Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 18:33:54 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/12_2021/5mz6_3583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/12_2021/5mz6_3583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/12_2021/5mz6_3583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/12_2021/5mz6_3583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/12_2021/5mz6_3583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mz6_3583/12_2021/5mz6_3583.pdb" } resolution = 3.8 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 "1 ARG 20": "NH1" <-> "NH2" Residue "1 ARG 84": "NH1" <-> "NH2" Residue "1 ARG 153": "NH1" <-> "NH2" Residue "1 ARG 217": "NH1" <-> "NH2" Residue "1 ARG 252": "NH1" <-> "NH2" Residue "1 ARG 315": "NH1" <-> "NH2" Residue "1 ARG 492": "NH1" <-> "NH2" Residue "1 ARG 494": "NH1" <-> "NH2" Residue "1 ARG 504": "NH1" <-> "NH2" Residue "1 ARG 559": "NH1" <-> "NH2" Residue "1 ARG 631": "NH1" <-> "NH2" Residue "1 ARG 691": "NH1" <-> "NH2" Residue "1 ARG 697": "NH1" <-> "NH2" Residue "1 ARG 869": "NH1" <-> "NH2" Residue "1 ARG 930": "NH1" <-> "NH2" Residue "1 ARG 1044": "NH1" <-> "NH2" Residue "1 ARG 1116": "NH1" <-> "NH2" Residue "1 ARG 1120": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 8401 Number of models: 1 Model: "" Number of chains: 2 Chain: "1" Number of atoms: 7968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7968 Classifications: {'peptide': 1018} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 32, 'TRANS': 985} Chain breaks: 4 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 433 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 106 Time building chain proxies: 5.05, per 1000 atoms: 0.60 Number of scatterers: 8401 At special positions: 0 Unit cell: (88.66, 124.41, 74.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1535 8.00 N 1457 7.00 C 5339 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 11031 " - pdb=" SG CYS 11066 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 3.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2090 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 63.6% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain '1' and resid 12 through 41 removed outlier: 3.938A pdb=" N LEU 1 16 " --> pdb=" O HIS 1 12 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU 1 18 " --> pdb=" O GLU 1 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS 1 21 " --> pdb=" O ASP 1 17 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 49 removed outlier: 4.045A pdb=" N ILE 1 46 " --> pdb=" O SER 1 42 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 56 through 58 No H-bonds generated for 'chain '1' and resid 56 through 58' Processing helix chain '1' and resid 59 through 72 removed outlier: 3.940A pdb=" N ARG 1 65 " --> pdb=" O SER 1 61 " (cutoff:3.500A) Processing helix chain '1' and resid 78 through 96 removed outlier: 4.198A pdb=" N TYR 1 82 " --> pdb=" O GLY 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 102 Processing helix chain '1' and resid 103 through 104 No H-bonds generated for 'chain '1' and resid 103 through 104' Processing helix chain '1' and resid 105 through 109 removed outlier: 3.531A pdb=" N ARG 1 108 " --> pdb=" O SER 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 125 removed outlier: 3.955A pdb=" N LEU 1 118 " --> pdb=" O ILE 1 114 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE 1 123 " --> pdb=" O CYS 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 127 through 143 removed outlier: 4.068A pdb=" N VAL 1 133 " --> pdb=" O CYS 1 129 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS 1 134 " --> pdb=" O ARG 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 144 through 149 Processing helix chain '1' and resid 150 through 158 removed outlier: 3.820A pdb=" N LEU 1 155 " --> pdb=" O ALA 1 151 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET 1 156 " --> pdb=" O LEU 1 152 " (cutoff:3.500A) Processing helix chain '1' and resid 160 through 171 removed outlier: 3.751A pdb=" N ILE 1 164 " --> pdb=" O GLU 1 160 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU 1 165 " --> pdb=" O THR 1 161 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS 1 166 " --> pdb=" O GLU 1 162 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 1 170 " --> pdb=" O LYS 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 193 removed outlier: 3.630A pdb=" N ALA 1 183 " --> pdb=" O ASP 1 179 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR 1 184 " --> pdb=" O MET 1 180 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU 1 191 " --> pdb=" O ALA 1 187 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS 1 192 " --> pdb=" O MET 1 188 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS 1 193 " --> pdb=" O ASN 1 189 " (cutoff:3.500A) Processing helix chain '1' and resid 198 through 214 removed outlier: 3.848A pdb=" N GLU 1 202 " --> pdb=" O VAL 1 198 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP 1 209 " --> pdb=" O MET 1 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS 1 212 " --> pdb=" O ARG 1 208 " (cutoff:3.500A) Processing helix chain '1' and resid 218 through 232 removed outlier: 3.701A pdb=" N TYR 1 227 " --> pdb=" O GLU 1 223 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER 1 229 " --> pdb=" O ALA 1 225 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 237 removed outlier: 4.267A pdb=" N SER 1 236 " --> pdb=" O SER 1 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN 1 237 " --> pdb=" O THR 1 234 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 233 through 237' Processing helix chain '1' and resid 251 through 257 removed outlier: 4.165A pdb=" N HIS 1 255 " --> pdb=" O ASP 1 251 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN 1 257 " --> pdb=" O VAL 1 253 " (cutoff:3.500A) Processing helix chain '1' and resid 258 through 271 removed outlier: 3.613A pdb=" N SER 1 263 " --> pdb=" O ALA 1 259 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP 1 264 " --> pdb=" O ALA 1 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL 1 267 " --> pdb=" O SER 1 263 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG 1 268 " --> pdb=" O ASP 1 264 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN 1 269 " --> pdb=" O SER 1 265 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG 1 270 " --> pdb=" O LEU 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 275 removed outlier: 4.123A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 272 through 275' Processing helix chain '1' and resid 304 through 321 removed outlier: 3.634A pdb=" N ILE 1 308 " --> pdb=" O ILE 1 304 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU 1 317 " --> pdb=" O GLU 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 329 through 346 removed outlier: 3.564A pdb=" N ALA 1 334 " --> pdb=" O ASP 1 330 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE 1 336 " --> pdb=" O MET 1 332 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN 1 338 " --> pdb=" O ALA 1 334 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL 1 341 " --> pdb=" O LEU 1 337 " (cutoff:3.500A) Processing helix chain '1' and resid 347 through 365 removed outlier: 3.632A pdb=" N THR 1 354 " --> pdb=" O ARG 1 350 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR 1 357 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER 1 362 " --> pdb=" O LEU 1 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER 1 363 " --> pdb=" O ALA 1 359 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 386 removed outlier: 4.175A pdb=" N VAL 1 379 " --> pdb=" O LYS 1 375 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER 1 380 " --> pdb=" O LEU 1 376 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL 1 382 " --> pdb=" O ARG 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 451 through 456 removed outlier: 3.897A pdb=" N ILE 1 455 " --> pdb=" O ASN 1 451 " (cutoff:3.500A) Processing helix chain '1' and resid 459 through 475 removed outlier: 3.563A pdb=" N ALA 1 464 " --> pdb=" O SER 1 460 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET 1 467 " --> pdb=" O ALA 1 463 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 495 removed outlier: 3.545A pdb=" N ASP 1 486 " --> pdb=" O LYS 1 482 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU 1 487 " --> pdb=" O HIS 1 483 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 1 489 " --> pdb=" O ASN 1 485 " (cutoff:3.500A) Processing helix chain '1' and resid 495 through 504 removed outlier: 3.829A pdb=" N GLN 1 499 " --> pdb=" O GLY 1 495 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET 1 502 " --> pdb=" O SER 1 498 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS 1 503 " --> pdb=" O GLN 1 499 " (cutoff:3.500A) Processing helix chain '1' and resid 513 through 535 removed outlier: 3.519A pdb=" N LYS 1 530 " --> pdb=" O ARG 1 526 " (cutoff:3.500A) Processing helix chain '1' and resid 539 through 554 removed outlier: 3.960A pdb=" N MET 1 543 " --> pdb=" O ASP 1 539 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS 1 551 " --> pdb=" O ASN 1 547 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL 1 553 " --> pdb=" O ALA 1 549 " (cutoff:3.500A) Processing helix chain '1' and resid 560 through 576 removed outlier: 3.826A pdb=" N ALA 1 566 " --> pdb=" O ASP 1 562 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL 1 567 " --> pdb=" O MET 1 563 " (cutoff:3.500A) Processing helix chain '1' and resid 629 through 645 removed outlier: 3.987A pdb=" N VAL 1 635 " --> pdb=" O ARG 1 631 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG 1 636 " --> pdb=" O PHE 1 632 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA 1 638 " --> pdb=" O LYS 1 634 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN 1 641 " --> pdb=" O LEU 1 637 " (cutoff:3.500A) Processing helix chain '1' and resid 651 through 666 removed outlier: 3.589A pdb=" N ARG 1 657 " --> pdb=" O GLU 1 653 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA 1 660 " --> pdb=" O CYS 1 656 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR 1 661 " --> pdb=" O ARG 1 657 " (cutoff:3.500A) Processing helix chain '1' and resid 669 through 679 removed outlier: 3.604A pdb=" N TYR 1 674 " --> pdb=" O TRP 1 670 " (cutoff:3.500A) Processing helix chain '1' and resid 681 through 693 removed outlier: 3.903A pdb=" N ALA 1 687 " --> pdb=" O GLY 1 683 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 1 688 " --> pdb=" O ALA 1 684 " (cutoff:3.500A) Processing helix chain '1' and resid 703 through 715 removed outlier: 3.630A pdb=" N ARG 1 707 " --> pdb=" O SER 1 703 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR 1 710 " --> pdb=" O ASP 1 706 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS 1 711 " --> pdb=" O ARG 1 707 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 1 712 " --> pdb=" O PHE 1 708 " (cutoff:3.500A) Processing helix chain '1' and resid 751 through 774 removed outlier: 3.645A pdb=" N LYS 1 760 " --> pdb=" O GLU 1 756 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 1 767 " --> pdb=" O PHE 1 763 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP 1 768 " --> pdb=" O LEU 1 764 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 1 771 " --> pdb=" O GLU 1 767 " (cutoff:3.500A) Processing helix chain '1' and resid 779 through 805 removed outlier: 3.597A pdb=" N TRP 1 784 " --> pdb=" O PRO 1 780 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG 1 787 " --> pdb=" O PHE 1 783 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE 1 789 " --> pdb=" O LYS 1 785 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 1 790 " --> pdb=" O ARG 1 786 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP 1 799 " --> pdb=" O MET 1 795 " (cutoff:3.500A) Processing helix chain '1' and resid 806 through 814 removed outlier: 3.626A pdb=" N ALA 1 810 " --> pdb=" O GLY 1 807 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET 1 814 " --> pdb=" O SER 1 811 " (cutoff:3.500A) Processing helix chain '1' and resid 823 through 834 removed outlier: 3.628A pdb=" N ALA 1 827 " --> pdb=" O ALA 1 823 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE 1 828 " --> pdb=" O ALA 1 824 " (cutoff:3.500A) Processing helix chain '1' and resid 839 through 847 removed outlier: 3.869A pdb=" N GLU 1 845 " --> pdb=" O GLY 1 841 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET 1 846 " --> pdb=" O GLU 1 842 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL 1 847 " --> pdb=" O ALA 1 843 " (cutoff:3.500A) Processing helix chain '1' and resid 854 through 867 removed outlier: 3.605A pdb=" N LEU 1 863 " --> pdb=" O GLU 1 859 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS 1 866 " --> pdb=" O ILE 1 862 " (cutoff:3.500A) Processing helix chain '1' and resid 872 through 878 removed outlier: 3.572A pdb=" N LYS 1 876 " --> pdb=" O ASP 1 872 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER 1 877 " --> pdb=" O GLU 1 873 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE 1 878 " --> pdb=" O LYS 1 874 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 872 through 878' Processing helix chain '1' and resid 879 through 891 removed outlier: 4.012A pdb=" N HIS 1 883 " --> pdb=" O LEU 1 879 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU 1 888 " --> pdb=" O ARG 1 884 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN 1 891 " --> pdb=" O VAL 1 887 " (cutoff:3.500A) Processing helix chain '1' and resid 933 through 947 Processing helix chain '1' and resid 956 through 959 removed outlier: 3.873A pdb=" N ASN 1 959 " --> pdb=" O ASP 1 956 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 956 through 959' Processing helix chain '1' and resid 965 through 969 removed outlier: 3.755A pdb=" N ASN 1 968 " --> pdb=" O ASP 1 965 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN 1 969 " --> pdb=" O PRO 1 966 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 965 through 969' Processing helix chain '1' and resid 971 through 984 removed outlier: 3.636A pdb=" N LYS 1 975 " --> pdb=" O GLY 1 971 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL 1 978 " --> pdb=" O GLN 1 974 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU 1 979 " --> pdb=" O LYS 1 975 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR 1 980 " --> pdb=" O ARG 1 976 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 1 983 " --> pdb=" O GLU 1 979 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE 1 984 " --> pdb=" O TYR 1 980 " (cutoff:3.500A) Processing helix chain '1' and resid 995 through 1006 Processing helix chain '1' and resid 1022 through 1027 removed outlier: 3.683A pdb=" N LEU 11026 " --> pdb=" O PRO 11022 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS 11027 " --> pdb=" O ARG 11023 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 1022 through 1027' Processing helix chain '1' and resid 1057 through 1064 removed outlier: 3.683A pdb=" N TYR 11061 " --> pdb=" O ALA 11057 " (cutoff:3.500A) Processing helix chain '1' and resid 1079 through 1094 removed outlier: 3.517A pdb=" N ASP 11090 " --> pdb=" O ILE 11086 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP 11091 " --> pdb=" O ARG 11087 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE 11093 " --> pdb=" O ILE 11089 " (cutoff:3.500A) Processing helix chain '1' and resid 1107 through 1119 removed outlier: 3.595A pdb=" N HIS 11113 " --> pdb=" O SER 11109 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER 11117 " --> pdb=" O HIS 11113 " (cutoff:3.500A) Processing helix chain '1' and resid 1125 through 1129 removed outlier: 3.753A pdb=" N VAL 11129 " --> pdb=" O GLY 11126 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 176 removed outlier: 3.543A pdb=" N ALA B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 744 through 750 removed outlier: 7.004A pdb=" N ILE 1 732 " --> pdb=" O LEU 1 748 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN 1 931 " --> pdb=" O THR 1 903 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU 1 905 " --> pdb=" O GLN 1 931 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 953 through 955 removed outlier: 5.257A pdb=" N LEU 1 953 " --> pdb=" O VAL 11137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '1' and resid 987 through 990 removed outlier: 3.942A pdb=" N THR 1 989 " --> pdb=" O TYR 1 962 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU 1 964 " --> pdb=" O THR 1 989 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2719 1.34 - 1.46: 1952 1.46 - 1.58: 3780 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 8566 Sorted by residual: bond pdb=" C ARG B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.30e+00 bond pdb=" C LEU 1 879 " pdb=" N PRO 1 880 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.11e-02 8.12e+03 3.20e+00 bond pdb=" C LEU 11134 " pdb=" N PRO 11135 " ideal model delta sigma weight residual 1.331 1.354 -0.023 1.31e-02 5.83e+03 3.17e+00 bond pdb=" CB ASP 1 137 " pdb=" CG ASP 1 137 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.03e+00 bond pdb=" C ILE 1 114 " pdb=" N PRO 1 115 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.70e+00 ... (remaining 8561 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.81: 161 105.81 - 112.87: 4512 112.87 - 119.93: 2845 119.93 - 126.99: 3965 126.99 - 134.05: 102 Bond angle restraints: 11585 Sorted by residual: angle pdb=" N PRO B 148 " pdb=" CA PRO B 148 " pdb=" CB PRO B 148 " ideal model delta sigma weight residual 103.36 110.53 -7.17 8.80e-01 1.29e+00 6.64e+01 angle pdb=" N PRO B 168 " pdb=" CA PRO B 168 " pdb=" CB PRO B 168 " ideal model delta sigma weight residual 103.08 110.27 -7.19 9.70e-01 1.06e+00 5.50e+01 angle pdb=" N PRO B 169 " pdb=" CA PRO B 169 " pdb=" CB PRO B 169 " ideal model delta sigma weight residual 103.25 109.99 -6.74 1.05e+00 9.07e-01 4.12e+01 angle pdb=" N PRO B 172 " pdb=" CA PRO B 172 " pdb=" CB PRO B 172 " ideal model delta sigma weight residual 103.44 110.10 -6.66 1.12e+00 7.97e-01 3.53e+01 angle pdb=" CA ALA 11064 " pdb=" C ALA 11064 " pdb=" O ALA 11064 " ideal model delta sigma weight residual 119.43 113.44 5.99 1.21e+00 6.83e-01 2.45e+01 ... (remaining 11580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 4813 15.03 - 30.07: 263 30.07 - 45.10: 94 45.10 - 60.13: 12 60.13 - 75.16: 6 Dihedral angle restraints: 5188 sinusoidal: 1973 harmonic: 3215 Sorted by residual: dihedral pdb=" CA ILE 1 951 " pdb=" C ILE 1 951 " pdb=" N PRO 1 952 " pdb=" CA PRO 1 952 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA HIS 1 255 " pdb=" C HIS 1 255 " pdb=" N ILE 1 256 " pdb=" CA ILE 1 256 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PRO B 141 " pdb=" C PRO B 141 " pdb=" N TYR B 142 " pdb=" CA TYR B 142 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 5185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1098 0.065 - 0.131: 185 0.131 - 0.196: 21 0.196 - 0.261: 4 0.261 - 0.327: 2 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CB VAL 1 928 " pdb=" CA VAL 1 928 " pdb=" CG1 VAL 1 928 " pdb=" CG2 VAL 1 928 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB ILE 1 271 " pdb=" CA ILE 1 271 " pdb=" CG1 ILE 1 271 " pdb=" CG2 ILE 1 271 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA PRO B 169 " pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CB PRO B 169 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1307 not shown) Planarity restraints: 1473 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 1 951 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO 1 952 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO 1 952 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO 1 952 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR 1 733 " -0.016 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR 1 733 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR 1 733 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 1 733 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR 1 733 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR 1 733 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR 1 733 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR 1 733 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 484 " -0.018 2.00e-02 2.50e+03 1.72e-02 5.19e+00 pdb=" CG PHE 1 484 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 484 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 484 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 484 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 484 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE 1 484 " 0.001 2.00e-02 2.50e+03 ... (remaining 1470 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2343 2.79 - 3.32: 8018 3.32 - 3.85: 13964 3.85 - 4.37: 17024 4.37 - 4.90: 28108 Nonbonded interactions: 69457 Sorted by model distance: nonbonded pdb=" OH TYR 1 902 " pdb=" OE1 GLN 11107 " model vdw 2.269 2.440 nonbonded pdb=" O ILE 1 934 " pdb=" OG1 THR 1 937 " model vdw 2.279 2.440 nonbonded pdb=" CB ALA 1 772 " pdb=" OD2 ASP B 125 " model vdw 2.288 3.460 nonbonded pdb=" O ASP 1 539 " pdb=" OG1 THR 1 542 " model vdw 2.327 2.440 nonbonded pdb=" OH TYR 1 124 " pdb=" O SER 1 345 " model vdw 2.331 2.440 ... (remaining 69452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5339 2.51 5 N 1457 2.21 5 O 1535 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 Write .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: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.040 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 25.040 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 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 : 0.005 0.053 8566 Z= 0.354 Angle : 1.046 14.517 11585 Z= 0.613 Chirality : 0.051 0.327 1310 Planarity : 0.007 0.071 1473 Dihedral : 11.570 75.163 3095 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -5.37 (0.18), residues: 1080 helix: -4.17 (0.10), residues: 573 sheet: -2.86 (0.74), residues: 45 loop : -2.57 (0.24), residues: 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 319 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 319 average time/residue: 0.2253 time to fit residues: 95.3850 Evaluate side-chains 206 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 33 GLN 1 38 GLN 1 58 ASN 1 303 HIS 1 311 HIS 1 338 ASN 1 353 GLN 1 383 ASN 1 483 HIS 1 517 ASN ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 705 HIS 1 713 GLN 1 818 GLN 1 913 GLN 1 935 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8566 Z= 0.195 Angle : 0.633 8.147 11585 Z= 0.326 Chirality : 0.040 0.155 1310 Planarity : 0.005 0.057 1473 Dihedral : 5.448 26.873 1184 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 3.24 % 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: -3.36 (0.21), residues: 1080 helix: -2.11 (0.16), residues: 610 sheet: -2.00 (0.79), residues: 45 loop : -2.22 (0.27), residues: 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 247 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 264 average time/residue: 0.2047 time to fit residues: 74.7400 Evaluate side-chains 216 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0827 time to fit residues: 3.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 237 ASN 1 303 HIS ** 1 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 485 ASN ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 713 GLN 1 910 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8566 Z= 0.205 Angle : 0.633 7.982 11585 Z= 0.315 Chirality : 0.041 0.167 1310 Planarity : 0.005 0.126 1473 Dihedral : 5.039 26.954 1184 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 3.36 % 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: -1.89 (0.24), residues: 1080 helix: -0.82 (0.19), residues: 604 sheet: -0.49 (0.92), residues: 40 loop : -1.83 (0.28), residues: 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 237 average time/residue: 0.1887 time to fit residues: 62.3343 Evaluate side-chains 215 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0842 time to fit residues: 3.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 104 optimal weight: 30.0000 chunk 51 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 303 HIS 1 353 GLN ** 1 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 883 HIS ** 1 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8566 Z= 0.191 Angle : 0.621 13.725 11585 Z= 0.309 Chirality : 0.040 0.148 1310 Planarity : 0.004 0.079 1473 Dihedral : 4.839 26.243 1184 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 1.74 % 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: -1.22 (0.25), residues: 1080 helix: -0.22 (0.20), residues: 615 sheet: -0.06 (0.94), residues: 40 loop : -1.67 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 223 average time/residue: 0.2050 time to fit residues: 63.4934 Evaluate side-chains 204 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0848 time to fit residues: 2.5329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 8566 Z= 0.321 Angle : 0.704 13.161 11585 Z= 0.353 Chirality : 0.044 0.203 1310 Planarity : 0.005 0.065 1473 Dihedral : 5.093 26.548 1184 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 3.13 % 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: -1.06 (0.25), residues: 1080 helix: -0.08 (0.20), residues: 607 sheet: -0.92 (0.86), residues: 45 loop : -1.49 (0.30), residues: 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 1.038 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 223 average time/residue: 0.1924 time to fit residues: 60.4536 Evaluate side-chains 207 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0851 time to fit residues: 3.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN 1 644 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 892 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 8566 Z= 0.198 Angle : 0.629 10.749 11585 Z= 0.314 Chirality : 0.040 0.135 1310 Planarity : 0.006 0.122 1473 Dihedral : 4.785 25.542 1184 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.04 % 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 (0.26), residues: 1080 helix: 0.29 (0.21), residues: 615 sheet: 0.16 (0.90), residues: 40 loop : -1.36 (0.31), residues: 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 219 average time/residue: 0.1889 time to fit residues: 58.9735 Evaluate side-chains 195 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0842 time to fit residues: 1.9184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN 1 573 GLN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 8566 Z= 0.200 Angle : 0.654 16.206 11585 Z= 0.319 Chirality : 0.040 0.129 1310 Planarity : 0.005 0.095 1473 Dihedral : 4.699 25.404 1184 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 2.09 % 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: -0.40 (0.26), residues: 1080 helix: 0.46 (0.21), residues: 613 sheet: 0.31 (0.89), residues: 40 loop : -1.34 (0.30), residues: 427 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 214 average time/residue: 0.1984 time to fit residues: 59.7550 Evaluate side-chains 200 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0801 time to fit residues: 2.9697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.0030 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 517 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 892 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8566 Z= 0.180 Angle : 0.666 17.137 11585 Z= 0.322 Chirality : 0.040 0.135 1310 Planarity : 0.005 0.083 1473 Dihedral : 4.533 24.265 1184 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.93 % 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: -0.28 (0.26), residues: 1080 helix: 0.57 (0.21), residues: 615 sheet: 0.67 (0.88), residues: 40 loop : -1.35 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 208 average time/residue: 0.1871 time to fit residues: 55.4017 Evaluate side-chains 196 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0854 time to fit residues: 2.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 303 HIS 1 517 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 892 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8566 Z= 0.212 Angle : 0.686 16.353 11585 Z= 0.333 Chirality : 0.040 0.138 1310 Planarity : 0.005 0.078 1473 Dihedral : 4.556 24.148 1184 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.46 % 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: -0.24 (0.26), residues: 1080 helix: 0.60 (0.21), residues: 614 sheet: 0.76 (0.88), residues: 40 loop : -1.34 (0.30), residues: 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 200 average time/residue: 0.2009 time to fit residues: 56.2620 Evaluate side-chains 192 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0879 time to fit residues: 1.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 0.0570 chunk 99 optimal weight: 0.0060 chunk 85 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.5514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 517 ASN ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8566 Z= 0.200 Angle : 0.691 16.319 11585 Z= 0.335 Chirality : 0.040 0.156 1310 Planarity : 0.005 0.075 1473 Dihedral : 4.523 23.909 1184 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.46 % 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: -0.14 (0.26), residues: 1080 helix: 0.67 (0.21), residues: 615 sheet: 0.86 (0.88), residues: 40 loop : -1.28 (0.30), residues: 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 196 average time/residue: 0.1956 time to fit residues: 54.2655 Evaluate side-chains 190 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0950 time to fit residues: 1.8534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124318 restraints weight = 14695.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127078 restraints weight = 9065.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129038 restraints weight = 6385.557| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 8566 Z= 0.207 Angle : 0.697 16.165 11585 Z= 0.338 Chirality : 0.041 0.170 1310 Planarity : 0.005 0.073 1473 Dihedral : 4.545 23.889 1184 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.70 % 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: -0.05 (0.26), residues: 1080 helix: 0.80 (0.21), residues: 606 sheet: 1.00 (0.89), residues: 40 loop : -1.32 (0.30), residues: 434 =============================================================================== Job complete usr+sys time: 2017.79 seconds wall clock time: 37 minutes 21.16 seconds (2241.16 seconds total)