Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 12:50:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifr_9656/07_2023/6ifr_9656_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifr_9656/07_2023/6ifr_9656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifr_9656/07_2023/6ifr_9656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifr_9656/07_2023/6ifr_9656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifr_9656/07_2023/6ifr_9656_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ifr_9656/07_2023/6ifr_9656_updated.pdb" } resolution = 3.4 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 12006 2.51 5 N 3256 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 715": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "G PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F ARG 188": "NH1" <-> "NH2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 292": "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: 19219 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5549 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 685} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 55 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: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1703 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1610 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2289 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2832 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 18, 'TRANS': 334} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 18} Chain: "J" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 752 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 13} Link IDs: {'rna2p': 4, 'rna3p': 30} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 9.71, per 1000 atoms: 0.51 Number of scatterers: 19219 At special positions: 0 Unit cell: (92.56, 135.2, 170.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 76 15.00 Mg 2 11.99 O 3843 8.00 N 3256 7.00 C 12006 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.05 Conformation dependent library (CDL) restraints added in 2.7 seconds 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 19 sheets defined 31.7% alpha, 8.6% beta 22 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.653A pdb=" N ASP A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 31 through 40 removed outlier: 4.040A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.610A pdb=" N ASN A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 removed outlier: 3.735A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR A 154 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 159 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 160 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.763A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 267 through 289 removed outlier: 3.503A pdb=" N ALA A 271 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 275 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 278 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 281 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 283 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 286 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 287 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 334 removed outlier: 3.669A pdb=" N VAL A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 329 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 353 removed outlier: 3.739A pdb=" N ILE A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 353' Processing helix chain 'A' and resid 363 through 377 removed outlier: 3.900A pdb=" N TYR A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.888A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN A 427 " --> pdb=" O ARG A 423 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 542 through 556 removed outlier: 3.688A pdb=" N PHE A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 Processing helix chain 'A' and resid 585 through 603 removed outlier: 3.664A pdb=" N ILE A 589 " --> pdb=" O TRP A 585 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 628 removed outlier: 3.569A pdb=" N HIS A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 removed outlier: 3.566A pdb=" N THR A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.606A pdb=" N ASN A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 711 removed outlier: 3.786A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.870A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TRP A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 753 removed outlier: 3.768A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.720A pdb=" N ASN D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 78 removed outlier: 4.009A pdb=" N ARG D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.520A pdb=" N LEU D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 removed outlier: 3.815A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.670A pdb=" N ARG D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 113 " --> pdb=" O CYS D 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 37 through 54 removed outlier: 3.722A pdb=" N ASN C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 78 removed outlier: 4.009A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.520A pdb=" N LEU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 removed outlier: 3.815A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 121 removed outlier: 3.671A pdb=" N ARG C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 113 " --> pdb=" O CYS C 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 60 removed outlier: 3.503A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 74 No H-bonds generated for 'chain 'G' and resid 72 through 74' Processing helix chain 'G' and resid 80 through 83 No H-bonds generated for 'chain 'G' and resid 80 through 83' Processing helix chain 'G' and resid 106 through 109 No H-bonds generated for 'chain 'G' and resid 106 through 109' Processing helix chain 'G' and resid 129 through 131 No H-bonds generated for 'chain 'G' and resid 129 through 131' Processing helix chain 'G' and resid 162 through 176 removed outlier: 3.656A pdb=" N LYS G 168 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP G 172 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU G 176 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 213 No H-bonds generated for 'chain 'G' and resid 210 through 213' Processing helix chain 'F' and resid 49 through 62 removed outlier: 3.801A pdb=" N LYS F 55 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 109 No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 163 through 176 removed outlier: 3.565A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.593A 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 'E' and resid 49 through 61 removed outlier: 3.539A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 83 No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 106 through 109 No H-bonds generated for 'chain 'E' and resid 106 through 109' Processing helix chain 'E' and resid 170 through 178 Processing helix chain 'E' and resid 210 through 213 No H-bonds generated for 'chain 'E' and resid 210 through 213' Processing helix chain 'B' and resid 29 through 42 Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.656A pdb=" N GLU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 99 removed outlier: 4.052A pdb=" N ALA B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.531A 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 173 removed outlier: 3.809A pdb=" N SER B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 222 through 227 removed outlier: 4.087A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'H' and resid 43 through 52 Processing helix chain 'H' and resid 56 through 62 Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 129 through 142 removed outlier: 3.614A pdb=" N GLY H 134 " --> pdb=" O SER H 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' 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 259 removed outlier: 3.554A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ILE H 243 " --> pdb=" O ALA H 239 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU H 245 " --> pdb=" O ARG H 241 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS H 248 " --> pdb=" O GLU H 244 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA H 252 " --> pdb=" O LYS H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 303 removed outlier: 3.962A pdb=" N GLN H 300 " --> pdb=" O ASP H 296 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG H 301 " --> pdb=" O GLY H 297 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG H 302 " --> pdb=" O ILE H 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR H 303 " --> pdb=" O LEU H 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 296 through 303' Processing sheet with id= A, first strand: chain 'A' and resid 243 through 245 Processing sheet with id= B, first strand: chain 'A' and resid 436 through 438 removed outlier: 3.698A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 609 through 616 removed outlier: 3.588A pdb=" N PHE A 580 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR A 573 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER A 584 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 569 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 193 through 196 removed outlier: 4.665A pdb=" N GLU G 150 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG G 99 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 118 through 122 Processing sheet with id= F, first strand: chain 'G' and resid 5 through 8 removed outlier: 3.623A pdb=" N PHE G 204 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS G 7 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N THR G 202 " --> pdb=" O LYS G 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 96 through 98 removed outlier: 3.952A pdb=" N LYS F 5 " --> pdb=" O PHE F 204 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS F 7 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR F 202 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER F 9 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA F 200 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 146 through 149 removed outlier: 3.562A pdb=" N ALA F 194 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 118 through 122 Processing sheet with id= J, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.668A pdb=" N PHE E 204 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS E 7 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR E 202 " --> pdb=" O LYS E 7 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 149 Processing sheet with id= L, first strand: chain 'E' and resid 118 through 123 Processing sheet with id= M, first strand: chain 'B' and resid 5 through 8 Processing sheet with id= N, first strand: chain 'B' and resid 71 through 73 Processing sheet with id= O, first strand: chain 'B' and resid 129 through 134 Processing sheet with id= P, first strand: chain 'H' and resid 226 through 231 removed outlier: 3.858A pdb=" N THR H 226 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 93 through 95 removed outlier: 4.313A pdb=" N ASN H 35 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N TYR H 39 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR H 33 " --> pdb=" O TYR H 39 " (cutoff:3.500A) 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 205 421 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.41 Time building geometry restraints manager: 8.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4020 1.33 - 1.45: 4869 1.45 - 1.57: 10621 1.57 - 1.69: 149 1.69 - 1.81: 67 Bond restraints: 19726 Sorted by residual: bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" C5 ATP A 802 " pdb=" C6 ATP A 802 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.57e+01 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.47e+01 bond pdb=" C4 ATP A 802 " pdb=" N9 ATP A 802 " ideal model delta sigma weight residual 1.374 1.327 0.047 1.00e-02 1.00e+04 2.17e+01 ... (remaining 19721 not shown) Histogram of bond angle deviations from ideal: 89.52 - 98.88: 2 98.88 - 108.24: 1429 108.24 - 117.60: 13010 117.60 - 126.96: 12183 126.96 - 136.32: 317 Bond angle restraints: 26941 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 119.25 20.62 1.00e+00 1.00e+00 4.25e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 120.03 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 123.95 15.92 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 123.83 13.00 1.00e+00 1.00e+00 1.69e+02 angle pdb=" N GLY G 186 " pdb=" CA GLY G 186 " pdb=" C GLY G 186 " ideal model delta sigma weight residual 112.73 126.68 -13.95 1.20e+00 6.94e-01 1.35e+02 ... (remaining 26936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.08: 11292 27.08 - 54.16: 367 54.16 - 81.24: 20 81.24 - 108.32: 7 108.32 - 135.40: 1 Dihedral angle restraints: 11687 sinusoidal: 5204 harmonic: 6483 Sorted by residual: dihedral pdb=" CA ASN A 604 " pdb=" C ASN A 604 " pdb=" N GLY A 605 " pdb=" CA GLY A 605 " ideal model delta harmonic sigma weight residual 180.00 -137.81 -42.19 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA LEU E 112 " pdb=" C LEU E 112 " pdb=" N GLY E 113 " pdb=" CA GLY E 113 " ideal model delta harmonic sigma weight residual -180.00 -147.02 -32.98 0 5.00e+00 4.00e-02 4.35e+01 dihedral pdb=" CA ARG H 87 " pdb=" C ARG H 87 " pdb=" N SER H 88 " pdb=" CA SER H 88 " ideal model delta harmonic sigma weight residual 180.00 148.14 31.86 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 11684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2702 0.091 - 0.181: 301 0.181 - 0.272: 26 0.272 - 0.362: 9 0.362 - 0.453: 4 Chirality restraints: 3042 Sorted by residual: chirality pdb=" CA GLN G 162 " pdb=" N GLN G 162 " pdb=" C GLN G 162 " pdb=" CB GLN G 162 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA TYR A 224 " pdb=" N TYR A 224 " pdb=" C TYR A 224 " pdb=" CB TYR A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA THR A 188 " pdb=" N THR A 188 " pdb=" C THR A 188 " pdb=" CB THR A 188 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 3039 not shown) Planarity restraints: 3196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 221 " -0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C ARG A 221 " 0.080 2.00e-02 2.50e+03 pdb=" O ARG A 221 " -0.031 2.00e-02 2.50e+03 pdb=" N HIS A 222 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP A 802 " -0.013 2.00e-02 2.50e+03 2.46e-02 1.67e+01 pdb=" C2 ATP A 802 " 0.006 2.00e-02 2.50e+03 pdb=" C4 ATP A 802 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ATP A 802 " 0.031 2.00e-02 2.50e+03 pdb=" C6 ATP A 802 " -0.069 2.00e-02 2.50e+03 pdb=" C8 ATP A 802 " -0.005 2.00e-02 2.50e+03 pdb=" N1 ATP A 802 " 0.022 2.00e-02 2.50e+03 pdb=" N3 ATP A 802 " -0.001 2.00e-02 2.50e+03 pdb=" N6 ATP A 802 " 0.010 2.00e-02 2.50e+03 pdb=" N7 ATP A 802 " 0.012 2.00e-02 2.50e+03 pdb=" N9 ATP A 802 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP A 732 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.006 2.00e-02 2.50e+03 ... (remaining 3193 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 16 2.23 - 2.89: 7403 2.89 - 3.56: 27174 3.56 - 4.23: 48277 4.23 - 4.90: 79199 Nonbonded interactions: 162069 Sorted by model distance: nonbonded pdb=" OG SER G 187 " pdb=" NZ LYS H 133 " model vdw 1.558 2.520 nonbonded pdb=" NH1 ARG G 81 " pdb=" OE1 GLN G 162 " model vdw 1.600 2.520 nonbonded pdb=" N GLN H 294 " pdb=" OE1 GLN H 294 " model vdw 2.076 2.520 nonbonded pdb=" N ASP E 39 " pdb=" OD1 ASP E 39 " model vdw 2.082 2.520 nonbonded pdb=" O2A ATP A 802 " pdb="MG MG A 804 " model vdw 2.099 2.170 ... (remaining 162064 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 92 or (resid 93 and (name N or name CA or name C \ or name O or name CB )) or resid 94 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 through 217)) selection = (chain 'F' and (resid 2 through 65 or resid 77 through 217)) selection = (chain 'G' and (resid 2 through 65 or resid 77 through 92 or (resid 93 and (name \ N or name CA or name C or name O or name CB )) or resid 94 through 157 or (resi \ d 158 and (name N or name CA or name C or name O or name CB )) or resid 159 or ( \ resid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 \ 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: 0.340 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: 3.620 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 53.360 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.007 0.077 19726 Z= 0.430 Angle : 1.156 20.620 26941 Z= 0.657 Chirality : 0.061 0.453 3042 Planarity : 0.006 0.056 3196 Dihedral : 12.477 135.402 7505 Min Nonbonded Distance : 1.558 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.02 % Favored : 87.66 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.42 (0.13), residues: 2188 helix: -4.31 (0.08), residues: 737 sheet: -3.00 (0.26), residues: 322 loop : -3.27 (0.15), residues: 1129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 575 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 4 residues processed: 590 average time/residue: 0.3855 time to fit residues: 322.2722 Evaluate side-chains 271 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 267 time to evaluate : 2.183 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1736 time to fit residues: 4.1943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 203 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 HIS A 223 ASN A 252 GLN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 ASN A 436 HIS A 497 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN A 676 HIS D 76 GLN C 76 GLN C 106 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 144 ASN E 159 ASN E 161 ASN B 125 HIS ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 161 ASN B 249 ASN B 255 GLN B 288 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 19726 Z= 0.193 Angle : 0.694 10.619 26941 Z= 0.360 Chirality : 0.044 0.306 3042 Planarity : 0.004 0.050 3196 Dihedral : 11.087 132.290 3257 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.92 % Favored : 88.99 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.26 (0.15), residues: 2188 helix: -2.86 (0.14), residues: 724 sheet: -2.57 (0.28), residues: 312 loop : -2.90 (0.16), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 350 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 25 residues processed: 394 average time/residue: 0.3421 time to fit residues: 201.7159 Evaluate side-chains 290 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 265 time to evaluate : 2.339 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1914 time to fit residues: 11.9463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 202 optimal weight: 0.1980 chunk 69 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN A 661 ASN D 26 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 19726 Z= 0.329 Angle : 0.727 10.714 26941 Z= 0.376 Chirality : 0.046 0.294 3042 Planarity : 0.004 0.040 3196 Dihedral : 11.050 130.826 3257 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.16 % Favored : 87.75 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.68 (0.16), residues: 2188 helix: -2.10 (0.16), residues: 733 sheet: -2.39 (0.29), residues: 312 loop : -2.71 (0.17), residues: 1143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 26 residues processed: 317 average time/residue: 0.3331 time to fit residues: 161.7158 Evaluate side-chains 268 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2005 time to fit residues: 12.5362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 19726 Z= 0.356 Angle : 0.728 10.641 26941 Z= 0.377 Chirality : 0.046 0.299 3042 Planarity : 0.004 0.042 3196 Dihedral : 11.109 127.676 3257 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.88 % Favored : 88.03 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 (0.17), residues: 2188 helix: -1.68 (0.17), residues: 741 sheet: -2.40 (0.29), residues: 307 loop : -2.64 (0.17), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 278 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 310 average time/residue: 0.3274 time to fit residues: 155.4000 Evaluate side-chains 270 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1879 time to fit residues: 12.0503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 3 optimal weight: 40.0000 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 ASN ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 GLN ** 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 19726 Z= 0.259 Angle : 0.664 10.523 26941 Z= 0.345 Chirality : 0.044 0.269 3042 Planarity : 0.004 0.041 3196 Dihedral : 10.959 130.517 3257 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.07 % Favored : 87.84 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.14 (0.17), residues: 2188 helix: -1.26 (0.18), residues: 742 sheet: -2.36 (0.29), residues: 306 loop : -2.61 (0.17), residues: 1140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 270 time to evaluate : 2.130 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 16 residues processed: 298 average time/residue: 0.3322 time to fit residues: 151.1138 Evaluate side-chains 254 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 238 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2278 time to fit residues: 9.1049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 113 optimal weight: 0.0270 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN A 628 GLN D 26 ASN D 72 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19726 Z= 0.193 Angle : 0.633 14.178 26941 Z= 0.328 Chirality : 0.042 0.275 3042 Planarity : 0.004 0.054 3196 Dihedral : 10.779 130.855 3257 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.11 % Favored : 88.80 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.17), residues: 2188 helix: -1.05 (0.18), residues: 762 sheet: -2.26 (0.29), residues: 308 loop : -2.59 (0.18), residues: 1118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 278 average time/residue: 0.3280 time to fit residues: 139.8259 Evaluate side-chains 256 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1733 time to fit residues: 7.0679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 0.2980 chunk 121 optimal weight: 10.0000 chunk 215 optimal weight: 30.0000 chunk 135 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 19726 Z= 0.150 Angle : 0.612 12.471 26941 Z= 0.314 Chirality : 0.041 0.295 3042 Planarity : 0.004 0.056 3196 Dihedral : 10.544 129.487 3257 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.42 % Favored : 89.49 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.65 (0.17), residues: 2188 helix: -0.68 (0.19), residues: 751 sheet: -2.09 (0.30), residues: 308 loop : -2.46 (0.18), residues: 1129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 282 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 294 average time/residue: 0.3300 time to fit residues: 150.5663 Evaluate side-chains 249 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1838 time to fit residues: 5.7769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN H 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19726 Z= 0.274 Angle : 0.675 14.138 26941 Z= 0.346 Chirality : 0.044 0.263 3042 Planarity : 0.004 0.061 3196 Dihedral : 10.639 125.175 3257 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.52 % Favored : 88.39 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.75 (0.17), residues: 2188 helix: -0.69 (0.19), residues: 754 sheet: -2.30 (0.30), residues: 302 loop : -2.54 (0.17), residues: 1132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 251 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 263 average time/residue: 0.3172 time to fit residues: 128.0999 Evaluate side-chains 243 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1717 time to fit residues: 5.4485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19726 Z= 0.281 Angle : 0.684 13.830 26941 Z= 0.351 Chirality : 0.044 0.265 3042 Planarity : 0.004 0.059 3196 Dihedral : 10.722 124.720 3257 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.88 % Favored : 88.03 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.67 (0.17), residues: 2188 helix: -0.64 (0.19), residues: 740 sheet: -2.29 (0.30), residues: 302 loop : -2.44 (0.18), residues: 1146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 240 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 247 average time/residue: 0.3291 time to fit residues: 125.4420 Evaluate side-chains 231 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 225 time to evaluate : 2.171 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1806 time to fit residues: 4.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 129 optimal weight: 0.0770 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 overall best weight: 4.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 19726 Z= 0.378 Angle : 0.744 13.720 26941 Z= 0.383 Chirality : 0.047 0.287 3042 Planarity : 0.004 0.059 3196 Dihedral : 10.927 123.583 3257 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.98 % Favored : 86.97 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.87 (0.17), residues: 2188 helix: -0.86 (0.18), residues: 761 sheet: -2.32 (0.29), residues: 314 loop : -2.56 (0.18), residues: 1113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 231 average time/residue: 0.3727 time to fit residues: 131.5195 Evaluate side-chains 219 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 215 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1838 time to fit residues: 4.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 177 optimal weight: 0.0070 chunk 74 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 overall best weight: 1.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 GLN ** 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 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099432 restraints weight = 37069.560| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.00 r_work: 0.3194 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19726 Z= 0.202 Angle : 0.671 13.310 26941 Z= 0.342 Chirality : 0.043 0.271 3042 Planarity : 0.004 0.059 3196 Dihedral : 10.787 128.869 3257 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.83 % Favored : 89.12 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.64 (0.17), residues: 2188 helix: -0.60 (0.19), residues: 755 sheet: -2.16 (0.30), residues: 300 loop : -2.49 (0.18), residues: 1133 =============================================================================== Job complete usr+sys time: 4148.38 seconds wall clock time: 76 minutes 17.35 seconds (4577.35 seconds total)