Starting phenix.real_space_refine (version: dev) on Mon Feb 27 10:31:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/02_2023/7x2a_32963_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/02_2023/7x2a_32963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/02_2023/7x2a_32963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/02_2023/7x2a_32963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/02_2023/7x2a_32963_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/02_2023/7x2a_32963_neut.pdb" } resolution = 2.49 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2935 atoms to isotropic. 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 GLU 188": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "A TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 1039": "OE1" <-> "OE2" Residue "B GLU 1090": "OE1" <-> "OE2" Residue "B GLU 1148": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 357": "OE1" <-> "OE2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1039": "OE1" <-> "OE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C GLU 1148": "OE1" <-> "OE2" Residue "C TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K GLU 196": "OE1" <-> "OE2" 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: 26800 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8940 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 3, 'PTRANS': 58, 'TRANS': 1097} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7313 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 44, 'TRANS': 902} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 7313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7313 Classifications: {'peptide': 947} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 44, 'TRANS': 902} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 16.23, per 1000 atoms: 0.61 Number of scatterers: 26800 At special positions: 0 Unit cell: (149.385, 185.107, 239.232, 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 135 16.00 O 5202 8.00 N 4455 7.00 C 17008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.02 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.02 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.04 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.02 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.04 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.03 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: 10.65 Conformation dependent library (CDL) restraints added in 4.9 seconds 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6444 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 60 sheets defined 25.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.126A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 removed outlier: 3.556A pdb=" N PHE A 341 " --> pdb=" O ASP A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.513A pdb=" N SER A 598 " --> pdb=" O LYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 826 through 854 removed outlier: 3.575A pdb=" N LYS A 830 " --> pdb=" O GLN A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 922 through 931 Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.555A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1010 Processing helix chain 'A' and resid 1016 through 1042 removed outlier: 3.632A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 removed outlier: 3.843A pdb=" N ILE A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1106 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.056A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.722A pdb=" N VAL B 611 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 825 Processing helix chain 'B' and resid 826 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 916 Processing helix chain 'B' and resid 922 through 931 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.592A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1010 Processing helix chain 'B' and resid 1016 through 1042 removed outlier: 3.633A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B1037 " --> pdb=" O LEU B1033 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.591A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1223 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 268 through 273 removed outlier: 4.000A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 678 through 682 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 825 Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 922 through 931 Processing helix chain 'C' and resid 940 through 959 removed outlier: 3.597A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1010 Processing helix chain 'C' and resid 1016 through 1042 removed outlier: 3.518A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 removed outlier: 3.591A pdb=" N ILE C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.554A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1219 through 1223 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'K' and resid 122 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 4.334A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 3.514A pdb=" N GLN A 319 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.354A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER A 151 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N HIS A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 153 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE A 165 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 11.733A pdb=" N PHE A 164 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 166 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A 187 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.354A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER A 151 " --> pdb=" O HIS A 167 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N HIS A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 153 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE A 165 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 11.733A pdb=" N PHE A 164 " --> pdb=" O PRO A 189 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 166 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU A 187 " --> pdb=" O ASN A 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA9, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.208A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.631A pdb=" N VAL A 263 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.576A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 373 through 374 removed outlier: 4.202A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 630 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.476A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.628A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A 502 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TRP A 553 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 724 removed outlier: 7.864A pdb=" N SER A 761 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU A 722 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.640A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1121 through 1129 removed outlier: 5.868A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1121 through 1129 removed outlier: 5.868A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 803 removed outlier: 3.830A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC3, first strand: chain 'A' and resid 967 through 968 removed outlier: 6.768A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 967 through 968 removed outlier: 6.768A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 4.032A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AC7, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.451A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.919A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.410A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 151 " --> pdb=" O HIS B 167 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N HIS B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL B 153 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 165 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N PHE B 164 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN B 166 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 187 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.410A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 151 " --> pdb=" O HIS B 167 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N HIS B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL B 153 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE B 165 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 11.210A pdb=" N PHE B 164 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN B 166 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 187 " --> pdb=" O ASN B 166 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.302A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.510A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 664 " --> pdb=" O THR B 669 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 603 through 604 removed outlier: 4.089A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 707 through 709 Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 724 removed outlier: 7.916A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 722 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 729 " --> pdb=" O ALA B 737 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.634A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.856A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.856A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 801 through 803 removed outlier: 4.391A pdb=" N LYS B 801 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1202 through 1204 Processing sheet with id=AE4, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AE5, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.282A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.634A pdb=" N TYR C 314 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 88 through 90 removed outlier: 4.116A pdb=" N SER C 88 " --> pdb=" O HIS C 298 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 300 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.350A pdb=" N SER C 151 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N HIS C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL C 153 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 165 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N PHE C 164 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN C 166 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 187 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.350A pdb=" N SER C 151 " --> pdb=" O HIS C 167 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N HIS C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL C 153 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 165 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 11.607A pdb=" N PHE C 164 " --> pdb=" O PRO C 189 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASN C 166 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 187 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AF2, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.391A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 717 through 724 removed outlier: 3.685A pdb=" N VAL C 718 " --> pdb=" O MET C 757 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 732 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA C 737 " --> pdb=" O PRO C 730 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 801 through 803 removed outlier: 4.409A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1202 through 1204 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.969A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.526A pdb=" N THR H 117 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 116 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA H 92 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AF9, first strand: chain 'H' and resid 143 through 145 removed outlier: 6.599A pdb=" N SER H 184 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA H 175 " --> pdb=" O SER H 184 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 158 through 160 removed outlier: 5.008A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS H 207 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR H 212 " --> pdb=" O HIS H 207 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AG3, first strand: chain 'K' and resid 19 through 24 removed outlier: 3.590A pdb=" N ALA K 19 " --> pdb=" O ILE K 76 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 54 through 55 removed outlier: 3.814A pdb=" N SER K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 115 through 119 removed outlier: 3.543A pdb=" N VAL K 134 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 154 through 155 1192 hydrogen bonds defined for protein. 3214 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: 13.61 Time building geometry restraints manager: 11.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5125 1.33 - 1.45: 7003 1.45 - 1.58: 15108 1.58 - 1.70: 9 1.70 - 1.83: 176 Bond restraints: 27421 Sorted by residual: bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.235 1.363 -0.128 1.14e-02 7.69e+03 1.26e+02 bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.361 -0.125 1.21e-02 6.83e+03 1.07e+02 bond pdb=" CB HIS A 681 " pdb=" CG HIS A 681 " ideal model delta sigma weight residual 1.497 1.375 0.122 1.40e-02 5.10e+03 7.62e+01 bond pdb=" CB HIS C 681 " pdb=" CG HIS C 681 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.51e+01 bond pdb=" CB HIS B 681 " pdb=" CG HIS B 681 " ideal model delta sigma weight residual 1.497 1.376 0.121 1.40e-02 5.10e+03 7.50e+01 ... (remaining 27416 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.77: 855 106.77 - 113.67: 14527 113.67 - 120.58: 12727 120.58 - 127.48: 9066 127.48 - 134.39: 127 Bond angle restraints: 37302 Sorted by residual: angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.27 -11.89 1.09e+00 8.42e-01 1.19e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.19 -11.81 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA ASER H 160 " ideal model delta sigma weight residual 120.32 132.17 -11.85 1.11e+00 8.12e-01 1.14e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA BSER H 160 " ideal model delta sigma weight residual 120.32 132.12 -11.80 1.11e+00 8.12e-01 1.13e+02 angle pdb=" CD1 LEU C1222 " pdb=" CG LEU C1222 " pdb=" CD2 LEU C1222 " ideal model delta sigma weight residual 110.80 132.64 -21.84 2.20e+00 2.07e-01 9.85e+01 ... (remaining 37297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 14904 17.32 - 34.64: 1096 34.64 - 51.96: 265 51.96 - 69.28: 70 69.28 - 86.60: 6 Dihedral angle restraints: 16341 sinusoidal: 6235 harmonic: 10106 Sorted by residual: dihedral pdb=" C THR C 669 " pdb=" N THR C 669 " pdb=" CA THR C 669 " pdb=" CB THR C 669 " ideal model delta harmonic sigma weight residual -122.00 -137.01 15.01 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" C PHE A 850 " pdb=" N PHE A 850 " pdb=" CA PHE A 850 " pdb=" CB PHE A 850 " ideal model delta harmonic sigma weight residual -122.60 -134.56 11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" CB CYS C 620 " pdb=" SG CYS C 620 " pdb=" SG CYS C 650 " pdb=" CB CYS C 650 " ideal model delta sinusoidal sigma weight residual 93.00 54.03 38.97 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 16338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 3301 0.140 - 0.280: 842 0.280 - 0.420: 16 0.420 - 0.560: 3 0.560 - 0.700: 3 Chirality restraints: 4165 Sorted by residual: chirality pdb=" CG LEU A1222 " pdb=" CB LEU A1222 " pdb=" CD1 LEU A1222 " pdb=" CD2 LEU A1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU B1222 " pdb=" CB LEU B1222 " pdb=" CD1 LEU B1222 " pdb=" CD2 LEU B1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CG LEU C1222 " pdb=" CB LEU C1222 " pdb=" CD1 LEU C1222 " pdb=" CD2 LEU C1222 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 4162 not shown) Planarity restraints: 4856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 668 " -0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C LYS C 668 " 0.062 2.00e-02 2.50e+03 pdb=" O LYS C 668 " -0.023 2.00e-02 2.50e+03 pdb=" N THR C 669 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 669 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.70e+00 pdb=" C THR C 669 " -0.048 2.00e-02 2.50e+03 pdb=" O THR C 669 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS C 670 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 709 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C THR B 709 " 0.042 2.00e-02 2.50e+03 pdb=" O THR B 709 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 710 " -0.014 2.00e-02 2.50e+03 ... (remaining 4853 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 5 2.33 - 2.97: 12421 2.97 - 3.61: 39241 3.61 - 4.26: 65743 4.26 - 4.90: 107246 Nonbonded interactions: 224656 Sorted by model distance: nonbonded pdb=" OE2 GLU B 376 " pdb=" NE2 GLN B 377 " model vdw 1.682 2.520 nonbonded pdb=" N GLN B 627 " pdb=" OE1 GLN B 627 " model vdw 1.856 2.520 nonbonded pdb=" O GLU B 357 " pdb=" OH TYR B 361 " model vdw 2.022 2.440 nonbonded pdb=" O SER A 546 " pdb=" O GLU A 549 " model vdw 2.247 3.040 nonbonded pdb=" O ASP A 510 " pdb=" NZ LYS H 74 " model vdw 2.318 2.520 ... (remaining 224651 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 'B' selection = chain 'C' } 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 135 5.16 5 C 17008 2.51 5 N 4455 2.21 5 O 5202 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 9.180 Check model and map are aligned: 0.420 Process input model: 75.580 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4236 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 : 0.013 0.141 27421 Z= 0.887 Angle : 1.512 21.837 37302 Z= 1.175 Chirality : 0.109 0.700 4165 Planarity : 0.004 0.036 4856 Dihedral : 12.932 86.598 9756 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.20 % Favored : 97.59 % Rotamer Outliers : 6.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 3450 helix: 4.35 (0.17), residues: 754 sheet: 1.64 (0.19), residues: 710 loop : 0.44 (0.13), residues: 1986 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 445 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 195 outliers final: 31 residues processed: 596 average time/residue: 1.0759 time to fit residues: 772.6834 Evaluate side-chains 292 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 261 time to evaluate : 2.955 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.3328 time to fit residues: 7.9206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 0.9980 chunk 262 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 314 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 72 GLN A 78 GLN A 81 HIS A 166 ASN A 236 ASN A 521 ASN A 576 GLN A 582 ASN A 628 GLN ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 GLN A 832 ASN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 ASN A 987 GLN A1009 GLN A1056 GLN A1072 ASN A1213 ASN B 166 ASN B 236 ASN B 264 HIS B 277 ASN B 599 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 HIS B 733 GLN B 848 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 981 ASN B 987 GLN B 993 ASN B1009 GLN B1072 ASN B1213 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 236 ASN C 280 GLN C 298 HIS C 377 GLN C 592 ASN C 628 GLN C 812 ASN C 836 HIS ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 ASN C1009 GLN C1020 GLN C1056 GLN C1072 ASN C1213 ASN H 6 GLN H 112 GLN H 178 GLN H 204 ASN K 125 GLN ** K 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4796 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.123 27421 Z= 0.278 Angle : 0.707 16.369 37302 Z= 0.372 Chirality : 0.046 0.228 4165 Planarity : 0.005 0.051 4856 Dihedral : 4.652 28.147 3771 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.14 % Rotamer Outliers : 4.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 1.18 (0.13), residues: 3450 helix: 2.28 (0.18), residues: 774 sheet: 0.89 (0.18), residues: 786 loop : 0.17 (0.13), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 268 time to evaluate : 3.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 46 residues processed: 369 average time/residue: 1.1136 time to fit residues: 500.3679 Evaluate side-chains 263 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 2.989 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 36 residues processed: 10 average time/residue: 0.3486 time to fit residues: 10.2754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 213 optimal weight: 0.2980 chunk 86 optimal weight: 10.0000 chunk 314 optimal weight: 30.0000 chunk 340 optimal weight: 50.0000 chunk 280 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 252 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 167 HIS A 670 HIS A 839 ASN A1132 ASN B 592 ASN B 988 GLN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN C 733 GLN C 800 GLN C 988 GLN C1042 ASN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN K 161 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5075 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 27421 Z= 0.235 Angle : 0.623 14.131 37302 Z= 0.328 Chirality : 0.044 0.357 4165 Planarity : 0.004 0.051 4856 Dihedral : 4.443 22.423 3771 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 0.90 (0.13), residues: 3450 helix: 2.10 (0.18), residues: 775 sheet: 0.68 (0.18), residues: 768 loop : -0.01 (0.13), residues: 1907 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 253 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 52 residues processed: 343 average time/residue: 0.9804 time to fit residues: 415.4774 Evaluate side-chains 262 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 210 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 43 residues processed: 10 average time/residue: 0.4400 time to fit residues: 10.5640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 150 optimal weight: 0.3980 chunk 211 optimal weight: 0.0970 chunk 315 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN B1110 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 988 GLN ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 162 ASN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 27421 Z= 0.235 Angle : 0.631 14.549 37302 Z= 0.331 Chirality : 0.044 0.215 4165 Planarity : 0.005 0.096 4856 Dihedral : 4.535 27.737 3771 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 0.61 (0.13), residues: 3450 helix: 1.97 (0.18), residues: 772 sheet: 0.40 (0.18), residues: 744 loop : -0.20 (0.13), residues: 1934 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 247 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 51 residues processed: 339 average time/residue: 1.0268 time to fit residues: 431.1918 Evaluate side-chains 264 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 213 time to evaluate : 3.001 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 45 residues processed: 7 average time/residue: 0.4987 time to fit residues: 9.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 0.5980 chunk 189 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 249 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 170 optimal weight: 0.8980 chunk 300 optimal weight: 0.5980 chunk 84 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN C 988 GLN H 1 GLN H 3 GLN K 39 GLN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 27421 Z= 0.193 Angle : 0.607 14.021 37302 Z= 0.312 Chirality : 0.043 0.350 4165 Planarity : 0.004 0.059 4856 Dihedral : 4.331 23.584 3771 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.47 % Favored : 97.48 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 0.59 (0.13), residues: 3450 helix: 2.16 (0.19), residues: 757 sheet: 0.35 (0.18), residues: 749 loop : -0.26 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 223 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 61 residues processed: 308 average time/residue: 0.9956 time to fit residues: 384.9740 Evaluate side-chains 268 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 207 time to evaluate : 3.091 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 54 residues processed: 8 average time/residue: 0.4662 time to fit residues: 9.8475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 112 optimal weight: 2.9990 chunk 301 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 334 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 154 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 81 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 27421 Z= 0.305 Angle : 0.692 18.855 37302 Z= 0.364 Chirality : 0.047 0.277 4165 Planarity : 0.005 0.066 4856 Dihedral : 4.731 24.621 3771 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 0.29 (0.13), residues: 3450 helix: 1.84 (0.18), residues: 755 sheet: 0.14 (0.18), residues: 746 loop : -0.42 (0.13), residues: 1949 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 272 time to evaluate : 3.170 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: 120 outliers final: 58 residues processed: 368 average time/residue: 0.9830 time to fit residues: 451.2316 Evaluate side-chains 279 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 50 residues processed: 10 average time/residue: 0.4405 time to fit residues: 11.1384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 244 optimal weight: 0.0370 chunk 189 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 186 optimal weight: 0.2980 chunk 333 optimal weight: 30.0000 chunk 208 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 81 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN B 836 HIS ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN C1079 ASN C1110 GLN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.7489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 27421 Z= 0.230 Angle : 0.664 16.094 37302 Z= 0.342 Chirality : 0.045 0.384 4165 Planarity : 0.005 0.063 4856 Dihedral : 4.547 21.773 3771 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.13 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 0.25 (0.14), residues: 3450 helix: 1.88 (0.19), residues: 759 sheet: 0.07 (0.18), residues: 756 loop : -0.46 (0.13), residues: 1935 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 239 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 56 residues processed: 317 average time/residue: 0.9870 time to fit residues: 393.5324 Evaluate side-chains 264 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 208 time to evaluate : 3.029 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 52 residues processed: 5 average time/residue: 0.3705 time to fit residues: 6.9822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 212 optimal weight: 0.0370 chunk 227 optimal weight: 0.6980 chunk 164 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 262 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN C 36 GLN C 72 GLN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.123 27421 Z= 0.191 Angle : 0.642 17.088 37302 Z= 0.327 Chirality : 0.044 0.379 4165 Planarity : 0.004 0.062 4856 Dihedral : 4.433 22.652 3771 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: 0.31 (0.14), residues: 3450 helix: 2.04 (0.19), residues: 747 sheet: 0.08 (0.18), residues: 745 loop : -0.45 (0.13), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 223 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 55 residues processed: 291 average time/residue: 0.9513 time to fit residues: 347.1175 Evaluate side-chains 260 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 205 time to evaluate : 2.925 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 48 residues processed: 8 average time/residue: 0.3388 time to fit residues: 9.2864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 9.9990 chunk 319 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 167 HIS ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 636 GLN B1132 ASN C 72 GLN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.9968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.115 27421 Z= 0.643 Angle : 0.999 15.998 37302 Z= 0.545 Chirality : 0.061 0.486 4165 Planarity : 0.007 0.117 4856 Dihedral : 6.352 36.992 3771 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.58 % Favored : 95.27 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % Twisted Proline : 0.60 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 3450 helix: 0.65 (0.18), residues: 742 sheet: -0.10 (0.18), residues: 736 loop : -1.11 (0.13), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 293 time to evaluate : 3.151 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: 89 outliers final: 46 residues processed: 365 average time/residue: 1.0728 time to fit residues: 487.7781 Evaluate side-chains 265 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 3.053 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 41 residues processed: 6 average time/residue: 0.4079 time to fit residues: 8.3194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 0.9990 chunk 328 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 228 optimal weight: 0.8980 chunk 344 optimal weight: 40.0000 chunk 317 optimal weight: 30.0000 chunk 274 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 167 HIS ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN B 91 HIS B 155 ASN B 166 ASN B 808 GLN B1072 ASN C 166 ASN ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 GLN C1110 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 1.0126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 27421 Z= 0.249 Angle : 0.753 17.824 37302 Z= 0.390 Chirality : 0.047 0.419 4165 Planarity : 0.005 0.071 4856 Dihedral : 5.354 27.244 3771 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: -0.48 (0.13), residues: 3450 helix: 1.34 (0.19), residues: 732 sheet: -0.31 (0.18), residues: 755 loop : -0.97 (0.13), residues: 1963 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6900 Ramachandran restraints generated. 3450 Oldfield, 0 Emsley, 3450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 3.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 43 residues processed: 290 average time/residue: 1.0672 time to fit residues: 384.8654 Evaluate side-chains 251 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 208 time to evaluate : 3.418 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 39 residues processed: 4 average time/residue: 0.2722 time to fit residues: 6.7340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 218 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN A1160 ASN ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1110 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.151852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.109073 restraints weight = 88707.792| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.52 r_work: 0.3463 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 1.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.109 27421 Z= 0.366 Angle : 0.816 17.275 37302 Z= 0.427 Chirality : 0.050 0.449 4165 Planarity : 0.006 0.069 4856 Dihedral : 5.456 27.251 3771 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % 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: -0.54 (0.13), residues: 3450 helix: 1.26 (0.19), residues: 736 sheet: -0.30 (0.18), residues: 711 loop : -1.02 (0.13), residues: 2003 =============================================================================== Job complete usr+sys time: 9250.18 seconds wall clock time: 166 minutes 17.37 seconds (9977.37 seconds total)