Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 15:36:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifk_9653/07_2023/6ifk_9653_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifk_9653/07_2023/6ifk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifk_9653/07_2023/6ifk_9653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifk_9653/07_2023/6ifk_9653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifk_9653/07_2023/6ifk_9653_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifk_9653/07_2023/6ifk_9653_updated.pdb" } 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 Residue "A ARG 121": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 74": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H ARG 158": "NH1" <-> "NH2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'GLU:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 1, 'ASP: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: {'RNA': 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: {'RNA': 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: 9.73, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 8.94 Conformation dependent library (CDL) restraints added in 2.7 seconds 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... running ksdssp... Secondary structure from input PDB file: 86 helices and 19 sheets defined 33.4% alpha, 8.4% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 6.56 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 18 through 25 removed outlier: 4.479A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 41 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) removed outlier: 4.406A pdb=" N ASP A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.573A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 150 through 161 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) removed outlier: 3.717A pdb=" N ALA A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 180 removed outlier: 3.919A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 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) Processing helix chain 'A' and resid 225 through 228 No H-bonds generated for 'chain 'A' and resid 225 through 228' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 267 through 273 removed outlier: 4.255A pdb=" N ARG A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 290 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 314 through 334 removed outlier: 3.562A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 364 through 377 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 384 through 388 Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 421 through 430 removed outlier: 4.723A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 removed outlier: 4.142A pdb=" N ALA A 499 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 501 " --> pdb=" O TYR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 542 through 563 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 602 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 622 through 637 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) Processing helix chain 'A' and resid 655 through 658 No H-bonds generated for 'chain 'A' and resid 655 through 658' Processing helix chain 'A' and resid 666 through 675 Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 697 through 711 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 720 through 733 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 741 through 754 Processing helix chain 'D' and resid 9 through 19 removed outlier: 3.538A pdb=" N LYS D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 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 63 through 77 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 81 through 84 No H-bonds generated for 'chain 'D' and resid 81 through 84' Processing helix chain 'D' and resid 86 through 89 No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.764A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 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 9 through 17 removed outlier: 3.581A pdb=" N ILE C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 41 through 51 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 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 63 through 79 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) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 95 No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 102 through 121 Processing helix chain 'G' and resid 49 through 59 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 61 through 64 No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 79 through 82 No H-bonds generated for 'chain 'G' and resid 79 through 82' Processing helix chain 'G' and resid 106 through 111 Processing helix chain 'G' and resid 167 through 179 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) removed outlier: 4.123A pdb=" N LEU G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 62 removed outlier: 3.544A pdb=" N MET F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 77 through 83 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 108 through 111 No H-bonds generated for 'chain 'F' and resid 108 through 111' Processing helix chain 'F' and resid 163 through 179 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 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 210 through 216 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 49 through 63 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 83 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 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 104 through 112 removed outlier: 4.656A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU E 108 " --> pdb=" O ASN E 105 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU E 109 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 172 through 179 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 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 213 through 216 No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 90 through 99 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 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 164 through 176 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 43 through 53 removed outlier: 3.980A pdb=" N GLU H 52 " --> pdb=" O ASN H 48 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 129 through 142 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 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 237 through 244 removed outlier: 3.601A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 258 removed outlier: 3.659A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 292 through 294 No H-bonds generated for 'chain 'H' and resid 292 through 294' Processing helix chain 'H' and resid 300 through 302 No H-bonds generated for 'chain 'H' and resid 300 through 302' Processing sheet with id= A, first strand: chain 'A' and resid 241 through 245 removed outlier: 3.624A pdb=" N GLY A 344 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.147A pdb=" N ARG A 468 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 451 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 453 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 612 through 617 removed outlier: 6.767A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER A 584 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 569 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 643 through 645 Processing sheet with id= E, first strand: chain 'G' and resid 152 through 155 removed outlier: 6.146A pdb=" N LYS G 7 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR G 202 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N SER G 9 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA G 200 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 11 through 15 removed outlier: 3.605A pdb=" N LYS G 192 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 118 through 122 Processing sheet with id= H, first strand: chain 'F' and resid 152 through 155 removed outlier: 3.864A pdb=" N PHE F 204 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS F 7 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR F 202 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N SER F 9 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA F 200 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 11 through 14 Processing sheet with id= J, first strand: chain 'F' and resid 118 through 126 Processing sheet with id= K, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= L, first strand: chain 'E' and resid 11 through 14 Processing sheet with id= M, first strand: chain 'E' and resid 118 through 123 Processing sheet with id= N, first strand: chain 'B' and resid 5 through 9 Processing sheet with id= O, first strand: chain 'B' and resid 71 through 73 Processing sheet with id= P, first strand: chain 'H' and resid 227 through 230 Processing sheet with id= Q, first strand: chain 'H' and resid 37 through 40 Processing sheet with id= R, first strand: chain 'H' and resid 184 through 186 Processing sheet with id= S, first strand: chain 'H' and resid 203 through 205 451 hydrogen bonds defined for protein. 1284 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: 5.85 Time building geometry restraints manager: 9.59 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: 97.97 - 106.23: 720 106.23 - 114.48: 11469 114.48 - 122.74: 12813 122.74 - 131.00: 2169 131.00 - 139.25: 71 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=" O4' G N 9 " pdb=" C1' G N 9 " pdb=" N9 G N 9 " ideal model delta sigma weight residual 108.20 115.79 -7.59 1.50e+00 4.44e-01 2.56e+01 ... (remaining 27237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 11632 33.96 - 67.93: 168 67.93 - 101.89: 18 101.89 - 135.86: 2 135.86 - 169.82: 3 Dihedral angle restraints: 11823 sinusoidal: 5222 harmonic: 6601 Sorted by residual: dihedral pdb=" CA PRO H 105 " pdb=" C PRO H 105 " pdb=" N ASN H 106 " pdb=" CA ASN H 106 " ideal model delta harmonic sigma weight residual 180.00 -135.66 -44.34 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" O4' C N 8 " pdb=" C1' C N 8 " pdb=" N1 C N 8 " pdb=" C2 C N 8 " ideal model delta sinusoidal sigma weight residual -128.00 41.82 -169.82 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" CA GLY H 90 " pdb=" C GLY H 90 " pdb=" N GLY H 91 " pdb=" CA GLY H 91 " ideal model delta harmonic sigma weight residual 180.00 -139.97 -40.03 0 5.00e+00 4.00e-02 6.41e+01 ... (remaining 11820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2582 0.084 - 0.167: 431 0.167 - 0.251: 40 0.251 - 0.334: 8 0.334 - 0.418: 5 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 2.44 2.05 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C1' G N 21 " pdb=" O4' G N 21 " pdb=" C2' G N 21 " pdb=" N9 G N 21 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.36 2.00e-01 2.50e+01 3.30e+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: 258 2.62 - 3.19: 16615 3.19 - 3.76: 31534 3.76 - 4.33: 45407 4.33 - 4.90: 72721 Nonbonded interactions: 166535 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 2.440 ... (remaining 166530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.710 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 58.420 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 19955 Z= 0.591 Angle : 1.199 22.953 27242 Z= 0.625 Chirality : 0.064 0.418 3066 Planarity : 0.007 0.073 3252 Dihedral : 12.738 169.820 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 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 19 poor density : 535 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 545 average time/residue: 0.4023 time to fit residues: 310.3258 Evaluate side-chains 297 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 291 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1894 time to fit residues: 5.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 268 GLN A 305 HIS A 312 ASN A 414 HIS A 491 GLN A 562 GLN A 604 ASN A 677 GLN D 106 GLN G 159 ASN F 11 GLN F 33 ASN F 213 ASN E 33 ASN E 134 ASN B 55 GLN B 152 ASN B 174 GLN B 284 HIS H 3 ASN H 72 ASN H 104 ASN H 115 ASN H 151 ASN H 194 ASN ** H 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19955 Z= 0.218 Angle : 0.690 15.931 27242 Z= 0.359 Chirality : 0.043 0.308 3066 Planarity : 0.004 0.048 3252 Dihedral : 12.029 171.129 3265 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.83 % Favored : 90.08 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.15), residues: 2228 helix: -2.39 (0.15), residues: 797 sheet: -2.58 (0.26), residues: 331 loop : -2.68 (0.16), residues: 1100 *********************** 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 360 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 326 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 348 average time/residue: 0.3492 time to fit residues: 182.3235 Evaluate side-chains 280 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1919 time to fit residues: 9.2819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 172 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 152 ASN B 167 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 19955 Z= 0.255 Angle : 0.659 14.878 27242 Z= 0.343 Chirality : 0.043 0.315 3066 Planarity : 0.004 0.041 3252 Dihedral : 11.735 171.311 3265 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.41 % Favored : 89.54 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 2228 helix: -1.79 (0.16), residues: 822 sheet: -2.35 (0.27), residues: 333 loop : -2.56 (0.17), residues: 1073 *********************** 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 335 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 25 residues processed: 319 average time/residue: 0.3385 time to fit residues: 163.7057 Evaluate side-chains 284 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1920 time to fit residues: 11.6027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 4.9990 chunk 155 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 463 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN F 85 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN F 213 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 19955 Z= 0.441 Angle : 0.759 15.697 27242 Z= 0.395 Chirality : 0.047 0.361 3066 Planarity : 0.005 0.044 3252 Dihedral : 11.827 169.805 3265 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.22 % Favored : 88.69 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.16), residues: 2228 helix: -1.46 (0.17), residues: 790 sheet: -2.29 (0.27), residues: 338 loop : -2.44 (0.17), residues: 1100 *********************** 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 302 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 290 average time/residue: 0.3371 time to fit residues: 147.8271 Evaluate side-chains 262 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2147 time to fit residues: 11.7887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 19955 Z= 0.321 Angle : 0.683 14.675 27242 Z= 0.355 Chirality : 0.044 0.331 3066 Planarity : 0.004 0.042 3252 Dihedral : 11.713 170.111 3265 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.50 % Favored : 89.45 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.17), residues: 2228 helix: -1.18 (0.17), residues: 792 sheet: -2.24 (0.27), residues: 339 loop : -2.33 (0.17), residues: 1097 *********************** 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 286 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 252 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 273 average time/residue: 0.3330 time to fit residues: 138.5768 Evaluate side-chains 256 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 239 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2588 time to fit residues: 10.4216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 328 ASN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 19955 Z= 0.161 Angle : 0.602 13.341 27242 Z= 0.310 Chirality : 0.041 0.290 3066 Planarity : 0.003 0.035 3252 Dihedral : 11.469 170.897 3265 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.05 % Favored : 89.90 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.17), residues: 2228 helix: -0.78 (0.18), residues: 803 sheet: -1.94 (0.28), residues: 327 loop : -2.25 (0.18), residues: 1098 *********************** 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 308 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 302 average time/residue: 0.3448 time to fit residues: 156.9620 Evaluate side-chains 260 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 251 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2213 time to fit residues: 6.4594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN B 11 GLN B 152 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19955 Z= 0.173 Angle : 0.599 12.441 27242 Z= 0.309 Chirality : 0.041 0.294 3066 Planarity : 0.003 0.033 3252 Dihedral : 11.293 170.602 3265 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.61 % Favored : 90.35 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.17), residues: 2228 helix: -0.59 (0.18), residues: 798 sheet: -1.80 (0.28), residues: 324 loop : -2.14 (0.18), residues: 1106 *********************** 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 291 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 281 average time/residue: 0.3657 time to fit residues: 154.1082 Evaluate side-chains 262 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 250 time to evaluate : 2.416 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1864 time to fit residues: 7.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 19955 Z= 0.359 Angle : 0.683 13.272 27242 Z= 0.354 Chirality : 0.045 0.330 3066 Planarity : 0.004 0.040 3252 Dihedral : 11.374 171.198 3265 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.28 % Favored : 89.68 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 2228 helix: -0.65 (0.18), residues: 790 sheet: -1.81 (0.28), residues: 324 loop : -2.17 (0.18), residues: 1114 *********************** 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 275 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 2.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 269 average time/residue: 0.3565 time to fit residues: 144.1160 Evaluate side-chains 248 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 237 time to evaluate : 2.336 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1893 time to fit residues: 6.9366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 19955 Z= 0.208 Angle : 0.618 12.116 27242 Z= 0.320 Chirality : 0.042 0.303 3066 Planarity : 0.003 0.036 3252 Dihedral : 11.282 170.807 3265 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.10 % Favored : 89.86 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.17), residues: 2228 helix: -0.44 (0.18), residues: 789 sheet: -1.59 (0.29), residues: 317 loop : -2.15 (0.18), residues: 1122 *********************** 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 271 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 265 average time/residue: 0.3606 time to fit residues: 143.0254 Evaluate side-chains 253 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 246 time to evaluate : 2.164 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1871 time to fit residues: 5.3727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19955 Z= 0.237 Angle : 0.628 12.025 27242 Z= 0.326 Chirality : 0.042 0.313 3066 Planarity : 0.003 0.035 3252 Dihedral : 11.178 170.876 3265 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.19 % Favored : 89.77 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.17), residues: 2228 helix: -0.42 (0.18), residues: 794 sheet: -1.56 (0.29), residues: 321 loop : -2.16 (0.18), residues: 1113 ********************** 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 265 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 253 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 262 average time/residue: 0.3606 time to fit residues: 141.6826 Evaluate side-chains 249 residues out of total 1952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1804 time to fit residues: 4.2625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 186 optimal weight: 0.0980 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 322 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111375 restraints weight = 30988.551| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.79 r_work: 0.3236 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 19955 Z= 0.227 Angle : 0.629 11.992 27242 Z= 0.324 Chirality : 0.042 0.311 3066 Planarity : 0.003 0.034 3252 Dihedral : 11.113 170.967 3265 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.19 % Favored : 89.77 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.17), residues: 2228 helix: -0.36 (0.18), residues: 796 sheet: -1.49 (0.29), residues: 315 loop : -2.14 (0.18), residues: 1117 =============================================================================== Job complete usr+sys time: 4170.05 seconds wall clock time: 77 minutes 6.59 seconds (4626.59 seconds total)