Starting phenix.real_space_refine (version: dev) on Fri Feb 24 21:44:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf2_14696/02_2023/7zf2_14696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf2_14696/02_2023/7zf2_14696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf2_14696/02_2023/7zf2_14696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf2_14696/02_2023/7zf2_14696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf2_14696/02_2023/7zf2_14696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zf2_14696/02_2023/7zf2_14696.pdb" } resolution = 3.86 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23822 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1704 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1781 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8699 Classifications: {'peptide': 1122} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1059} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 9879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1264, 9879 Classifications: {'peptide': 1264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1203} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 637 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 74} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1119 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19233 SG CYS D 891 77.823 25.379 97.890 1.00 77.37 S ATOM 19807 SG CYS D 968 78.667 28.744 97.624 1.00 71.40 S ATOM 19849 SG CYS D 975 74.930 27.669 98.642 1.00 61.72 S ATOM 19867 SG CYS D 978 77.642 27.763 101.091 1.00 63.75 S ATOM 12660 SG CYS D 60 66.937 42.577 33.661 1.00154.40 S ATOM 12678 SG CYS D 62 68.408 42.874 30.301 1.00163.42 S ATOM 12787 SG CYS D 75 67.845 39.336 31.624 1.00153.90 S ATOM 12813 SG CYS D 78 70.576 41.436 33.031 1.00153.87 S Time building chain proxies: 13.45, per 1000 atoms: 0.56 Number of scatterers: 23822 At special positions: 0 Unit cell: (181.5, 132, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 87 16.00 Mg 1 11.99 O 4567 8.00 N 4230 7.00 C 14935 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: 9.59 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1401 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 978 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 968 " pdb="ZN ZN D1401 " - pdb=" SG CYS D 975 " pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " Number of angles added : 12 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5638 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 41 sheets defined 41.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.845A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.095A pdb=" N SER A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.547A pdb=" N ARG A 153 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 154 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 155 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 156 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.205A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.726A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.719A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 83 " --> pdb=" O ASN B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.835A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.086A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE C 61 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 78 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 removed outlier: 4.018A pdb=" N ARG C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 302 removed outlier: 3.968A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 350 Processing helix chain 'C' and resid 380 through 407 removed outlier: 4.084A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.997A pdb=" N PHE C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.641A pdb=" N ARG C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.865A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 564 through 566 No H-bonds generated for 'chain 'C' and resid 564 through 566' Processing helix chain 'C' and resid 582 through 587 removed outlier: 4.546A pdb=" N MET C 586 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 587 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 3.575A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 610 removed outlier: 3.542A pdb=" N MET C 607 " --> pdb=" O ASN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.590A pdb=" N ALA C 615 " --> pdb=" O GLN C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 639 removed outlier: 4.480A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 779 through 783 removed outlier: 3.592A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP C 783 " --> pdb=" O VAL C 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 779 through 783' Processing helix chain 'C' and resid 815 through 825 removed outlier: 3.688A pdb=" N PHE C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 900 through 904 removed outlier: 3.586A pdb=" N MET C 904 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 926 removed outlier: 3.823A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 removed outlier: 3.516A pdb=" N LEU C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 960 through 964 Processing helix chain 'C' and resid 981 through 990 removed outlier: 3.604A pdb=" N SER C 990 " --> pdb=" O GLN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1040 removed outlier: 3.702A pdb=" N ASP C1039 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1079 removed outlier: 3.787A pdb=" N TYR C1079 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing helix chain 'C' and resid 1082 through 1090 Processing helix chain 'C' and resid 1097 through 1109 Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.613A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 104 through 109 removed outlier: 3.524A pdb=" N GLY D 109 " --> pdb=" O TRP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 188 removed outlier: 4.950A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.786A pdb=" N LYS D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 285 through 306 removed outlier: 3.774A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY D 306 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 338 through 359 removed outlier: 3.942A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 401 through 406 Processing helix chain 'D' and resid 445 through 452 removed outlier: 4.395A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.020A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 488 " --> pdb=" O TRP D 484 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 589 removed outlier: 4.162A pdb=" N THR D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 3.592A pdb=" N MET D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 removed outlier: 3.681A pdb=" N GLU D 649 " --> pdb=" O GLU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.643A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 725 removed outlier: 3.600A pdb=" N VAL D 709 " --> pdb=" O PRO D 705 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 741 through 762 Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.974A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.945A pdb=" N ARG D 857 " --> pdb=" O THR D 853 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LYS D 858 " --> pdb=" O HIS D 854 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP D 869 " --> pdb=" O LEU D 865 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY D 871 " --> pdb=" O THR D 867 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 873 " --> pdb=" O ASP D 869 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR D 874 " --> pdb=" O SER D 870 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 876 " --> pdb=" O TYR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 3.632A pdb=" N ALA D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 995 through 1005 Processing helix chain 'D' and resid 1006 through 1009 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1146 removed outlier: 3.593A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.087A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D1157 " --> pdb=" O HIS D1153 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1197 Processing helix chain 'D' and resid 1209 through 1216 removed outlier: 3.618A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1240 removed outlier: 3.604A pdb=" N ASN D1239 " --> pdb=" O ASP D1235 " (cutoff:3.500A) Processing helix chain 'D' and resid 1248 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.980A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 4.030A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 101 removed outlier: 3.515A pdb=" N ILE E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 43 through 65 removed outlier: 4.148A pdb=" N GLU F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG F 51 " --> pdb=" O GLU F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 89 Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing helix chain 'F' and resid 94 through 104 removed outlier: 4.083A pdb=" N SER F 100 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.254A pdb=" N GLN F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 157 removed outlier: 3.673A pdb=" N TRP F 145 " --> pdb=" O TYR F 141 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN F 148 " --> pdb=" O TRP F 144 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 5.917A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 99 removed outlier: 7.545A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 141 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.869A pdb=" N GLU B 24 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 10 removed outlier: 3.869A pdb=" N GLU B 24 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.741A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.772A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 removed outlier: 7.028A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.513A pdb=" N THR C 136 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB4, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.663A pdb=" N SER C 177 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB6, first strand: chain 'C' and resid 212 through 216 Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 3.516A pdb=" N LYS C 518 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.946A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.533A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 676 through 677 removed outlier: 3.645A pdb=" N ALA C 676 " --> pdb=" O ALA C 684 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 3.970A pdb=" N ALA C 886 " --> pdb=" O MET C1031 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR C1024 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 750 through 760 removed outlier: 3.647A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 removed outlier: 3.538A pdb=" N GLU C 768 " --> pdb=" O VAL C 806 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 806 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.597A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1042 through 1044 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.677A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.704A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS D 420 " --> pdb=" O PHE C1068 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1144 through 1145 removed outlier: 4.420A pdb=" N VAL C1137 " --> pdb=" O ILE C1145 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.080A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 11.001A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 135 through 139 removed outlier: 7.167A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD7, first strand: chain 'D' and resid 392 through 393 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE1, first strand: chain 'D' and resid 897 through 900 removed outlier: 4.521A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 902 through 903 Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1080 removed outlier: 3.724A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D1105 " --> pdb=" O GLY D1051 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 1034 hydrogen bonds defined for protein. 2865 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: 10.48 Time building geometry restraints manager: 10.33 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: 8231 1.34 - 1.46: 4805 1.46 - 1.58: 11034 1.58 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 24223 Sorted by residual: bond pdb=" CA SER D 805 " pdb=" C SER D 805 " ideal model delta sigma weight residual 1.524 1.470 0.053 2.25e-02 1.98e+03 5.59e+00 bond pdb=" CB VAL D 543 " pdb=" CG2 VAL D 543 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB ILE D 509 " pdb=" CG2 ILE D 509 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB THR D 583 " pdb=" CG2 THR D 583 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" CB LYS D1152 " pdb=" CG LYS D1152 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.80e+00 ... (remaining 24218 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.79: 618 105.79 - 112.85: 13189 112.85 - 119.91: 8343 119.91 - 126.97: 10411 126.97 - 134.03: 252 Bond angle restraints: 32813 Sorted by residual: angle pdb=" N GLY E 34 " pdb=" CA GLY E 34 " pdb=" C GLY E 34 " ideal model delta sigma weight residual 110.77 116.82 -6.05 1.93e+00 2.68e-01 9.82e+00 angle pdb=" C PRO C 725 " pdb=" N TRP C 726 " pdb=" CA TRP C 726 " ideal model delta sigma weight residual 122.76 118.34 4.42 1.63e+00 3.76e-01 7.35e+00 angle pdb=" C VAL D 880 " pdb=" CA VAL D 880 " pdb=" CB VAL D 880 " ideal model delta sigma weight residual 112.16 108.04 4.12 1.63e+00 3.76e-01 6.38e+00 angle pdb=" C PHE C 554 " pdb=" N VAL C 555 " pdb=" CA VAL C 555 " ideal model delta sigma weight residual 122.97 120.65 2.32 9.80e-01 1.04e+00 5.62e+00 angle pdb=" C LEU B 43 " pdb=" N SER B 44 " pdb=" CA SER B 44 " ideal model delta sigma weight residual 122.50 118.22 4.28 1.82e+00 3.02e-01 5.53e+00 ... (remaining 32808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13562 17.93 - 35.85: 1037 35.85 - 53.78: 205 53.78 - 71.71: 34 71.71 - 89.64: 13 Dihedral angle restraints: 14851 sinusoidal: 6076 harmonic: 8775 Sorted by residual: dihedral pdb=" CA GLY D 855 " pdb=" C GLY D 855 " pdb=" N ALA D 856 " pdb=" CA ALA D 856 " ideal model delta harmonic sigma weight residual -180.00 -157.98 -22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ARG D 414 " pdb=" C ARG D 414 " pdb=" N GLN D 415 " pdb=" CA GLN D 415 " ideal model delta harmonic sigma weight residual 180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY C 979 " pdb=" C GLY C 979 " pdb=" N ALA C 980 " pdb=" CA ALA C 980 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 14848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1951 0.029 - 0.059: 1104 0.059 - 0.088: 451 0.088 - 0.117: 194 0.117 - 0.146: 35 Chirality restraints: 3735 Sorted by residual: chirality pdb=" CA ILE C 594 " pdb=" N ILE C 594 " pdb=" C ILE C 594 " pdb=" CB ILE C 594 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA PHE C 300 " pdb=" N PHE C 300 " pdb=" C PHE C 300 " pdb=" CB PHE C 300 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE D 832 " pdb=" N ILE D 832 " pdb=" C ILE D 832 " pdb=" CB ILE D 832 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 3732 not shown) Planarity restraints: 4333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 24 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 25 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO D 321 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 815 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO C 816 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 816 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 816 " 0.023 5.00e-02 4.00e+02 ... (remaining 4330 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1048 2.71 - 3.26: 24549 3.26 - 3.80: 36677 3.80 - 4.35: 42734 4.35 - 4.90: 74852 Nonbonded interactions: 179860 Sorted by model distance: nonbonded pdb=" OG1 THR B 74 " pdb=" OE1 GLU B 75 " model vdw 2.162 2.440 nonbonded pdb=" OE2 GLU D 81 " pdb=" OG1 THR D 83 " model vdw 2.211 2.440 nonbonded pdb=" OG1 THR C 356 " pdb=" OE1 GLU C 362 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR E 56 " pdb=" O GLU E 105 " model vdw 2.214 2.440 nonbonded pdb=" O LEU D1176 " pdb=" OG SER D1179 " model vdw 2.223 2.440 ... (remaining 179855 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' and (resid 3 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 226)) selection = (chain 'B' and (resid 3 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 226)) } 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 87 5.16 5 C 14935 2.51 5 N 4230 2.21 5 O 4567 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: 3.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.820 Check model and map are aligned: 0.340 Process input model: 66.290 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 24223 Z= 0.432 Angle : 0.623 6.752 32813 Z= 0.333 Chirality : 0.044 0.146 3735 Planarity : 0.004 0.045 4333 Dihedral : 13.324 89.635 9213 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 5.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.01 (0.15), residues: 3054 helix: 1.11 (0.16), residues: 1084 sheet: -0.24 (0.27), residues: 374 loop : -0.66 (0.16), residues: 1596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 331 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 88 residues processed: 451 average time/residue: 0.3775 time to fit residues: 268.1411 Evaluate side-chains 361 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 273 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 0 residues processed: 88 average time/residue: 0.2301 time to fit residues: 41.1699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 0.0570 chunk 78 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 0.0070 chunk 145 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 ASN D 415 GLN D 687 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 24223 Z= 0.155 Angle : 0.528 8.871 32813 Z= 0.272 Chirality : 0.042 0.163 3735 Planarity : 0.004 0.049 4333 Dihedral : 4.012 19.038 3368 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.34 (0.15), residues: 3054 helix: 1.33 (0.16), residues: 1128 sheet: 0.09 (0.28), residues: 358 loop : -0.52 (0.16), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 330 time to evaluate : 2.915 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: 52 outliers final: 23 residues processed: 368 average time/residue: 0.3676 time to fit residues: 213.9039 Evaluate side-chains 309 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 3.086 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2442 time to fit residues: 14.2592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 275 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 222 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 GLN ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 24223 Z= 0.303 Angle : 0.563 7.871 32813 Z= 0.289 Chirality : 0.043 0.245 3735 Planarity : 0.004 0.052 4333 Dihedral : 4.098 17.761 3368 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.30 (0.15), residues: 3054 helix: 1.32 (0.16), residues: 1131 sheet: 0.07 (0.28), residues: 362 loop : -0.57 (0.16), residues: 1561 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 289 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 39 residues processed: 342 average time/residue: 0.3654 time to fit residues: 199.2108 Evaluate side-chains 305 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 266 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2233 time to fit residues: 20.5936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1227 GLN F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 24223 Z= 0.247 Angle : 0.540 9.433 32813 Z= 0.276 Chirality : 0.043 0.219 3735 Planarity : 0.004 0.048 4333 Dihedral : 4.054 16.943 3368 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.35 (0.15), residues: 3054 helix: 1.36 (0.16), residues: 1130 sheet: 0.08 (0.28), residues: 364 loop : -0.53 (0.16), residues: 1560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 299 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 349 average time/residue: 0.3689 time to fit residues: 203.1522 Evaluate side-chains 311 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 2.778 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2247 time to fit residues: 17.4040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 0.4980 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 121 optimal weight: 0.0050 chunk 251 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN D1227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 24223 Z= 0.357 Angle : 0.601 11.793 32813 Z= 0.307 Chirality : 0.044 0.217 3735 Planarity : 0.004 0.045 4333 Dihedral : 4.252 18.158 3368 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.13 (0.15), residues: 3054 helix: 1.14 (0.15), residues: 1142 sheet: -0.06 (0.27), residues: 372 loop : -0.65 (0.16), residues: 1540 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 284 time to evaluate : 3.104 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: 75 outliers final: 51 residues processed: 341 average time/residue: 0.3725 time to fit residues: 200.2999 Evaluate side-chains 320 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 269 time to evaluate : 2.797 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2380 time to fit residues: 26.8371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 295 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 24223 Z= 0.313 Angle : 0.584 12.422 32813 Z= 0.298 Chirality : 0.044 0.303 3735 Planarity : 0.004 0.044 4333 Dihedral : 4.228 18.343 3368 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.12 (0.15), residues: 3054 helix: 1.16 (0.15), residues: 1136 sheet: -0.08 (0.27), residues: 372 loop : -0.66 (0.16), residues: 1546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 308 average time/residue: 0.4102 time to fit residues: 198.2940 Evaluate side-chains 287 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 270 time to evaluate : 2.649 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2168 time to fit residues: 10.5487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 164 optimal weight: 0.0370 chunk 293 optimal weight: 0.0270 chunk 183 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 24223 Z= 0.149 Angle : 0.537 13.343 32813 Z= 0.268 Chirality : 0.042 0.299 3735 Planarity : 0.003 0.046 4333 Dihedral : 3.866 16.273 3368 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.43 (0.16), residues: 3054 helix: 1.39 (0.16), residues: 1139 sheet: 0.10 (0.28), residues: 359 loop : -0.47 (0.16), residues: 1556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 310 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 325 average time/residue: 0.3930 time to fit residues: 200.6176 Evaluate side-chains 295 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 3.046 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2928 time to fit residues: 11.1797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 200 optimal weight: 0.0670 chunk 145 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24223 Z= 0.200 Angle : 0.553 13.346 32813 Z= 0.278 Chirality : 0.043 0.293 3735 Planarity : 0.004 0.045 4333 Dihedral : 3.870 16.419 3368 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.43 (0.16), residues: 3054 helix: 1.36 (0.16), residues: 1142 sheet: 0.16 (0.28), residues: 368 loop : -0.46 (0.16), residues: 1544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 293 time to evaluate : 2.896 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: 22 outliers final: 10 residues processed: 309 average time/residue: 0.3764 time to fit residues: 184.2212 Evaluate side-chains 294 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 284 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2178 time to fit residues: 8.1979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 256 optimal weight: 0.3980 chunk 273 optimal weight: 0.0670 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 215 optimal weight: 0.0870 chunk 84 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 24223 Z= 0.153 Angle : 0.550 13.740 32813 Z= 0.272 Chirality : 0.042 0.303 3735 Planarity : 0.003 0.045 4333 Dihedral : 3.752 21.172 3368 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.53 (0.16), residues: 3054 helix: 1.49 (0.16), residues: 1135 sheet: 0.29 (0.28), residues: 362 loop : -0.46 (0.16), residues: 1557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 299 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 303 average time/residue: 0.3964 time to fit residues: 188.6047 Evaluate side-chains 279 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 275 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2408 time to fit residues: 5.6232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 1.9990 chunk 289 optimal weight: 0.8980 chunk 176 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 201 optimal weight: 1.9990 chunk 303 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 24223 Z= 0.289 Angle : 0.606 12.362 32813 Z= 0.304 Chirality : 0.044 0.315 3735 Planarity : 0.004 0.046 4333 Dihedral : 3.959 19.464 3368 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.45 (0.16), residues: 3054 helix: 1.42 (0.16), residues: 1131 sheet: 0.14 (0.28), residues: 368 loop : -0.47 (0.16), residues: 1555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 285 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 290 average time/residue: 0.3845 time to fit residues: 175.6051 Evaluate side-chains 285 residues out of total 2581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2467 time to fit residues: 6.8324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.091798 restraints weight = 45117.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091098 restraints weight = 35857.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.091806 restraints weight = 37396.596| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 24223 Z= 0.217 Angle : 0.585 12.002 32813 Z= 0.291 Chirality : 0.043 0.299 3735 Planarity : 0.004 0.045 4333 Dihedral : 3.910 19.162 3368 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % 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: 0.47 (0.16), residues: 3054 helix: 1.41 (0.16), residues: 1135 sheet: 0.17 (0.28), residues: 368 loop : -0.44 (0.16), residues: 1551 =============================================================================== Job complete usr+sys time: 4587.81 seconds wall clock time: 84 minutes 54.63 seconds (5094.63 seconds total)