Starting phenix.real_space_refine (version: dev) on Wed Dec 14 09:39:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/12_2022/6zy7_11553_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/12_2022/6zy7_11553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/12_2022/6zy7_11553.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/12_2022/6zy7_11553.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/12_2022/6zy7_11553_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zy7_11553/12_2022/6zy7_11553_updated.pdb" } resolution = 4.64 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= 0.004 sd= 0.060 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 200": "NH1" <-> "NH2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 870": "NH1" <-> "NH2" Residue "B ARG 1148": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19979 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 9310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9310 Classifications: {'peptide': 1160} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 1114} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 9305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9305 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 45, 'TRANS': 1113} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.40, per 1000 atoms: 0.57 Number of scatterers: 19979 At special positions: 0 Unit cell: (119.053, 116.039, 197.417, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 62 15.00 O 3881 8.00 N 3417 7.00 C 12527 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=0, symmetry=0 Time building additional restraints: 7.96 Conformation dependent library (CDL) restraints added in 2.8 seconds 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 15 sheets defined 40.6% alpha, 9.2% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 8.38 Creating SS restraints... Processing helix chain 'B' and resid 39 through 45 removed outlier: 3.799A pdb=" N ILE B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 79 through 98 removed outlier: 4.052A pdb=" N ILE B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 removed outlier: 3.839A pdb=" N CYS B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.529A pdb=" N PHE B 226 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 233 through 249 removed outlier: 3.519A pdb=" N ASP B 245 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.544A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 341 removed outlier: 4.137A pdb=" N ASP B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 396 through 402 removed outlier: 3.762A pdb=" N ALA B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 432 removed outlier: 3.796A pdb=" N GLN B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 464 through 476 removed outlier: 3.577A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 505 through 514 Processing helix chain 'B' and resid 525 through 530 Processing helix chain 'B' and resid 544 through 560 removed outlier: 4.013A pdb=" N ASN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 removed outlier: 3.576A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 631 through 634 No H-bonds generated for 'chain 'B' and resid 631 through 634' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 658 through 678 removed outlier: 3.594A pdb=" N PHE B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 701 Processing helix chain 'B' and resid 703 through 713 Processing helix chain 'B' and resid 724 through 735 removed outlier: 3.546A pdb=" N VAL B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.774A pdb=" N MET B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 817 No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 847 through 851 removed outlier: 4.217A pdb=" N ASN B 851 " --> pdb=" O VAL B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 869 through 881 removed outlier: 3.726A pdb=" N ASP B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 944 removed outlier: 4.588A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix Processing helix chain 'B' and resid 974 through 983 Processing helix chain 'B' and resid 985 through 988 No H-bonds generated for 'chain 'B' and resid 985 through 988' Processing helix chain 'B' and resid 1015 through 1060 removed outlier: 3.884A pdb=" N TYR B1029 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR B1030 " --> pdb=" O ARG B1026 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY B1039 " --> pdb=" O GLU B1035 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1040 " --> pdb=" O TRP B1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B1042 " --> pdb=" O LEU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1080 removed outlier: 3.640A pdb=" N GLN B1079 " --> pdb=" O LYS B1075 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B1080 " --> pdb=" O VAL B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1095 Processing helix chain 'B' and resid 1133 through 1136 Processing helix chain 'B' and resid 1138 through 1160 removed outlier: 3.998A pdb=" N GLU B1143 " --> pdb=" O GLU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1192 removed outlier: 4.133A pdb=" N TRP B1167 " --> pdb=" O PRO B1163 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B1168 " --> pdb=" O SER B1164 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B1180 " --> pdb=" O GLU B1176 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B1189 " --> pdb=" O GLU B1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 33 No H-bonds generated for 'chain 'A' and resid 30 through 33' Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.790A pdb=" N ILE A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 79 through 98 removed outlier: 3.539A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 removed outlier: 3.723A pdb=" N CYS A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.624A pdb=" N LEU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.802A pdb=" N ASP A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 274' Processing helix chain 'A' and resid 324 through 342 removed outlier: 3.512A pdb=" N VAL A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.906A pdb=" N ASN A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N HIS A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 407 through 429 removed outlier: 3.555A pdb=" N LYS A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 464 through 476 removed outlier: 3.578A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 544 through 560 removed outlier: 4.013A pdb=" N ASN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 removed outlier: 3.576A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 631 through 634 No H-bonds generated for 'chain 'A' and resid 631 through 634' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 658 through 678 removed outlier: 3.596A pdb=" N PHE A 668 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.546A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.772A pdb=" N MET A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 817 No H-bonds generated for 'chain 'A' and resid 814 through 817' Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 847 through 851 removed outlier: 4.215A pdb=" N ASN A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 removed outlier: 3.726A pdb=" N ASP A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 944 removed outlier: 4.588A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix Processing helix chain 'A' and resid 974 through 983 Processing helix chain 'A' and resid 985 through 988 No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 1015 through 1060 removed outlier: 3.885A pdb=" N TYR A1029 " --> pdb=" O LEU A1025 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1030 " --> pdb=" O ARG A1026 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLY A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 removed outlier: 3.605A pdb=" N GLN A1079 " --> pdb=" O LYS A1075 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 Processing helix chain 'A' and resid 1133 through 1136 Processing helix chain 'A' and resid 1138 through 1160 removed outlier: 3.998A pdb=" N GLU A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1192 removed outlier: 3.782A pdb=" N VAL A1191 " --> pdb=" O ASP A1188 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 57 through 65 removed outlier: 3.602A pdb=" N ARG B 73 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 65 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 254 through 257 removed outlier: 3.915A pdb=" N ILE B 116 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 219 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 176 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 192 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 309 through 311 Processing sheet with id= D, first strand: chain 'B' and resid 483 through 485 removed outlier: 8.575A pdb=" N PHE B 484 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 458 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS B 535 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 459 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET B 537 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 853 through 856 Processing sheet with id= F, first strand: chain 'B' and resid 898 through 901 Processing sheet with id= G, first strand: chain 'B' and resid 956 through 959 removed outlier: 6.340A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 290 through 294 removed outlier: 3.966A pdb=" N GLU B 291 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 299 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 56 through 65 removed outlier: 3.635A pdb=" N PHE A 77 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 61 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 73 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 65 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 254 through 257 removed outlier: 3.698A pdb=" N ILE A 116 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 192 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 181 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 190 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 361 through 364 removed outlier: 3.570A pdb=" N THR A 302 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 300 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 299 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLN A 292 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU A 301 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N HIS A 290 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 483 through 485 removed outlier: 8.574A pdb=" N PHE A 484 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 458 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS A 535 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU A 459 " --> pdb=" O LYS A 535 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET A 537 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 853 through 856 Processing sheet with id= N, first strand: chain 'A' and resid 898 through 901 Processing sheet with id= O, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.342A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 8.60 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: 3464 1.32 - 1.45: 5374 1.45 - 1.57: 11393 1.57 - 1.69: 122 1.69 - 1.82: 158 Bond restraints: 20511 Sorted by residual: bond pdb=" N3B ANP B1601 " pdb=" PG ANP B1601 " ideal model delta sigma weight residual 1.795 1.630 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N3B ANP A1601 " pdb=" PG ANP A1601 " ideal model delta sigma weight residual 1.795 1.632 0.163 2.00e-02 2.50e+03 6.60e+01 bond pdb=" O3A ANP B1601 " pdb=" PB ANP B1601 " ideal model delta sigma weight residual 1.700 1.599 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3A ANP A1601 " pdb=" PB ANP A1601 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N ILE B 864 " pdb=" CA ILE B 864 " ideal model delta sigma weight residual 1.454 1.485 -0.031 7.70e-03 1.69e+04 1.57e+01 ... (remaining 20506 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.45: 890 106.45 - 113.90: 11726 113.90 - 121.35: 10779 121.35 - 128.79: 4380 128.79 - 136.24: 168 Bond angle restraints: 27943 Sorted by residual: angle pdb=" CA HIS B 605 " pdb=" C HIS B 605 " pdb=" O HIS B 605 " ideal model delta sigma weight residual 121.47 116.88 4.59 1.15e+00 7.56e-01 1.59e+01 angle pdb=" CA HIS A 605 " pdb=" C HIS A 605 " pdb=" O HIS A 605 " ideal model delta sigma weight residual 121.47 116.89 4.58 1.15e+00 7.56e-01 1.59e+01 angle pdb=" N VAL B1191 " pdb=" CA VAL B1191 " pdb=" C VAL B1191 " ideal model delta sigma weight residual 110.72 106.72 4.00 1.01e+00 9.80e-01 1.57e+01 angle pdb=" N VAL A1191 " pdb=" CA VAL A1191 " pdb=" C VAL A1191 " ideal model delta sigma weight residual 110.72 106.78 3.94 1.01e+00 9.80e-01 1.52e+01 angle pdb=" C LYS B 606 " pdb=" CA LYS B 606 " pdb=" CB LYS B 606 " ideal model delta sigma weight residual 109.83 113.67 -3.84 9.90e-01 1.02e+00 1.51e+01 ... (remaining 27938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 11809 28.12 - 56.23: 310 56.23 - 84.35: 51 84.35 - 112.47: 3 112.47 - 140.58: 2 Dihedral angle restraints: 12175 sinusoidal: 5424 harmonic: 6751 Sorted by residual: dihedral pdb=" C4' DC C 9 " pdb=" C3' DC C 9 " pdb=" O3' DC C 9 " pdb=" P DG C 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.42 140.58 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " pdb=" O3' DC E 9 " pdb=" P DG E 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.45 140.55 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C TYR B 830 " pdb=" N TYR B 830 " pdb=" CA TYR B 830 " pdb=" CB TYR B 830 " ideal model delta harmonic sigma weight residual -122.60 -131.78 9.18 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 12172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1877 0.057 - 0.114: 770 0.114 - 0.171: 325 0.171 - 0.228: 93 0.228 - 0.285: 16 Chirality restraints: 3081 Sorted by residual: chirality pdb=" CA ILE B 915 " pdb=" N ILE B 915 " pdb=" C ILE B 915 " pdb=" CB ILE B 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' ANP B1601 " pdb=" C2' ANP B1601 " pdb=" C4' ANP B1601 " pdb=" O3' ANP B1601 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3078 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 824 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C HIS B 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS B 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 824 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C HIS A 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS A 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 815 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ARG B 815 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 815 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 816 " 0.014 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2206 2.75 - 3.29: 19602 3.29 - 3.83: 31409 3.83 - 4.36: 38634 4.36 - 4.90: 62557 Nonbonded interactions: 154408 Sorted by model distance: nonbonded pdb=" O6 DG E 13 " pdb=" O13 EVP F 101 " model vdw 2.218 2.440 nonbonded pdb=" OG SER A 312 " pdb=" OG1 THR A 319 " model vdw 2.300 2.440 nonbonded pdb=" ND2 ASN B 315 " pdb=" O ILE B 368 " model vdw 2.331 2.520 nonbonded pdb=" OG SER A 304 " pdb=" O GLY A 307 " model vdw 2.337 2.440 nonbonded pdb=" OH TYR A 270 " pdb=" OH TYR A 274 " model vdw 2.341 2.440 ... (remaining 154403 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 'A' selection = (chain 'B' and (resid 29 through 345 or resid 351 through 1215 or resid 1601)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 62 5.49 5 S 92 5.16 5 C 12527 2.51 5 N 3417 2.21 5 O 3881 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.170 Process input model: 56.870 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 0.165 20511 Z= 0.601 Angle : 1.010 10.829 27943 Z= 0.737 Chirality : 0.076 0.285 3081 Planarity : 0.006 0.038 3339 Dihedral : 12.283 140.584 7821 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.17), residues: 2307 helix: 0.43 (0.17), residues: 912 sheet: -1.68 (0.29), residues: 343 loop : -2.40 (0.17), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.4237 time to fit residues: 97.0076 Evaluate side-chains 100 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 0.3980 chunk 184 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 213 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 HIS B 508 ASN ** B 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN A 420 GLN A 498 HIS A 508 ASN A 558 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 20511 Z= 0.152 Angle : 0.466 6.328 27943 Z= 0.253 Chirality : 0.038 0.236 3081 Planarity : 0.004 0.038 3339 Dihedral : 15.517 139.406 3093 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.16 (0.18), residues: 2307 helix: 0.86 (0.18), residues: 926 sheet: -1.62 (0.28), residues: 374 loop : -2.00 (0.19), residues: 1007 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.4210 time to fit residues: 67.9344 Evaluate side-chains 88 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 chunk 230 optimal weight: 0.4980 chunk 190 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 558 HIS ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 HIS B1051 GLN A 667 ASN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 HIS A 874 ASN A 875 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20511 Z= 0.208 Angle : 0.531 8.105 27943 Z= 0.285 Chirality : 0.039 0.202 3081 Planarity : 0.004 0.045 3339 Dihedral : 15.788 142.420 3093 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.98 (0.18), residues: 2307 helix: 0.86 (0.17), residues: 940 sheet: -1.56 (0.28), residues: 384 loop : -1.75 (0.19), residues: 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.3839 time to fit residues: 56.8612 Evaluate side-chains 82 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 2.327 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2231 time to fit residues: 3.5012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 8.9990 chunk 160 optimal weight: 0.0870 chunk 110 optimal weight: 0.2980 chunk 23 optimal weight: 20.0000 chunk 102 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 227 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 559 HIS ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN A 393 GLN ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 20511 Z= 0.130 Angle : 0.452 11.466 27943 Z= 0.240 Chirality : 0.038 0.462 3081 Planarity : 0.003 0.071 3339 Dihedral : 15.762 142.664 3093 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.18), residues: 2307 helix: 1.22 (0.18), residues: 925 sheet: -1.38 (0.30), residues: 362 loop : -1.67 (0.19), residues: 1020 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.3427 time to fit residues: 49.9916 Evaluate side-chains 80 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 157 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 HIS ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN A 150 ASN A 567 HIS ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1050 ASN A1051 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20511 Z= 0.189 Angle : 0.502 7.066 27943 Z= 0.269 Chirality : 0.038 0.206 3081 Planarity : 0.003 0.040 3339 Dihedral : 15.877 144.362 3093 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.18), residues: 2307 helix: 1.20 (0.18), residues: 934 sheet: -1.17 (0.31), residues: 333 loop : -1.57 (0.19), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3541 time to fit residues: 48.2396 Evaluate side-chains 78 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 50.0000 chunk 56 optimal weight: 0.9990 chunk 227 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 105 optimal weight: 0.0000 chunk 18 optimal weight: 50.0000 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 GLN B 938 GLN A 637 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 20511 Z= 0.279 Angle : 0.633 6.970 27943 Z= 0.337 Chirality : 0.041 0.281 3081 Planarity : 0.004 0.057 3339 Dihedral : 16.499 148.778 3093 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.18), residues: 2307 helix: 0.70 (0.17), residues: 942 sheet: -1.34 (0.31), residues: 327 loop : -1.56 (0.19), residues: 1038 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.223 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: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3577 time to fit residues: 48.2716 Evaluate side-chains 75 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 126 optimal weight: 50.0000 chunk 226 optimal weight: 3.9990 chunk 141 optimal weight: 20.0000 chunk 138 optimal weight: 40.0000 chunk 104 optimal weight: 5.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 20511 Z= 0.184 Angle : 0.514 7.764 27943 Z= 0.274 Chirality : 0.039 0.187 3081 Planarity : 0.003 0.046 3339 Dihedral : 16.429 148.211 3093 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.18), residues: 2307 helix: 0.92 (0.17), residues: 945 sheet: -1.37 (0.30), residues: 339 loop : -1.37 (0.20), residues: 1023 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3590 time to fit residues: 48.2459 Evaluate side-chains 76 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.2980 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 50.0000 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 50.0000 chunk 178 optimal weight: 8.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20511 Z= 0.249 Angle : 0.590 7.481 27943 Z= 0.313 Chirality : 0.040 0.219 3081 Planarity : 0.004 0.046 3339 Dihedral : 16.654 149.808 3093 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.79 (0.18), residues: 2307 helix: 0.70 (0.17), residues: 943 sheet: -1.26 (0.31), residues: 335 loop : -1.40 (0.20), residues: 1029 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3194 time to fit residues: 42.9019 Evaluate side-chains 73 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.319 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 210 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 917 ASN A 558 HIS A 637 GLN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 20511 Z= 0.154 Angle : 0.507 7.682 27943 Z= 0.268 Chirality : 0.039 0.189 3081 Planarity : 0.003 0.044 3339 Dihedral : 16.530 148.931 3093 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.18), residues: 2307 helix: 0.95 (0.17), residues: 951 sheet: -1.31 (0.30), residues: 344 loop : -1.29 (0.20), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.3265 time to fit residues: 43.3392 Evaluate side-chains 74 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 155 optimal weight: 0.3980 chunk 234 optimal weight: 50.0000 chunk 215 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 917 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 20511 Z= 0.223 Angle : 0.569 7.790 27943 Z= 0.301 Chirality : 0.040 0.188 3081 Planarity : 0.004 0.041 3339 Dihedral : 16.642 149.268 3093 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.18), residues: 2307 helix: 0.76 (0.17), residues: 952 sheet: -1.51 (0.29), residues: 363 loop : -1.24 (0.21), residues: 992 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4614 Ramachandran restraints generated. 2307 Oldfield, 0 Emsley, 2307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3401 time to fit residues: 44.0399 Evaluate side-chains 73 residues out of total 2076 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 27 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 GLN B 834 GLN B 917 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.035945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.022708 restraints weight = 329364.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.023155 restraints weight = 214102.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.023428 restraints weight = 155847.550| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 20511 Z= 0.197 Angle : 0.542 7.662 27943 Z= 0.287 Chirality : 0.039 0.188 3081 Planarity : 0.003 0.044 3339 Dihedral : 16.690 149.474 3093 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.18), residues: 2307 helix: 0.85 (0.17), residues: 942 sheet: -1.52 (0.29), residues: 351 loop : -1.16 (0.21), residues: 1014 =============================================================================== Job complete usr+sys time: 2868.36 seconds wall clock time: 54 minutes 42.03 seconds (3282.03 seconds total)