Starting phenix.real_space_refine on Thu Mar 21 10:07:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/03_2024/7x2a_32963_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/03_2024/7x2a_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_32963/03_2024/7x2a_32963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/03_2024/7x2a_32963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/03_2024/7x2a_32963_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2a_32963/03_2024/7x2a_32963_neut.pdb" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.83, per 1000 atoms: 0.52 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: 9.98 Conformation dependent library (CDL) restraints added in 5.4 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: 3.51 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: 13.78 Time building geometry restraints manager: 10.95 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 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 7.940 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 74.200 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4056 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 % Allowed : 7.93 % Favored : 85.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.004 0.001 HIS C1138 PHE 0.013 0.002 PHE C1172 TYR 0.032 0.002 TYR C1171 ARG 0.005 0.001 ARG B 269 *********************** 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 : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 940 ASP cc_start: 0.4933 (OUTLIER) cc_final: 0.4355 (t0) REVERT: B 608 LEU cc_start: -0.3691 (OUTLIER) cc_final: -0.4005 (pp) REVERT: B 809 TYR cc_start: 0.4021 (t80) cc_final: 0.3743 (t80) REVERT: C 214 CYS cc_start: 0.0317 (OUTLIER) cc_final: -0.0293 (m) outliers start: 195 outliers final: 31 residues processed: 596 average time/residue: 1.0705 time to fit residues: 771.4140 Evaluate side-chains 295 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 261 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 909 TYR Chi-restraints excluded: chain A residue 940 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 626 ARG Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 836 HIS Chi-restraints excluded: chain B residue 912 CYS Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain C residue 208 HIS Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 836 HIS Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 164 VAL 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 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 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 348 HIS C 377 GLN C 592 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 812 ASN ** 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 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN 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: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4568 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 27421 Z= 0.278 Angle : 0.697 16.888 37302 Z= 0.368 Chirality : 0.045 0.228 4165 Planarity : 0.005 0.052 4856 Dihedral : 5.691 59.355 3825 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.71 % Favored : 98.23 % Rotamer: Outliers : 4.37 % Allowed : 16.37 % Favored : 79.25 % 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: 1.25 (0.13), residues: 3450 helix: 2.41 (0.18), residues: 772 sheet: 0.92 (0.18), residues: 793 loop : 0.18 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP H 47 HIS 0.011 0.002 HIS A 836 PHE 0.026 0.002 PHE C 156 TYR 0.025 0.002 TYR B 932 ARG 0.005 0.001 ARG C 629 *********************** 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 393 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 266 time to evaluate : 2.471 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: A 148 MET cc_start: -0.0245 (mmm) cc_final: -0.1219 (tmt) REVERT: A 230 GLU cc_start: 0.2951 (OUTLIER) cc_final: 0.2386 (pt0) REVERT: A 374 VAL cc_start: -0.4284 (OUTLIER) cc_final: -0.4580 (m) REVERT: A 960 TRP cc_start: 0.4917 (OUTLIER) cc_final: 0.4503 (t60) REVERT: B 303 ILE cc_start: 0.0154 (OUTLIER) cc_final: -0.0194 (pp) REVERT: B 608 LEU cc_start: -0.3869 (OUTLIER) cc_final: -0.4114 (pp) REVERT: B 630 PHE cc_start: -0.0041 (OUTLIER) cc_final: -0.0487 (p90) outliers start: 127 outliers final: 42 residues processed: 366 average time/residue: 1.0119 time to fit residues: 451.8993 Evaluate side-chains 265 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 217 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 836 HIS Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 909 TYR Chi-restraints excluded: chain A residue 912 CYS Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 606 TYR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 836 HIS Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 836 HIS Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 314 optimal weight: 30.0000 chunk 340 optimal weight: 40.0000 chunk 280 optimal weight: 0.7980 chunk 312 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 252 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 167 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 ASN A 988 GLN A1132 ASN B 81 HIS ** B 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 HIS B 988 GLN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN C 800 GLN C 832 ASN C 988 GLN ** 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** H 204 ASN K 39 GLN K 161 GLN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5361 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 27421 Z= 0.410 Angle : 0.820 16.874 37302 Z= 0.444 Chirality : 0.052 0.343 4165 Planarity : 0.006 0.066 4856 Dihedral : 5.924 51.500 3793 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 5.32 % Allowed : 15.83 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.16 (0.13), residues: 3450 helix: 1.38 (0.18), residues: 765 sheet: 0.20 (0.18), residues: 758 loop : -0.40 (0.13), residues: 1927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 44 HIS 0.031 0.003 HIS C 670 PHE 0.038 0.003 PHE A 827 TYR 0.036 0.003 TYR A 361 ARG 0.013 0.001 ARG C 614 *********************** 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 459 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 304 time to evaluate : 2.873 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: A 230 GLU cc_start: 0.3585 (OUTLIER) cc_final: 0.2731 (pt0) REVERT: A 577 TYR cc_start: 0.4037 (OUTLIER) cc_final: 0.3541 (t80) REVERT: A 836 HIS cc_start: 0.5173 (OUTLIER) cc_final: 0.4907 (m90) REVERT: B 142 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5493 (ttmt) REVERT: B 303 ILE cc_start: 0.0348 (OUTLIER) cc_final: 0.0081 (pp) REVERT: B 608 LEU cc_start: -0.3603 (OUTLIER) cc_final: -0.3915 (pp) REVERT: B 847 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8077 (ttp-170) REVERT: B 961 THR cc_start: 0.5464 (OUTLIER) cc_final: 0.5140 (t) outliers start: 155 outliers final: 59 residues processed: 416 average time/residue: 0.9781 time to fit residues: 500.4481 Evaluate side-chains 297 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 230 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 836 HIS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 909 TYR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 986 THR Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 771 ASP Chi-restraints excluded: chain B residue 836 HIS Chi-restraints excluded: chain B residue 847 ARG Chi-restraints excluded: chain B residue 943 MET Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 836 HIS Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 983 VAL Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 310 optimal weight: 9.9990 chunk 236 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 211 optimal weight: 0.2980 chunk 315 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 299 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 167 HIS ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 988 GLN ** B1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 832 ASN C 836 HIS C 988 GLN C1042 ASN C1079 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 moved from start: 0.6337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27421 Z= 0.221 Angle : 0.648 15.849 37302 Z= 0.338 Chirality : 0.044 0.180 4165 Planarity : 0.005 0.055 4856 Dihedral : 5.201 53.610 3787 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.80 % Rotamer: Outliers : 3.56 % Allowed : 19.29 % Favored : 77.15 % 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: 0.33 (0.13), residues: 3450 helix: 1.80 (0.18), residues: 764 sheet: 0.19 (0.18), residues: 748 loop : -0.37 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 47 HIS 0.015 0.001 HIS A 836 PHE 0.024 0.002 PHE B 617 TYR 0.033 0.002 TYR H 80 ARG 0.012 0.000 ARG B 269 *********************** 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 344 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 241 time to evaluate : 2.976 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: A 230 GLU cc_start: 0.3308 (OUTLIER) cc_final: 0.2736 (tm-30) REVERT: A 577 TYR cc_start: 0.3957 (OUTLIER) cc_final: 0.3468 (t80) REVERT: B 608 LEU cc_start: -0.3671 (OUTLIER) cc_final: -0.3994 (pp) REVERT: C 120 ILE cc_start: 0.1489 (OUTLIER) cc_final: 0.1175 (mt) REVERT: H 46 GLU cc_start: 0.3091 (OUTLIER) cc_final: 0.2767 (pp20) outliers start: 103 outliers final: 46 residues processed: 318 average time/residue: 1.0271 time to fit residues: 399.3475 Evaluate side-chains 265 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 577 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 909 TYR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 836 HIS Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 1217 ASN Chi-restraints excluded: chain C residue 114 ASN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 1071 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 278 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 249 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 300 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 1 GLN H 3 GLN ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5437 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 27421 Z= 0.220 Angle : 0.633 17.363 37302 Z= 0.326 Chirality : 0.044 0.498 4165 Planarity : 0.004 0.055 4856 Dihedral : 4.923 54.449 3784 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.22 % Rotamer: Outliers : 3.49 % Allowed : 19.69 % Favored : 76.81 % 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: 0.33 (0.13), residues: 3450 helix: 1.91 (0.18), residues: 762 sheet: 0.15 (0.18), residues: 740 loop : -0.40 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 47 HIS 0.016 0.001 HIS A 836 PHE 0.023 0.002 PHE B 617 TYR 0.030 0.002 TYR A 932 ARG 0.006 0.000 ARG B 62 *********************** 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 329 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 228 time to evaluate : 3.199 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: A 230 GLU cc_start: 0.3230 (OUTLIER) cc_final: 0.2766 (tm-30) REVERT: B 110 LYS cc_start: 0.6106 (OUTLIER) cc_final: 0.5744 (mmtm) REVERT: B 608 LEU cc_start: -0.3679 (OUTLIER) cc_final: -0.3982 (pp) REVERT: B 961 THR cc_start: 0.5327 (OUTLIER) cc_final: 0.5003 (t) outliers start: 101 outliers final: 51 residues processed: 311 average time/residue: 0.9471 time to fit residues: 368.0702 Evaluate side-chains 272 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 217 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 909 TYR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 1042 ASN Chi-restraints excluded: chain C residue 1071 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU 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: 0.6980 chunk 66 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 334 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 154 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 HIS ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 264 HIS B 636 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 GLN ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 988 GLN H 162 ASN ** K 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27421 Z= 0.343 Angle : 0.759 18.134 37302 Z= 0.402 Chirality : 0.049 0.576 4165 Planarity : 0.006 0.067 4856 Dihedral : 5.387 51.368 3782 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 4.24 % Allowed : 19.15 % Favored : 76.61 % 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: -0.01 (0.13), residues: 3450 helix: 1.65 (0.18), residues: 747 sheet: -0.07 (0.17), residues: 770 loop : -0.62 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP H 47 HIS 0.017 0.002 HIS B 91 PHE 0.080 0.003 PHE C 101 TYR 0.036 0.003 TYR B 332 ARG 0.009 0.001 ARG C 614 *********************** 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 395 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 272 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.3855 (OUTLIER) cc_final: 0.3055 (tm-30) REVERT: A 240 MET cc_start: 0.2575 (OUTLIER) cc_final: 0.2259 (tmt) REVERT: A 332 TYR cc_start: 0.1816 (m-80) cc_final: 0.1119 (m-80) REVERT: B 110 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6178 (mmtm) REVERT: B 232 PHE cc_start: 0.3221 (OUTLIER) cc_final: 0.2881 (m-10) REVERT: B 608 LEU cc_start: -0.3565 (OUTLIER) cc_final: -0.3839 (pp) REVERT: B 630 PHE cc_start: 0.0917 (OUTLIER) cc_final: 0.0399 (p90) REVERT: B 961 THR cc_start: 0.5479 (OUTLIER) cc_final: 0.5073 (t) REVERT: C 296 ILE cc_start: 0.5349 (OUTLIER) cc_final: 0.5065 (mt) REVERT: C 1008 MET cc_start: 0.6524 (tmm) cc_final: 0.6254 (ttp) outliers start: 123 outliers final: 48 residues processed: 370 average time/residue: 0.9847 time to fit residues: 450.0251 Evaluate side-chains 261 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 205 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 664 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 810 VAL Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1071 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 322 optimal weight: 0.0570 chunk 37 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 333 optimal weight: 40.0000 chunk 208 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 280 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 GLN B1072 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 moved from start: 0.8733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27421 Z= 0.276 Angle : 0.708 16.383 37302 Z= 0.363 Chirality : 0.046 0.407 4165 Planarity : 0.005 0.066 4856 Dihedral : 5.119 45.779 3780 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 3.25 % Allowed : 21.05 % Favored : 75.69 % Cbeta Deviations : 0.03 % 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: -0.00 (0.14), residues: 3450 helix: 1.64 (0.19), residues: 749 sheet: -0.04 (0.17), residues: 770 loop : -0.62 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP H 47 HIS 0.018 0.002 HIS A 836 PHE 0.027 0.002 PHE C 281 TYR 0.024 0.002 TYR A 635 ARG 0.014 0.001 ARG A 269 *********************** 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 327 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 233 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.3488 (OUTLIER) cc_final: 0.2913 (tm-30) REVERT: A 332 TYR cc_start: 0.3074 (m-80) cc_final: 0.2027 (m-80) REVERT: B 232 PHE cc_start: 0.2969 (OUTLIER) cc_final: 0.2619 (m-10) REVERT: B 608 LEU cc_start: -0.3516 (OUTLIER) cc_final: -0.3795 (pp) REVERT: B 630 PHE cc_start: 0.1061 (OUTLIER) cc_final: 0.0493 (p90) outliers start: 94 outliers final: 49 residues processed: 309 average time/residue: 1.0157 time to fit residues: 387.1831 Evaluate side-chains 260 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 207 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1031 GLN Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 844 ASP Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1063 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 206 optimal weight: 0.3980 chunk 133 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 262 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 HIS ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1217 ASN K 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.9031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27421 Z= 0.236 Angle : 0.657 16.196 37302 Z= 0.340 Chirality : 0.044 0.387 4165 Planarity : 0.005 0.068 4856 Dihedral : 4.949 50.673 3778 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 2.88 % Allowed : 21.42 % Favored : 75.69 % 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: 0.02 (0.14), residues: 3450 helix: 1.74 (0.19), residues: 750 sheet: -0.14 (0.17), residues: 769 loop : -0.60 (0.13), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP H 47 HIS 0.017 0.001 HIS A 836 PHE 0.029 0.002 PHE C 101 TYR 0.104 0.002 TYR H 80 ARG 0.008 0.001 ARG A 269 *********************** 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 306 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 223 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ASP cc_start: 0.1278 (OUTLIER) cc_final: 0.1009 (p0) REVERT: B 232 PHE cc_start: 0.3048 (OUTLIER) cc_final: 0.2831 (m-10) REVERT: B 608 LEU cc_start: -0.3511 (OUTLIER) cc_final: -0.3753 (pp) REVERT: B 630 PHE cc_start: 0.1013 (OUTLIER) cc_final: 0.0473 (p90) outliers start: 83 outliers final: 49 residues processed: 294 average time/residue: 0.9929 time to fit residues: 362.0232 Evaluate side-chains 259 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 806 CYS Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 844 ASP Chi-restraints excluded: chain C residue 1063 GLN Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 303 optimal weight: 20.0000 chunk 319 optimal weight: 20.0000 chunk 291 optimal weight: 4.9990 chunk 310 optimal weight: 20.0000 chunk 187 optimal weight: 4.9990 chunk 135 optimal weight: 0.0970 chunk 244 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 280 optimal weight: 0.9990 chunk 293 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 91 HIS B 280 GLN ** B 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 1.0033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 27421 Z= 0.362 Angle : 0.778 15.808 37302 Z= 0.408 Chirality : 0.049 0.415 4165 Planarity : 0.006 0.082 4856 Dihedral : 5.484 59.779 3778 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 2.85 % Allowed : 21.73 % Favored : 75.42 % 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: -0.38 (0.13), residues: 3450 helix: 1.32 (0.18), residues: 752 sheet: -0.30 (0.18), residues: 748 loop : -0.86 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP H 47 HIS 0.024 0.002 HIS A 836 PHE 0.035 0.002 PHE C 327 TYR 0.035 0.002 TYR A 332 ARG 0.019 0.001 ARG A 269 *********************** 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 329 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 247 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.3579 (OUTLIER) cc_final: 0.2718 (tm-30) REVERT: A 757 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.7021 (mtm) REVERT: B 608 LEU cc_start: -0.3584 (OUTLIER) cc_final: -0.3853 (pp) REVERT: B 630 PHE cc_start: 0.1379 (OUTLIER) cc_final: 0.0793 (p90) REVERT: C 1071 ILE cc_start: 0.4035 (OUTLIER) cc_final: 0.3706 (mp) outliers start: 82 outliers final: 53 residues processed: 313 average time/residue: 1.0003 time to fit residues: 386.0818 Evaluate side-chains 267 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 209 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASP Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 757 MET Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain C residue 1063 GLN Chi-restraints excluded: chain C residue 1071 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 204 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 200 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 344 optimal weight: 20.0000 chunk 317 optimal weight: 40.0000 chunk 274 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1079 ASN B 348 HIS B 708 GLN C 72 GLN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1079 ASN C1217 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 1.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 27421 Z= 0.464 Angle : 0.865 16.522 37302 Z= 0.454 Chirality : 0.051 0.439 4165 Planarity : 0.007 0.104 4856 Dihedral : 5.827 36.350 3778 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 2.41 % Allowed : 22.78 % Favored : 74.81 % 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: -0.62 (0.13), residues: 3450 helix: 1.09 (0.19), residues: 740 sheet: -0.39 (0.18), residues: 737 loop : -1.01 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP H 47 HIS 0.020 0.002 HIS A 836 PHE 0.089 0.003 PHE C 232 TYR 0.071 0.003 TYR C 270 ARG 0.034 0.001 ARG A 62 ********************** 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 325 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 256 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.3790 (OUTLIER) cc_final: 0.3450 (t) REVERT: B 608 LEU cc_start: -0.3756 (OUTLIER) cc_final: -0.4064 (pp) REVERT: B 630 PHE cc_start: 0.1029 (OUTLIER) cc_final: 0.0648 (p90) REVERT: B 1105 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7036 (tt0) outliers start: 69 outliers final: 45 residues processed: 308 average time/residue: 0.9923 time to fit residues: 375.8971 Evaluate side-chains 264 residues out of total 2957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 215 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 332 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 438 TYR Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 630 PHE Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 900 ILE Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1041 SER Chi-restraints excluded: chain B residue 1051 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain B residue 1209 VAL Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 728 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 188 GLU 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: 2.9990 chunk 84 optimal weight: 0.0070 chunk 253 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 282 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** A 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A1079 ASN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 111 GLN B1072 ASN C 72 GLN C 167 HIS C 636 GLN ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1217 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.151080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.109274 restraints weight = 89311.763| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.79 r_work: 0.3463 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 1.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27421 Z= 0.229 Angle : 0.717 16.989 37302 Z= 0.369 Chirality : 0.045 0.423 4165 Planarity : 0.005 0.052 4856 Dihedral : 5.209 30.373 3777 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 1.86 % Allowed : 24.10 % Favored : 74.03 % 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: -0.33 (0.14), residues: 3450 helix: 1.49 (0.19), residues: 746 sheet: -0.31 (0.18), residues: 756 loop : -0.86 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP H 47 HIS 0.021 0.001 HIS A 836 PHE 0.040 0.002 PHE A 630 TYR 0.022 0.002 TYR B 648 ARG 0.009 0.001 ARG A 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9074.47 seconds wall clock time: 162 minutes 27.22 seconds (9747.22 seconds total)