Starting phenix.real_space_refine on Sat Sep 12 23:17:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.map" model { file = "/net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ifk_9653/09_2026/6ifk_9653.cif" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.019 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 73 5.49 5 Mg 2 5.21 5 S 37 5.16 5 C 12148 2.51 5 N 3307 2.21 5 O 3880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19448 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5812 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1697 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2347 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2786 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 715 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 2, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2925 SG CYS A 401 58.703 31.302 67.415 1.00 59.23 S ATOM 2948 SG CYS A 404 56.038 32.182 65.030 1.00 58.39 S ATOM 3070 SG CYS A 419 59.384 30.986 63.808 1.00 60.57 S ATOM 3092 SG CYS A 422 59.244 34.801 64.709 1.00 59.65 S Time building chain proxies: 4.16, per 1000 atoms: 0.21 Number of scatterers: 19448 At special positions: 0 Unit cell: (93.6, 137.28, 173.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 73 15.00 Mg 2 11.99 O 3880 8.00 N 3307 7.00 C 12148 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 815.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 419 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 422 " Number of angles added : 6 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 25 sheets defined 39.7% alpha, 12.7% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.540A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 removed outlier: 4.094A pdb=" N GLY A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.573A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.629A pdb=" N SER A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.767A pdb=" N VAL A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.658A pdb=" N TYR A 141 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.890A pdb=" N ILE A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.845A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.777A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.568A pdb=" N PHE A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.561A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 266 through 274 removed outlier: 4.255A pdb=" N ARG A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.548A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 313 through 335 removed outlier: 3.562A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 removed outlier: 4.056A pdb=" N SER A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 363 through 378 removed outlier: 3.984A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.595A pdb=" N GLN A 416 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.723A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.575A pdb=" N LYS A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 4.408A pdb=" N ALA A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 541 through 564 removed outlier: 3.882A pdb=" N SER A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 603 removed outlier: 3.779A pdb=" N PHE A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.980A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.631A pdb=" N HIS A 676 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 removed outlier: 3.613A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.798A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 removed outlier: 4.057A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 755 removed outlier: 3.760A pdb=" N ALA A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 36 through 54 removed outlier: 3.698A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.858A pdb=" N ILE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.764A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.558A pdb=" N LEU D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 113 " --> pdb=" O CYS D 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 removed outlier: 3.581A pdb=" N ILE C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.654A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.595A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'G' and resid 48 through 60 removed outlier: 3.617A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 removed outlier: 3.537A pdb=" N ASN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 166 through 178 removed outlier: 3.811A pdb=" N ARG G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.578A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.881A pdb=" N ARG F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.721A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.153A pdb=" N GLU F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU F 215 " --> pdb=" O THR F 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 64 removed outlier: 3.609A pdb=" N LEU E 52 " --> pdb=" O PRO E 48 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 84 removed outlier: 3.843A pdb=" N ARG E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 4.268A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 113 removed outlier: 4.155A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 167 removed outlier: 3.895A pdb=" N VAL E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU E 164 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 180 removed outlier: 3.688A pdb=" N LEU E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.608A pdb=" N ARG E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.600A pdb=" N THR E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.777A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.658A pdb=" N LEU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 removed outlier: 4.248A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.599A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.807A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.620A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 148 removed outlier: 3.771A pdb=" N ASN H 148 " --> pdb=" O PRO H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.601A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 3.659A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 Processing helix chain 'H' and resid 285 through 289 removed outlier: 3.624A pdb=" N THR H 288 " --> pdb=" O GLY H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 295 removed outlier: 3.639A pdb=" N ALA H 295 " --> pdb=" O PHE H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 303 removed outlier: 3.559A pdb=" N ARG H 302 " --> pdb=" O LEU H 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.624A pdb=" N GLY A 344 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.566A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 468 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 491 removed outlier: 4.245A pdb=" N TYR A 490 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 574 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 579 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.976A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.976A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN G 11 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN G 197 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG G 13 " --> pdb=" O PHE G 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE G 195 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA8, first strand: chain 'F' and resid 148 through 149 Processing sheet with id=AA9, first strand: chain 'F' and resid 148 through 149 removed outlier: 6.650A pdb=" N LYS F 5 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN F 11 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASN F 197 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG F 13 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N PHE F 195 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 126 Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 97 removed outlier: 7.239A pdb=" N LYS E 5 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR E 202 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS E 7 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA E 200 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER E 9 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU E 198 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.663A pdb=" N LEU E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB6, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.822A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 128 removed outlier: 3.515A pdb=" N VAL B 127 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AC3, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.887A pdb=" N ILE H 232 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.887A pdb=" N ILE H 232 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'H' and resid 37 through 40 Processing sheet with id=AC7, first strand: chain 'H' and resid 212 through 214 615 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 2.23 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: 3672 1.32 - 1.45: 5301 1.45 - 1.57: 10770 1.57 - 1.69: 145 1.69 - 1.81: 67 Bond restraints: 19955 Sorted by residual: bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 19950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 26935 4.59 - 9.18: 277 9.18 - 13.77: 25 13.77 - 18.36: 3 18.36 - 22.95: 2 Bond angle restraints: 27242 Sorted by residual: angle pdb=" N VAL H 336 " pdb=" CA VAL H 336 " pdb=" C VAL H 336 " ideal model delta sigma weight residual 110.62 120.90 -10.28 1.02e+00 9.61e-01 1.02e+02 angle pdb=" CA LEU H 199 " pdb=" CB LEU H 199 " pdb=" CG LEU H 199 " ideal model delta sigma weight residual 116.30 139.25 -22.95 3.50e+00 8.16e-02 4.30e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 107.88 19.07 3.00e+00 1.11e-01 4.04e+01 angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 109.21 17.74 3.00e+00 1.11e-01 3.50e+01 angle pdb=" C ARG E 143 " pdb=" N ASN E 144 " pdb=" CA ASN E 144 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 ... (remaining 27237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.94: 11380 28.94 - 57.88: 390 57.88 - 86.83: 50 86.83 - 115.77: 1 115.77 - 144.71: 2 Dihedral angle restraints: 11823 sinusoidal: 5222 harmonic: 6601 Sorted by residual: dihedral pdb=" C4' G N 3 " pdb=" C3' G N 3 " pdb=" C2' G N 3 " pdb=" C1' G N 3 " ideal model delta sinusoidal sigma weight residual 36.34 -39.62 75.96 1 3.10e+00 1.04e-01 7.57e+02 dihedral pdb=" C4' A N 26 " pdb=" C3' A N 26 " pdb=" C2' A N 26 " pdb=" C1' A N 26 " ideal model delta sinusoidal sigma weight residual 36.34 -38.84 75.18 1 3.10e+00 1.04e-01 7.43e+02 dihedral pdb=" C4' G N 9 " pdb=" C3' G N 9 " pdb=" C2' G N 9 " pdb=" C1' G N 9 " ideal model delta sinusoidal sigma weight residual 36.35 -38.78 75.13 1 3.10e+00 1.04e-01 7.43e+02 ... (remaining 11820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2481 0.084 - 0.167: 434 0.167 - 0.251: 106 0.251 - 0.334: 37 0.334 - 0.418: 8 Chirality restraints: 3066 Sorted by residual: chirality pdb=" CA VAL H 336 " pdb=" N VAL H 336 " pdb=" C VAL H 336 " pdb=" CB VAL H 336 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C1' G N 9 " pdb=" O4' G N 9 " pdb=" C2' G N 9 " pdb=" N9 G N 9 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" P C J 35 " pdb=" OP1 C J 35 " pdb=" OP2 C J 35 " pdb=" O5' C J 35 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 3063 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G N 9 " 0.059 2.00e-02 2.50e+03 2.49e-02 1.86e+01 pdb=" N9 G N 9 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G N 9 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G N 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G N 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G N 9 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G N 9 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G N 9 " 0.009 2.00e-02 2.50e+03 pdb=" C2 G N 9 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G N 9 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G N 9 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G N 9 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.033 2.00e-02 2.50e+03 2.45e-02 1.51e+01 pdb=" CG TRP A 732 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G N 21 " 0.048 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" N9 G N 21 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G N 21 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G N 21 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G N 21 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G N 21 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G N 21 " 0.015 2.00e-02 2.50e+03 pdb=" N1 G N 21 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G N 21 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G N 21 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G N 21 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G N 21 " -0.005 2.00e-02 2.50e+03 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 248 2.62 - 3.19: 16546 3.19 - 3.76: 31361 3.76 - 4.33: 45137 4.33 - 4.90: 72667 Nonbonded interactions: 165959 Sorted by model distance: nonbonded pdb=" O1A ANP A 801 " pdb="MG MG A 803 " model vdw 2.046 2.170 nonbonded pdb=" OD2 ASP A 519 " pdb="MG MG A 803 " model vdw 2.140 2.170 nonbonded pdb=" O2B ANP A 801 " pdb="MG MG A 803 " model vdw 2.141 2.170 nonbonded pdb=" OD1 ASP A 519 " pdb="MG MG A 803 " model vdw 2.168 2.170 nonbonded pdb=" O PHE B 71 " pdb=" OH TYR B 157 " model vdw 2.170 3.040 ... (remaining 165954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) selection = (chain 'F' and (resid 2 through 66 or resid 76 through 156 or (resid 157 through \ 158 and (name N or name CA or name C or name O or name CB )) or resid 159 or (r \ esid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 through 217)) } 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: 0.560 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.150 19961 Z= 0.417 Angle : 1.253 22.953 27248 Z= 0.631 Chirality : 0.077 0.418 3066 Planarity : 0.007 0.073 3252 Dihedral : 14.130 144.711 7565 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.73 % Favored : 88.96 % Rotamer: Outliers : 1.01 % Allowed : 5.61 % Favored : 93.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.27 % 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: -4.87 (0.13), residues: 2228 helix: -3.50 (0.11), residues: 805 sheet: -2.79 (0.25), residues: 332 loop : -3.13 (0.15), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG G 95 TYR 0.035 0.004 TYR H 218 PHE 0.060 0.004 PHE B 10 TRP 0.065 0.005 TRP A 732 HIS 0.016 0.003 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.41 (19955) covalent geometry : angle 1.24169 / 0.63 (27242) hydrogen bonds : bond 0.19239 / 12.70 ( 643) hydrogen bonds : angle 7.62905 / 5.26 ( 1776) metal coordination : bond 0.10934 / 5.53 ( 4) metal coordination : angle 11.26859 / 5.69 ( 6) Misc. bond : bond 0.00199 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 535 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7472 (t80) cc_final: 0.7120 (t80) REVERT: A 719 ARG cc_start: 0.7611 (ttt180) cc_final: 0.7127 (ttm-80) REVERT: C 14 GLU cc_start: 0.7859 (tp30) cc_final: 0.7599 (tp30) REVERT: G 138 ILE cc_start: 0.9133 (pt) cc_final: 0.8597 (mt) REVERT: F 11 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7643 (mp10) REVERT: E 12 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (tt) REVERT: B 132 THR cc_start: 0.8745 (t) cc_final: 0.8436 (m) REVERT: B 198 LEU cc_start: 0.8342 (mt) cc_final: 0.8023 (mp) REVERT: H 4 ASP cc_start: 0.5886 (t0) cc_final: 0.5537 (t0) REVERT: H 249 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.7949 (mtt-85) REVERT: H 307 LYS cc_start: 0.7418 (pmmt) cc_final: 0.7049 (pmmt) outliers start: 19 outliers final: 6 residues processed: 545 average time/residue: 0.1803 time to fit residues: 140.7516 Evaluate side-chains 303 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 296 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain H residue 218 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN A 78 ASN A 268 GLN A 305 HIS A 312 ASN ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN A 562 GLN A 604 ASN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN D 106 GLN G 159 ASN F 33 ASN F 85 ASN F 213 ASN E 33 ASN E 134 ASN B 11 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 125 HIS B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 284 HIS H 3 ASN ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN H 115 ASN H 151 ASN H 194 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116587 restraints weight = 30931.995| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.82 r_work: 0.3322 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19961 Z= 0.175 Angle : 0.989 19.024 27248 Z= 0.451 Chirality : 0.082 1.122 3066 Planarity : 0.005 0.072 3252 Dihedral : 12.631 142.769 3278 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 1.59 % Allowed : 12.24 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.83 (0.15), residues: 2228 helix: -2.23 (0.15), residues: 810 sheet: -2.57 (0.25), residues: 342 loop : -2.73 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 99 TYR 0.018 0.002 TYR E 181 PHE 0.022 0.002 PHE G 167 TRP 0.029 0.002 TRP A 732 HIS 0.008 0.001 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (19955) covalent geometry : angle 0.98849 / 0.45 (27242) hydrogen bonds : bond 0.04506 / 2.98 ( 643) hydrogen bonds : angle 5.47645 / 3.77 ( 1776) metal coordination : bond 0.00544 / 0.27 ( 4) metal coordination : angle 1.41151 / 0.81 ( 6) Misc. bond : bond 0.00086 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 339 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8041 (t80) cc_final: 0.7757 (t80) REVERT: A 521 ASP cc_start: 0.9084 (m-30) cc_final: 0.8597 (m-30) REVERT: D 85 ASP cc_start: 0.8655 (t0) cc_final: 0.8137 (t0) REVERT: C 20 LEU cc_start: 0.7567 (tt) cc_final: 0.7268 (mp) REVERT: G 144 ASN cc_start: 0.8084 (t0) cc_final: 0.7871 (t0) REVERT: F 123 GLU cc_start: 0.8413 (tt0) cc_final: 0.8077 (mt-10) REVERT: E 166 ASP cc_start: 0.8161 (m-30) cc_final: 0.7961 (m-30) REVERT: B 101 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7637 (mmtm) REVERT: B 152 ASN cc_start: 0.6710 (t160) cc_final: 0.6376 (p0) REVERT: B 229 MET cc_start: 0.8293 (mtp) cc_final: 0.7875 (mtp) REVERT: H 54 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7561 (mmp80) outliers start: 30 outliers final: 18 residues processed: 361 average time/residue: 0.1591 time to fit residues: 86.2477 Evaluate side-chains 289 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 86 optimal weight: 0.1980 chunk 127 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 64 optimal weight: 0.0470 chunk 48 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 158 ASN A 166 ASN A 414 HIS E 162 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 174 GLN H 19 HIS ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.116726 restraints weight = 31180.161| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.78 r_work: 0.3320 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19961 Z= 0.161 Angle : 0.837 14.611 27248 Z= 0.392 Chirality : 0.068 1.035 3066 Planarity : 0.004 0.040 3252 Dihedral : 12.451 145.409 3274 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.53 % Rotamer: Outliers : 2.97 % Allowed : 12.76 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.32 (0.16), residues: 2228 helix: -1.63 (0.16), residues: 832 sheet: -2.39 (0.26), residues: 339 loop : -2.57 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 107 TYR 0.019 0.001 TYR E 181 PHE 0.020 0.002 PHE A 655 TRP 0.020 0.002 TRP A 732 HIS 0.007 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (19955) covalent geometry : angle 0.83656 / 0.39 (27242) hydrogen bonds : bond 0.04095 / 2.70 ( 643) hydrogen bonds : angle 5.03774 / 3.47 ( 1776) metal coordination : bond 0.00324 / 0.16 ( 4) metal coordination : angle 1.52574 / 0.80 ( 6) Misc. bond : bond 0.00111 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8077 (t80) cc_final: 0.7766 (t80) REVERT: A 212 ILE cc_start: 0.9076 (mp) cc_final: 0.8871 (mp) REVERT: A 521 ASP cc_start: 0.9072 (m-30) cc_final: 0.8630 (m-30) REVERT: A 694 ASN cc_start: 0.8131 (m-40) cc_final: 0.7692 (m-40) REVERT: D 85 ASP cc_start: 0.8476 (t0) cc_final: 0.8038 (t0) REVERT: C 20 LEU cc_start: 0.7572 (tt) cc_final: 0.7300 (mp) REVERT: G 32 ILE cc_start: 0.8875 (mt) cc_final: 0.8580 (mp) REVERT: G 144 ASN cc_start: 0.8083 (t0) cc_final: 0.7756 (t0) REVERT: F 123 GLU cc_start: 0.8458 (tt0) cc_final: 0.8198 (mt-10) REVERT: B 5 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 157 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7944 (p90) REVERT: B 219 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 229 MET cc_start: 0.8379 (mtp) cc_final: 0.8006 (mtp) REVERT: H 54 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7497 (mmp80) outliers start: 56 outliers final: 33 residues processed: 339 average time/residue: 0.1626 time to fit residues: 83.0672 Evaluate side-chains 302 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 ASN A 463 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN H 349 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.114976 restraints weight = 31272.313| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.80 r_work: 0.3299 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19961 Z= 0.172 Angle : 0.811 14.460 27248 Z= 0.382 Chirality : 0.065 0.858 3066 Planarity : 0.004 0.037 3252 Dihedral : 12.511 163.227 3274 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.55 % Allowed : 13.77 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.95 (0.16), residues: 2228 helix: -1.21 (0.17), residues: 827 sheet: -2.14 (0.26), residues: 333 loop : -2.49 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 392 TYR 0.021 0.002 TYR E 181 PHE 0.023 0.002 PHE G 167 TRP 0.018 0.002 TRP A 732 HIS 0.007 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (19955) covalent geometry : angle 0.81119 / 0.38 (27242) hydrogen bonds : bond 0.03862 / 2.55 ( 643) hydrogen bonds : angle 4.87466 / 3.36 ( 1776) metal coordination : bond 0.00415 / 0.20 ( 4) metal coordination : angle 1.56115 / 0.81 ( 6) Misc. bond : bond 0.00089 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 279 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7229 (mp) REVERT: A 74 TYR cc_start: 0.8095 (t80) cc_final: 0.7781 (t80) REVERT: A 166 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7438 (p0) REVERT: A 521 ASP cc_start: 0.9084 (m-30) cc_final: 0.8788 (m-30) REVERT: D 104 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8248 (t) REVERT: C 20 LEU cc_start: 0.7484 (tt) cc_final: 0.7228 (mp) REVERT: G 32 ILE cc_start: 0.8850 (mt) cc_final: 0.8590 (mp) REVERT: G 144 ASN cc_start: 0.8170 (t0) cc_final: 0.7800 (t0) REVERT: E 117 TYR cc_start: 0.8799 (m-80) cc_final: 0.8540 (m-80) REVERT: B 5 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8567 (pp) REVERT: B 157 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8190 (p90) REVERT: B 229 MET cc_start: 0.8393 (mtp) cc_final: 0.8114 (mtp) REVERT: H 54 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7629 (mpp80) REVERT: H 262 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8047 (mt) outliers start: 67 outliers final: 45 residues processed: 328 average time/residue: 0.1524 time to fit residues: 76.3374 Evaluate side-chains 309 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN A 463 GLN B 14 HIS B 55 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 273 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.116655 restraints weight = 30974.148| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.68 r_work: 0.3327 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19961 Z= 0.144 Angle : 0.765 13.839 27248 Z= 0.361 Chirality : 0.060 0.656 3066 Planarity : 0.003 0.035 3252 Dihedral : 12.423 168.143 3274 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.39 % Allowed : 14.46 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.69 (0.17), residues: 2228 helix: -0.95 (0.17), residues: 830 sheet: -2.03 (0.27), residues: 335 loop : -2.38 (0.18), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 149 TYR 0.020 0.001 TYR D 75 PHE 0.025 0.001 PHE A 548 TRP 0.015 0.002 TRP A 732 HIS 0.007 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (19955) covalent geometry : angle 0.76493 / 0.36 (27242) hydrogen bonds : bond 0.03628 / 2.39 ( 643) hydrogen bonds : angle 4.73033 / 3.26 ( 1776) metal coordination : bond 0.00351 / 0.17 ( 4) metal coordination : angle 1.52703 / 0.78 ( 6) Misc. bond : bond 0.00083 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7267 (mp) REVERT: A 74 TYR cc_start: 0.8019 (t80) cc_final: 0.7721 (t80) REVERT: A 521 ASP cc_start: 0.9019 (m-30) cc_final: 0.8675 (m-30) REVERT: A 728 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8390 (tp) REVERT: D 21 GLU cc_start: 0.6834 (pm20) cc_final: 0.6507 (pm20) REVERT: D 85 ASP cc_start: 0.8463 (t0) cc_final: 0.8062 (t0) REVERT: D 104 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8236 (t) REVERT: C 20 LEU cc_start: 0.7416 (tt) cc_final: 0.7192 (mp) REVERT: G 32 ILE cc_start: 0.8834 (mt) cc_final: 0.8587 (mp) REVERT: G 93 MET cc_start: 0.8521 (mmt) cc_final: 0.8318 (mmt) REVERT: G 144 ASN cc_start: 0.8094 (t0) cc_final: 0.7684 (t0) REVERT: E 117 TYR cc_start: 0.8741 (m-80) cc_final: 0.8397 (m-80) REVERT: B 5 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 39 GLU cc_start: 0.7599 (tp30) cc_final: 0.7203 (tp30) REVERT: B 152 ASN cc_start: 0.6513 (OUTLIER) cc_final: 0.6023 (p0) REVERT: B 229 MET cc_start: 0.8246 (mtp) cc_final: 0.7959 (mtp) REVERT: H 54 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7495 (mpp80) REVERT: H 65 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: H 307 LYS cc_start: 0.7930 (pmmt) cc_final: 0.7632 (pmmt) outliers start: 64 outliers final: 37 residues processed: 338 average time/residue: 0.1573 time to fit residues: 80.6554 Evaluate side-chains 305 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 262 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 86 optimal weight: 8.9990 chunk 216 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 185 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 215 optimal weight: 0.4980 chunk 109 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114726 restraints weight = 30906.177| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.74 r_work: 0.3301 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19961 Z= 0.171 Angle : 0.777 13.975 27248 Z= 0.367 Chirality : 0.061 0.669 3066 Planarity : 0.004 0.036 3252 Dihedral : 12.360 165.424 3272 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 3.39 % Allowed : 14.67 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.57 (0.17), residues: 2228 helix: -0.79 (0.18), residues: 832 sheet: -1.96 (0.27), residues: 338 loop : -2.36 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 149 TYR 0.024 0.002 TYR B 157 PHE 0.027 0.002 PHE G 167 TRP 0.015 0.002 TRP A 732 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19955) covalent geometry : angle 0.77672 / 0.37 (27242) hydrogen bonds : bond 0.03624 / 2.40 ( 643) hydrogen bonds : angle 4.70080 / 3.24 ( 1776) metal coordination : bond 0.00480 / 0.24 ( 4) metal coordination : angle 1.59967 / 0.83 ( 6) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 277 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8270 (tt) cc_final: 0.7984 (tt) REVERT: A 42 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7318 (mp) REVERT: A 74 TYR cc_start: 0.8022 (t80) cc_final: 0.7733 (t80) REVERT: A 521 ASP cc_start: 0.9044 (m-30) cc_final: 0.8746 (m-30) REVERT: A 728 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8448 (tp) REVERT: C 20 LEU cc_start: 0.7436 (tt) cc_final: 0.7189 (mp) REVERT: G 18 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8725 (pt) REVERT: G 144 ASN cc_start: 0.8142 (t0) cc_final: 0.7702 (t0) REVERT: F 80 SER cc_start: 0.9203 (m) cc_final: 0.8905 (m) REVERT: E 117 TYR cc_start: 0.8757 (m-80) cc_final: 0.8408 (m-80) REVERT: B 5 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8331 (pp) REVERT: B 39 GLU cc_start: 0.7565 (tp30) cc_final: 0.7080 (tp30) REVERT: B 114 TYR cc_start: 0.8553 (t80) cc_final: 0.8315 (t80) REVERT: B 157 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8235 (p90) REVERT: B 252 TYR cc_start: 0.8467 (m-80) cc_final: 0.8246 (m-80) REVERT: H 54 ARG cc_start: 0.7975 (tpp80) cc_final: 0.7598 (mpt180) REVERT: H 65 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7440 (pt0) REVERT: H 307 LYS cc_start: 0.7869 (pmmt) cc_final: 0.7538 (pmmt) outliers start: 64 outliers final: 42 residues processed: 327 average time/residue: 0.1616 time to fit residues: 79.5992 Evaluate side-chains 302 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 209 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN A 322 GLN F 197 ASN B 134 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110452 restraints weight = 31212.055| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.84 r_work: 0.3225 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 19961 Z= 0.243 Angle : 0.841 14.182 27248 Z= 0.398 Chirality : 0.065 0.747 3066 Planarity : 0.004 0.047 3252 Dihedral : 12.654 157.764 3272 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.50 % Favored : 89.45 % Rotamer: Outliers : 3.65 % Allowed : 15.15 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.48 (0.17), residues: 2228 helix: -0.73 (0.18), residues: 810 sheet: -1.97 (0.26), residues: 346 loop : -2.24 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 219 TYR 0.025 0.002 TYR E 181 PHE 0.035 0.002 PHE B 58 TRP 0.017 0.002 TRP A 732 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (19955) covalent geometry : angle 0.84034 / 0.40 (27242) hydrogen bonds : bond 0.03906 / 2.59 ( 643) hydrogen bonds : angle 4.83732 / 3.33 ( 1776) metal coordination : bond 0.00674 / 0.33 ( 4) metal coordination : angle 1.79201 / 1.00 ( 6) Misc. bond : bond 0.00081 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 253 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7084 (tpp) cc_final: 0.6708 (tpp) REVERT: A 74 TYR cc_start: 0.8039 (t80) cc_final: 0.7729 (t80) REVERT: A 322 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (tm130) REVERT: A 521 ASP cc_start: 0.9139 (m-30) cc_final: 0.8732 (m-30) REVERT: D 85 ASP cc_start: 0.8524 (t0) cc_final: 0.8232 (t0) REVERT: G 18 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8689 (pt) REVERT: G 144 ASN cc_start: 0.8233 (t0) cc_final: 0.7781 (t0) REVERT: E 117 TYR cc_start: 0.8750 (m-80) cc_final: 0.8392 (m-80) REVERT: B 5 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8312 (pp) REVERT: B 58 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7074 (p90) REVERT: B 157 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8046 (p90) REVERT: H 54 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7673 (mpt180) REVERT: H 65 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: H 307 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7537 (pmmt) outliers start: 69 outliers final: 46 residues processed: 304 average time/residue: 0.1587 time to fit residues: 73.5299 Evaluate side-chains 294 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 177 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 63 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.0040 overall best weight: 0.8212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 GLN A 166 ASN E 159 ASN B 208 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117379 restraints weight = 31007.111| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.69 r_work: 0.3349 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19961 Z= 0.125 Angle : 0.743 13.201 27248 Z= 0.352 Chirality : 0.057 0.637 3066 Planarity : 0.003 0.036 3252 Dihedral : 12.488 170.971 3268 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.56 % Favored : 90.39 % Rotamer: Outliers : 2.86 % Allowed : 16.42 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -2.26 (0.17), residues: 2228 helix: -0.55 (0.18), residues: 817 sheet: -1.75 (0.27), residues: 335 loop : -2.15 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 657 TYR 0.023 0.001 TYR B 157 PHE 0.033 0.001 PHE A 548 TRP 0.017 0.001 TRP A 732 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (19955) covalent geometry : angle 0.74314 / 0.35 (27242) hydrogen bonds : bond 0.03465 / 2.28 ( 643) hydrogen bonds : angle 4.66315 / 3.22 ( 1776) metal coordination : bond 0.00326 / 0.16 ( 4) metal coordination : angle 1.57584 / 0.75 ( 6) Misc. bond : bond 0.00086 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7015 (tpp) cc_final: 0.6718 (tpp) REVERT: A 74 TYR cc_start: 0.8000 (t80) cc_final: 0.7705 (t80) REVERT: A 521 ASP cc_start: 0.8982 (m-30) cc_final: 0.8650 (m-30) REVERT: A 742 LYS cc_start: 0.8104 (mttm) cc_final: 0.7528 (ttpt) REVERT: D 21 GLU cc_start: 0.7356 (pm20) cc_final: 0.7156 (pm20) REVERT: D 58 GLU cc_start: 0.8172 (tp30) cc_final: 0.7799 (pm20) REVERT: D 80 GLU cc_start: 0.7456 (tp30) cc_final: 0.7159 (tm-30) REVERT: D 98 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7445 (tm-30) REVERT: G 18 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8698 (pt) REVERT: G 144 ASN cc_start: 0.8174 (t0) cc_final: 0.7750 (t0) REVERT: E 117 TYR cc_start: 0.8707 (m-80) cc_final: 0.8234 (m-80) REVERT: E 214 GLU cc_start: 0.7059 (mp0) cc_final: 0.6819 (pt0) REVERT: B 5 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 58 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6838 (p90) REVERT: B 132 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8471 (m) REVERT: B 157 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8293 (p90) REVERT: H 54 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7543 (mpp80) REVERT: H 65 GLN cc_start: 0.7739 (tt0) cc_final: 0.7404 (pt0) REVERT: H 307 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7404 (pmmt) REVERT: H 345 MET cc_start: 0.8528 (tpt) cc_final: 0.8280 (tpt) outliers start: 54 outliers final: 37 residues processed: 316 average time/residue: 0.1663 time to fit residues: 78.7898 Evaluate side-chains 296 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.0170 chunk 131 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 133 optimal weight: 0.5980 chunk 219 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN H 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120008 restraints weight = 30797.304| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.64 r_work: 0.3386 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19961 Z= 0.118 Angle : 0.723 13.114 27248 Z= 0.344 Chirality : 0.055 0.610 3066 Planarity : 0.003 0.038 3252 Dihedral : 12.227 170.999 3268 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.12 % Allowed : 17.80 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -2.07 (0.18), residues: 2228 helix: -0.38 (0.18), residues: 820 sheet: -1.59 (0.28), residues: 326 loop : -2.09 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 149 TYR 0.024 0.001 TYR B 157 PHE 0.034 0.001 PHE G 167 TRP 0.012 0.001 TRP H 203 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (19955) covalent geometry : angle 0.72272 / 0.34 (27242) hydrogen bonds : bond 0.03320 / 2.18 ( 643) hydrogen bonds : angle 4.51983 / 3.11 ( 1776) metal coordination : bond 0.00344 / 0.17 ( 4) metal coordination : angle 1.64332 / 0.76 ( 6) Misc. bond : bond 0.00086 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.6989 (tpp) cc_final: 0.6693 (tpp) REVERT: A 74 TYR cc_start: 0.7960 (t80) cc_final: 0.7654 (t80) REVERT: A 521 ASP cc_start: 0.8882 (m-30) cc_final: 0.8557 (m-30) REVERT: A 742 LYS cc_start: 0.8037 (mttm) cc_final: 0.7524 (ttpt) REVERT: D 58 GLU cc_start: 0.8134 (tp30) cc_final: 0.7866 (pm20) REVERT: C 6 ASP cc_start: 0.8370 (m-30) cc_final: 0.8116 (m-30) REVERT: G 18 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8675 (pt) REVERT: G 144 ASN cc_start: 0.7989 (t0) cc_final: 0.7683 (t0) REVERT: F 80 SER cc_start: 0.9227 (m) cc_final: 0.8947 (m) REVERT: E 117 TYR cc_start: 0.8657 (m-80) cc_final: 0.8161 (m-80) REVERT: E 165 GLU cc_start: 0.8092 (tp30) cc_final: 0.7661 (tp30) REVERT: E 214 GLU cc_start: 0.6971 (mp0) cc_final: 0.6552 (pt0) REVERT: B 5 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8395 (pp) REVERT: B 58 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6801 (p90) REVERT: B 132 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8449 (m) REVERT: H 8 PHE cc_start: 0.7943 (m-10) cc_final: 0.7729 (m-80) REVERT: H 54 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7517 (mpp80) REVERT: H 65 GLN cc_start: 0.7765 (tt0) cc_final: 0.7506 (pt0) REVERT: H 307 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7201 (pmmt) REVERT: H 345 MET cc_start: 0.8484 (tpt) cc_final: 0.8221 (tpt) outliers start: 40 outliers final: 29 residues processed: 312 average time/residue: 0.1638 time to fit residues: 76.7088 Evaluate side-chains 303 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 269 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 173 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 181 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 224 optimal weight: 7.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115221 restraints weight = 31042.042| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.70 r_work: 0.3301 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19961 Z= 0.177 Angle : 0.775 13.794 27248 Z= 0.369 Chirality : 0.059 0.655 3066 Planarity : 0.004 0.049 3252 Dihedral : 12.272 164.394 3268 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.44 % Rotamer: Outliers : 2.01 % Allowed : 18.17 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.06 (0.17), residues: 2228 helix: -0.38 (0.18), residues: 818 sheet: -1.50 (0.28), residues: 330 loop : -2.10 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 149 TYR 0.054 0.002 TYR B 157 PHE 0.032 0.002 PHE B 58 TRP 0.013 0.002 TRP A 732 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (19955) covalent geometry : angle 0.77406 / 0.37 (27242) hydrogen bonds : bond 0.03528 / 2.34 ( 643) hydrogen bonds : angle 4.56667 / 3.15 ( 1776) metal coordination : bond 0.00607 / 0.30 ( 4) metal coordination : angle 1.92584 / 0.95 ( 6) Misc. bond : bond 0.00085 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8000 (t80) cc_final: 0.7692 (t80) REVERT: A 521 ASP cc_start: 0.8973 (m-30) cc_final: 0.8672 (m-30) REVERT: A 548 PHE cc_start: 0.8389 (t80) cc_final: 0.8189 (t80) REVERT: D 58 GLU cc_start: 0.8157 (tp30) cc_final: 0.7952 (pm20) REVERT: C 6 ASP cc_start: 0.8399 (m-30) cc_final: 0.8169 (m-30) REVERT: G 18 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8688 (pt) REVERT: G 144 ASN cc_start: 0.8127 (t0) cc_final: 0.7837 (t0) REVERT: F 80 SER cc_start: 0.9212 (m) cc_final: 0.8943 (m) REVERT: E 117 TYR cc_start: 0.8711 (m-80) cc_final: 0.8309 (m-80) REVERT: E 165 GLU cc_start: 0.8155 (tp30) cc_final: 0.7725 (tp30) REVERT: E 214 GLU cc_start: 0.7063 (mp0) cc_final: 0.6829 (pt0) REVERT: B 5 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8431 (pp) REVERT: B 58 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6826 (p90) REVERT: B 132 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8411 (m) REVERT: H 34 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6594 (mm-30) REVERT: H 54 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7662 (mpt180) REVERT: H 65 GLN cc_start: 0.7817 (tt0) cc_final: 0.7588 (pt0) REVERT: H 307 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7238 (pmmt) outliers start: 38 outliers final: 30 residues processed: 290 average time/residue: 0.1624 time to fit residues: 71.1181 Evaluate side-chains 293 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 307 LYS Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 100 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 178 optimal weight: 0.4980 chunk 157 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 90 optimal weight: 0.0020 chunk 227 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN B 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122146 restraints weight = 30987.732| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.65 r_work: 0.3416 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19961 Z= 0.116 Angle : 0.717 13.000 27248 Z= 0.341 Chirality : 0.054 0.595 3066 Planarity : 0.003 0.039 3252 Dihedral : 12.173 173.740 3268 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.47 % Favored : 90.48 % Rotamer: Outliers : 1.69 % Allowed : 18.64 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.93 (0.18), residues: 2228 helix: -0.19 (0.19), residues: 821 sheet: -1.50 (0.28), residues: 328 loop : -2.08 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 149 TYR 0.050 0.001 TYR B 157 PHE 0.030 0.001 PHE B 58 TRP 0.014 0.001 TRP H 203 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (19955) covalent geometry : angle 0.71671 / 0.34 (27242) hydrogen bonds : bond 0.03236 / 2.11 ( 643) hydrogen bonds : angle 4.47530 / 3.09 ( 1776) metal coordination : bond 0.00326 / 0.16 ( 4) metal coordination : angle 1.85440 / 0.84 ( 6) Misc. bond : bond 0.00097 / 0.05 ( 2) =============================================================================== Job complete usr+sys time: 5251.57 seconds wall clock time: 90 minutes 51.98 seconds (5451.98 seconds total)