1.96903 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4648.35 seconds wall clock time: 79 minutes 54.53 seconds (4794.53 seconds total)