Starting phenix.real_space_refine on Fri Feb 23 02:43:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5k_31726/02_2024/7v5k_31726.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5k_31726/02_2024/7v5k_31726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5k_31726/02_2024/7v5k_31726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5k_31726/02_2024/7v5k_31726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5k_31726/02_2024/7v5k_31726.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v5k_31726/02_2024/7v5k_31726.pdb" } resolution = 2.8 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 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 192 5.16 5 C 23063 2.51 5 N 6010 2.21 5 O 7104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A ARG 694": "NH1" <-> "NH2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1105": "OE1" <-> "OE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B ARG 626": "NH1" <-> "NH2" Residue "B PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1062": "OE1" <-> "OE2" Residue "B ARG 1179": "NH1" <-> "NH2" Residue "B GLU 1183": "OE1" <-> "OE2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C GLU 549": "OE1" <-> "OE2" Residue "C ARG 626": "NH1" <-> "NH2" Residue "C ARG 691": "NH1" <-> "NH2" Residue "C GLU 818": "OE1" <-> "OE2" Residue "C GLU 823": "OE1" <-> "OE2" Residue "C ARG 887": "NH1" <-> "NH2" Residue "C TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1039": "OE1" <-> "OE2" Residue "C PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1062": "OE1" <-> "OE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36369 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8836 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 8836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8836 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 8836 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1141, 8830 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 1141, 8830 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 9023 Chain: "D" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "F" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "G" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain: "H" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "I" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1668 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER C 51 " occ=0.46 ... (10 atoms not shown) pdb=" OG BSER C 51 " occ=0.54 Time building chain proxies: 22.00, per 1000 atoms: 0.60 Number of scatterers: 36369 At special positions: 0 Unit cell: (214.335, 231.655, 182.942, 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 192 16.00 O 7104 8.00 N 6010 7.00 C 23063 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=2.05 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.05 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.06 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.02 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.05 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 151 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 151 " - pdb=" SG CYS I 207 " distance=2.01 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: 13.69 Conformation dependent library (CDL) restraints added in 8.8 seconds 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8786 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 83 sheets defined 19.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.84 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.520A pdb=" N ASP A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.995A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.000A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.035A pdb=" N LEU A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 390' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.854A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.563A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.798A pdb=" N GLN A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.220A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 825 through 854 removed outlier: 3.673A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 removed outlier: 3.557A pdb=" N VAL A 898 " --> pdb=" O LEU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 925 through 929 Processing helix chain 'A' and resid 940 through 959 removed outlier: 4.825A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 987 through 994 removed outlier: 3.592A pdb=" N GLN A 994 " --> pdb=" O LEU A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1011 removed outlier: 3.573A pdb=" N GLY A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1041 removed outlier: 3.852A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1107 removed outlier: 3.855A pdb=" N ALA A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.804A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.576A pdb=" N LYS B 52 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.952A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.980A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.107A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.516A pdb=" N GLN B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 825 through 854 removed outlier: 3.616A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 867 removed outlier: 4.173A pdb=" N GLY B 866 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 867 " --> pdb=" O PRO B 863 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 862 through 867' Processing helix chain 'B' and resid 888 through 898 removed outlier: 3.901A pdb=" N VAL B 898 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 915 Processing helix chain 'B' and resid 925 through 930 Processing helix chain 'B' and resid 940 through 959 removed outlier: 4.670A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 removed outlier: 3.608A pdb=" N GLY B 984 " --> pdb=" O LEU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 993 Processing helix chain 'B' and resid 996 through 1011 removed outlier: 3.748A pdb=" N GLY B1011 " --> pdb=" O ALA B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1040 removed outlier: 3.886A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1107 removed outlier: 3.659A pdb=" N ALA B1065 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.506A pdb=" N SER C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.716A pdb=" N SER C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.869A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.763A pdb=" N MET C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 453 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 588 through 588 No H-bonds generated for 'chain 'C' and resid 588 through 588' Processing helix chain 'C' and resid 595 through 598 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 825 through 854 Processing helix chain 'C' and resid 888 through 898 removed outlier: 3.539A pdb=" N VAL C 898 " --> pdb=" O LEU C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 915 Processing helix chain 'C' and resid 940 through 960 removed outlier: 4.807A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TRP C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 Processing helix chain 'C' and resid 987 through 994 removed outlier: 3.953A pdb=" N GLN C 994 " --> pdb=" O LEU C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1011 Processing helix chain 'C' and resid 1018 through 1040 removed outlier: 3.558A pdb=" N LYS C1035 " --> pdb=" O GLN C1031 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1059 through 1107 removed outlier: 4.044A pdb=" N ALA C1065 " --> pdb=" O LEU C1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 197 through 203 removed outlier: 4.332A pdb=" N GLY E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR E 202 " --> pdb=" O SER E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.196A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.577A pdb=" N GLY F 128 " --> pdb=" O GLN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 Processing helix chain 'G' and resid 197 through 203 removed outlier: 4.332A pdb=" N GLY G 201 " --> pdb=" O SER G 197 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR G 202 " --> pdb=" O SER G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.143A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.577A pdb=" N GLY H 128 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'I' and resid 197 through 203 removed outlier: 4.332A pdb=" N GLY I 201 " --> pdb=" O SER I 197 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR I 202 " --> pdb=" O SER I 198 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.499A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 647 " --> pdb=" O SER C 643 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR C 648 " --> pdb=" O CYS C 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.173A 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 removed outlier: 6.210A pdb=" N VAL A 263 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A 283 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 265 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.336A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.951A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 232 through 235 Processing sheet with id=AA8, first strand: chain 'A' and resid 232 through 235 removed outlier: 3.545A pdb=" N CYS A 185 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 367 removed outlier: 3.983A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.518A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 477 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N CYS A 425 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 479 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE A 423 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 481 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 407 through 409 Processing sheet with id=AB4, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.389A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AB6, first strand: chain 'A' and resid 630 through 632 Processing sheet with id=AB7, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.927A 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 778 through 782 Processing sheet with id=AB9, first strand: chain 'A' and resid 802 through 803 Processing sheet with id=AC1, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AC2, first strand: chain 'A' and resid 967 through 969 removed outlier: 4.234A pdb=" N LYS C 779 " --> pdb=" O ALA A 969 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1121 through 1130 removed outlier: 6.508A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.623A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.438A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.327A pdb=" N VAL B 263 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR B 283 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 265 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.043A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.524A pdb=" N GLU B 188 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AD1, first strand: chain 'B' and resid 127 through 129 removed outlier: 4.312A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AD3, first strand: chain 'B' and resid 360 through 367 removed outlier: 4.436A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.818A pdb=" N SER B 440 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP B 444 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 567 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR B 477 " --> pdb=" O CYS B 425 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS B 425 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 479 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 423 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 481 " --> pdb=" O ASN B 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 407 through 409 removed outlier: 6.555A pdb=" N CYS B 407 " --> pdb=" O CYS B 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.325A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 605 through 607 Processing sheet with id=AD8, first strand: chain 'B' and resid 617 through 618 Processing sheet with id=AD9, first strand: chain 'B' and resid 631 through 632 Processing sheet with id=AE1, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AE2, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AE3, first strand: chain 'B' and resid 1121 through 1130 removed outlier: 5.888A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1154 through 1156 Processing sheet with id=AE5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE6, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.210A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.332A pdb=" N VAL C 263 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 283 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU C 265 " --> pdb=" O PHE C 281 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 88 through 90 removed outlier: 7.359A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ARG C 301 " --> pdb=" O THR C 206 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS C 208 " --> pdb=" O ARG C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 127 through 130 removed outlier: 9.102A pdb=" N GLY C 128 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER C 135 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL C 130 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA C 309 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 139 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 232 through 241 removed outlier: 4.906A pdb=" N CYS C 237 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR C 184 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE C 239 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA C 182 " --> pdb=" O PHE C 239 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 147 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AF3, first strand: chain 'C' and resid 360 through 367 removed outlier: 5.608A pdb=" N SER C 362 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 661 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER C 364 " --> pdb=" O VAL C 659 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL C 659 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 374 through 375 removed outlier: 6.235A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 613 " --> pdb=" O TYR C 606 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.808A pdb=" N ILE C 573 " --> pdb=" O CYS C 478 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS C 478 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.785A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS C 502 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'C' and resid 1121 through 1130 removed outlier: 5.834A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.782A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AG2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.558A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.928A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.480A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.709A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.240A pdb=" N GLU E 10 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 131 through 135 removed outlier: 4.294A pdb=" N THR E 146 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 143 " --> pdb=" O THR E 146 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 131 through 135 removed outlier: 5.878A pdb=" N SER E 188 " --> pdb=" O ALA E 179 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 179 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER E 190 " --> pdb=" O PHE E 177 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 161 through 165 removed outlier: 4.591A pdb=" N TYR E 205 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS E 207 " --> pdb=" O LYS E 220 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS E 220 " --> pdb=" O CYS E 207 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.792A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH3, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.282A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.927A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.480A pdb=" N TRP F 148 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.686A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.238A pdb=" N GLU G 10 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 131 through 135 removed outlier: 4.295A pdb=" N THR G 146 " --> pdb=" O SER G 143 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER G 143 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 131 through 135 removed outlier: 5.879A pdb=" N SER G 188 " --> pdb=" O ALA G 179 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA G 179 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER G 190 " --> pdb=" O PHE G 177 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 162 through 165 removed outlier: 4.590A pdb=" N TYR G 205 " --> pdb=" O VAL G 222 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS G 207 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS G 220 " --> pdb=" O CYS G 207 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.817A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AI4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.280A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.928A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.478A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.538A pdb=" N ILE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.963A pdb=" N TYR I 112 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 142 through 143 removed outlier: 3.682A pdb=" N SER I 143 " --> pdb=" O THR I 146 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR I 146 " --> pdb=" O SER I 143 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER I 188 " --> pdb=" O ALA I 179 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA I 179 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER I 190 " --> pdb=" O PHE I 177 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 162 through 165 removed outlier: 4.590A pdb=" N TYR I 205 " --> pdb=" O VAL I 222 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS I 207 " --> pdb=" O LYS I 220 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS I 220 " --> pdb=" O CYS I 207 " (cutoff:3.500A) 1298 hydrogen bonds defined for protein. 3453 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: 17.27 Time building geometry restraints manager: 14.90 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: 7339 1.33 - 1.45: 9861 1.45 - 1.58: 19749 1.58 - 1.70: 0 1.70 - 1.83: 258 Bond restraints: 37207 Sorted by residual: bond pdb=" C MET A 696 " pdb=" N LEU A 697 " ideal model delta sigma weight residual 1.330 1.476 -0.146 1.44e-02 4.82e+03 1.03e+02 bond pdb=" C GLN B 319 " pdb=" N PRO B 320 " ideal model delta sigma weight residual 1.331 1.449 -0.118 1.20e-02 6.94e+03 9.61e+01 bond pdb=" C THR A1175 " pdb=" N ASN A1176 " ideal model delta sigma weight residual 1.328 1.461 -0.133 1.40e-02 5.10e+03 9.04e+01 bond pdb=" C THR C 693 " pdb=" N ARG C 694 " ideal model delta sigma weight residual 1.335 1.457 -0.122 1.31e-02 5.83e+03 8.67e+01 bond pdb=" C VAL H 104 " pdb=" N GLU H 105 " ideal model delta sigma weight residual 1.330 1.220 0.110 1.19e-02 7.06e+03 8.54e+01 ... (remaining 37202 not shown) Histogram of bond angle deviations from ideal: 77.52 - 88.89: 1 88.89 - 100.26: 36 100.26 - 111.64: 16511 111.64 - 123.01: 30163 123.01 - 134.38: 3905 Bond angle restraints: 50616 Sorted by residual: angle pdb=" O SER B1144 " pdb=" C SER B1144 " pdb=" N ASN B1145 " ideal model delta sigma weight residual 122.03 95.72 26.31 7.30e-01 1.88e+00 1.30e+03 angle pdb=" C TYR B 641 " pdb=" CA TYR B 641 " pdb=" CB TYR B 641 " ideal model delta sigma weight residual 110.42 77.52 32.90 1.99e+00 2.53e-01 2.73e+02 angle pdb=" N ARG F 142 " pdb=" CA ARG F 142 " pdb=" C ARG F 142 " ideal model delta sigma weight residual 113.19 102.11 11.08 1.19e+00 7.06e-01 8.67e+01 angle pdb=" CA PRO A1161 " pdb=" C PRO A1161 " pdb=" N THR A1162 " ideal model delta sigma weight residual 115.37 126.83 -11.46 1.32e+00 5.74e-01 7.54e+01 angle pdb=" CA SER B1144 " pdb=" C SER B1144 " pdb=" N ASN B1145 " ideal model delta sigma weight residual 118.57 126.10 -7.53 8.80e-01 1.29e+00 7.32e+01 ... (remaining 50611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 20183 17.83 - 35.66: 1599 35.66 - 53.49: 279 53.49 - 71.32: 61 71.32 - 89.15: 31 Dihedral angle restraints: 22153 sinusoidal: 8406 harmonic: 13747 Sorted by residual: dihedral pdb=" C TYR B 641 " pdb=" N TYR B 641 " pdb=" CA TYR B 641 " pdb=" CB TYR B 641 " ideal model delta harmonic sigma weight residual -122.60 -84.88 -37.72 0 2.50e+00 1.60e-01 2.28e+02 dihedral pdb=" C PHE E 157 " pdb=" N PHE E 157 " pdb=" CA PHE E 157 " pdb=" CB PHE E 157 " ideal model delta harmonic sigma weight residual -122.60 -149.08 26.48 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N TYR B 641 " pdb=" C TYR B 641 " pdb=" CA TYR B 641 " pdb=" CB TYR B 641 " ideal model delta harmonic sigma weight residual 122.80 97.68 25.12 0 2.50e+00 1.60e-01 1.01e+02 ... (remaining 22150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 5530 0.200 - 0.400: 154 0.400 - 0.601: 11 0.601 - 0.801: 1 0.801 - 1.001: 4 Chirality restraints: 5700 Sorted by residual: chirality pdb=" CA PHE E 157 " pdb=" N PHE E 157 " pdb=" C PHE E 157 " pdb=" CB PHE E 157 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA PHE G 157 " pdb=" N PHE G 157 " pdb=" C PHE G 157 " pdb=" CB PHE G 157 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA THR F 94 " pdb=" N THR F 94 " pdb=" C THR F 94 " pdb=" CB THR F 94 " both_signs ideal model delta sigma weight residual False 2.53 1.69 0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 5697 not shown) Planarity restraints: 6520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B1144 " -0.089 2.00e-02 2.50e+03 1.48e-01 2.20e+02 pdb=" C SER B1144 " 0.257 2.00e-02 2.50e+03 pdb=" O SER B1144 " -0.082 2.00e-02 2.50e+03 pdb=" N ASN B1145 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 640 " -0.058 2.00e-02 2.50e+03 1.15e-01 1.32e+02 pdb=" C GLY B 640 " 0.199 2.00e-02 2.50e+03 pdb=" O GLY B 640 " -0.074 2.00e-02 2.50e+03 pdb=" N TYR B 641 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C1190 " 0.046 2.00e-02 2.50e+03 8.97e-02 8.04e+01 pdb=" C SER C1190 " -0.155 2.00e-02 2.50e+03 pdb=" O SER C1190 " 0.057 2.00e-02 2.50e+03 pdb=" N PHE C1191 " 0.053 2.00e-02 2.50e+03 ... (remaining 6517 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 2 1.81 - 2.59: 319 2.59 - 3.36: 46434 3.36 - 4.13: 91760 4.13 - 4.90: 161795 Nonbonded interactions: 300310 Sorted by model distance: nonbonded pdb=" ND2 ASN A 406 " pdb=" ND2 ASN A 582 " model vdw 1.043 3.200 nonbonded pdb=" CG ASN A 406 " pdb=" ND2 ASN A 582 " model vdw 1.781 3.350 nonbonded pdb=" CB TYR B 641 " pdb=" N TYR B 642 " model vdw 2.008 2.816 nonbonded pdb=" OG1 THR F 109 " pdb=" O ASP F 170 " model vdw 2.091 2.440 nonbonded pdb=" OG1 THR H 109 " pdb=" O ASP H 170 " model vdw 2.091 2.440 ... (remaining 300305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 50 or resid 52 through 728 or (resid 729 and (n \ ame N or name CA or name C or name O or name CB )) or resid 730 through 739 or ( \ resid 740 and (name N or name CA or name C or name O or name CB )) or resid 741 \ through 1206)) selection = (chain 'B' and (resid 18 through 50 or resid 52 through 728 or (resid 729 and (n \ ame N or name CA or name C or name O or name CB )) or resid 730 through 739 or ( \ resid 740 and (name N or name CA or name C or name O or name CB )) or resid 741 \ through 1206)) selection = (chain 'C' and (resid 18 through 50 or resid 52 through 1206)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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=0.46 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: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.170 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 102.910 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.240 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.010 0.146 37207 Z= 0.676 Angle : 1.251 32.903 50616 Z= 0.861 Chirality : 0.085 1.001 5700 Planarity : 0.007 0.148 6520 Dihedral : 13.498 89.150 13226 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 1.43 % Allowed : 8.67 % Favored : 89.90 % Rotamer: Outliers : 2.76 % Allowed : 4.14 % Favored : 93.11 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4674 helix: 0.81 (0.20), residues: 717 sheet: -0.18 (0.15), residues: 1264 loop : -1.86 (0.11), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 553 HIS 0.022 0.002 HIS B 91 PHE 0.047 0.002 PHE B1044 TYR 0.034 0.002 TYR C1192 ARG 0.008 0.001 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 353 time to evaluate : 4.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "SER B 965 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8350 (m-40) cc_final: 0.8050 (p0) REVERT: A 988 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6408 (mm-40) REVERT: B 798 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7450 (t) REVERT: B 906 MET cc_start: 0.8476 (ptm) cc_final: 0.6911 (mpp) REVERT: B 1185 SER cc_start: 0.5733 (m) cc_final: 0.4724 (p) REVERT: C 27 LYS cc_start: 0.6038 (mmtm) cc_final: 0.5565 (tttt) REVERT: C 91 HIS cc_start: 0.4972 (t70) cc_final: 0.4499 (t70) REVERT: C 209 THR cc_start: 0.6846 (OUTLIER) cc_final: 0.6240 (m) REVERT: C 240 MET cc_start: 0.7624 (tmm) cc_final: 0.7111 (tmt) REVERT: C 241 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.4505 (p90) REVERT: C 243 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.4749 (p90) REVERT: C 985 ILE cc_start: 0.6198 (mt) cc_final: 0.5857 (mm) REVERT: E 155 ASP cc_start: 0.6452 (t0) cc_final: 0.5989 (p0) REVERT: F 4 MET cc_start: 0.7084 (mtp) cc_final: 0.6878 (mtp) REVERT: G 23 LYS cc_start: 0.9047 (tttm) cc_final: 0.8784 (ttpp) REVERT: G 73 ASP cc_start: 0.7542 (t0) cc_final: 0.7235 (t0) REVERT: G 166 ASN cc_start: 0.2280 (m110) cc_final: 0.1948 (m110) REVERT: H 137 ASN cc_start: 0.5461 (m-40) cc_final: 0.5212 (t0) REVERT: H 208 SER cc_start: 0.6112 (OUTLIER) cc_final: 0.5746 (t) REVERT: I 157 PHE cc_start: 0.6534 (OUTLIER) cc_final: 0.6118 (m-10) outliers start: 111 outliers final: 16 residues processed: 448 average time/residue: 1.2241 time to fit residues: 685.3829 Evaluate side-chains 239 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 988 GLN Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain I residue 157 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 397 optimal weight: 30.0000 chunk 356 optimal weight: 0.8980 chunk 198 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN A 167 HIS ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 HIS A 519 ASN A 981 ASN A 988 GLN A 993 ASN A 994 GLN A1042 ASN A1063 GLN A1119 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN B 107 GLN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 765 ASN B1201 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 244 ASN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 599 GLN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN C1020 GLN C1042 ASN ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 ASN ** G 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN I 99 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37207 Z= 0.205 Angle : 0.728 15.978 50616 Z= 0.382 Chirality : 0.047 0.273 5700 Planarity : 0.005 0.087 6520 Dihedral : 6.450 71.753 5144 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.11 % Favored : 91.42 % Rotamer: Outliers : 2.27 % Allowed : 10.10 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % 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: -1.17 (0.12), residues: 4674 helix: 1.10 (0.20), residues: 729 sheet: -0.12 (0.15), residues: 1283 loop : -1.73 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B1184 HIS 0.006 0.001 HIS A1138 PHE 0.022 0.002 PHE B1044 TYR 0.030 0.002 TYR B 641 ARG 0.013 0.001 ARG C 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 245 time to evaluate : 4.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8309 (m-40) cc_final: 0.8042 (p0) REVERT: A 988 GLN cc_start: 0.7078 (mm110) cc_final: 0.6789 (mm-40) REVERT: B 127 THR cc_start: 0.7739 (OUTLIER) cc_final: 0.7399 (p) REVERT: B 563 MET cc_start: 0.6359 (mtp) cc_final: 0.5919 (mtt) REVERT: B 599 GLN cc_start: 0.2807 (OUTLIER) cc_final: 0.2465 (tp-100) REVERT: B 642 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.3591 (p90) REVERT: B 764 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.4596 (p90) REVERT: B 906 MET cc_start: 0.8320 (ptm) cc_final: 0.6886 (mpp) REVERT: B 1183 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: C 27 LYS cc_start: 0.5978 (mmtm) cc_final: 0.5522 (tttt) REVERT: C 241 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.5104 (p90) REVERT: C 243 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.5093 (p90) REVERT: C 563 MET cc_start: 0.2615 (tpp) cc_final: 0.2235 (mmm) REVERT: C 759 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6177 (pp) REVERT: D 28 ASP cc_start: 0.8647 (t0) cc_final: 0.8408 (t0) REVERT: D 138 ASN cc_start: 0.6195 (m110) cc_final: 0.5691 (t0) REVERT: E 10 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6856 (mm-30) REVERT: E 67 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7838 (ttp80) REVERT: F 173 TYR cc_start: 0.6836 (m-80) cc_final: 0.6174 (m-80) REVERT: G 73 ASP cc_start: 0.7815 (t0) cc_final: 0.7472 (t0) REVERT: H 137 ASN cc_start: 0.5301 (m-40) cc_final: 0.4947 (t0) REVERT: I 157 PHE cc_start: 0.6191 (OUTLIER) cc_final: 0.5956 (m-10) outliers start: 91 outliers final: 35 residues processed: 310 average time/residue: 1.3825 time to fit residues: 527.9143 Evaluate side-chains 245 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 201 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain G residue 210 ASN Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 45 MET Chi-restraints excluded: chain I residue 157 PHE Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 50.0000 chunk 291 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 428 optimal weight: 4.9990 chunk 462 optimal weight: 0.9980 chunk 381 optimal weight: 20.0000 chunk 424 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 343 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 519 ASN ** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 GLN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1063 GLN ** C1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 37207 Z= 0.474 Angle : 0.842 12.705 50616 Z= 0.448 Chirality : 0.053 0.288 5700 Planarity : 0.006 0.072 6520 Dihedral : 6.824 69.883 5126 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.57 % Favored : 89.94 % Rotamer: Outliers : 3.00 % Allowed : 11.57 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.25 % 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: -1.42 (0.12), residues: 4674 helix: 0.65 (0.20), residues: 743 sheet: -0.37 (0.15), residues: 1350 loop : -1.80 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 553 HIS 0.043 0.002 HIS A 486 PHE 0.034 0.003 PHE C1172 TYR 0.041 0.003 TYR C 85 ARG 0.010 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 223 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8451 (m-40) cc_final: 0.8119 (p0) REVERT: A 295 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 642 TYR cc_start: 0.5398 (p90) cc_final: 0.5100 (p90) REVERT: A 734 SER cc_start: 0.6338 (m) cc_final: 0.6054 (t) REVERT: A 994 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: A 1117 CYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 563 MET cc_start: 0.6034 (mtp) cc_final: 0.5614 (mtt) REVERT: B 642 TYR cc_start: 0.4782 (OUTLIER) cc_final: 0.3841 (p90) REVERT: B 764 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.5004 (p90) REVERT: C 178 THR cc_start: 0.6946 (OUTLIER) cc_final: 0.6609 (m) REVERT: C 241 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.5595 (p90) REVERT: C 243 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6147 (p90) REVERT: C 563 MET cc_start: 0.3018 (tpp) cc_final: 0.2635 (mmm) REVERT: C 1192 TYR cc_start: 0.5496 (OUTLIER) cc_final: 0.5264 (m-80) REVERT: D 24 ARG cc_start: 0.7768 (mmp-170) cc_final: 0.7310 (mmp-170) REVERT: D 138 ASN cc_start: 0.6262 (m110) cc_final: 0.5881 (t0) REVERT: E 10 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6921 (mm-30) REVERT: E 157 PHE cc_start: 0.6297 (m-80) cc_final: 0.5918 (m-80) REVERT: G 73 ASP cc_start: 0.7835 (t0) cc_final: 0.7592 (t0) REVERT: H 4 MET cc_start: 0.7269 (mtm) cc_final: 0.7063 (mmm) REVERT: H 137 ASN cc_start: 0.5507 (m-40) cc_final: 0.5173 (t0) REVERT: I 73 ASP cc_start: 0.7808 (t0) cc_final: 0.7408 (t0) REVERT: I 101 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8742 (p) outliers start: 121 outliers final: 49 residues processed: 322 average time/residue: 1.2250 time to fit residues: 494.5504 Evaluate side-chains 252 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 193 time to evaluate : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 797 THR Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 GLN Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain A residue 1187 THR Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain C residue 1181 VAL Chi-restraints excluded: chain C residue 1192 TYR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain G residue 154 LYS Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 423 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 287 optimal weight: 0.0270 chunk 430 optimal weight: 9.9990 chunk 455 optimal weight: 0.0050 chunk 224 optimal weight: 0.8980 chunk 407 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 overall best weight: 0.9854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A1160 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN H 6 GLN I 166 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37207 Z= 0.194 Angle : 0.676 10.953 50616 Z= 0.353 Chirality : 0.045 0.262 5700 Planarity : 0.005 0.073 6520 Dihedral : 6.059 65.496 5121 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.48 % Favored : 91.16 % Rotamer: Outliers : 2.19 % Allowed : 13.12 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.20 (0.12), residues: 4674 helix: 1.08 (0.20), residues: 734 sheet: -0.25 (0.15), residues: 1323 loop : -1.70 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1184 HIS 0.006 0.001 HIS A 486 PHE 0.018 0.002 PHE B 674 TYR 0.024 0.001 TYR B 77 ARG 0.009 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 206 time to evaluate : 4.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8374 (m-40) cc_final: 0.8066 (p0) REVERT: A 734 SER cc_start: 0.5986 (m) cc_final: 0.5721 (t) REVERT: A 928 TYR cc_start: 0.5010 (OUTLIER) cc_final: 0.4646 (m-80) REVERT: A 1117 CYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7755 (m) REVERT: A 1169 ASN cc_start: 0.4762 (p0) cc_final: 0.4539 (p0) REVERT: B 563 MET cc_start: 0.6124 (mtp) cc_final: 0.5708 (mtt) REVERT: B 642 TYR cc_start: 0.4456 (OUTLIER) cc_final: 0.3890 (p90) REVERT: B 764 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.5031 (p90) REVERT: C 241 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.5503 (p90) REVERT: C 243 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.6449 (p90) REVERT: C 563 MET cc_start: 0.3075 (tpp) cc_final: 0.2718 (mmm) REVERT: C 759 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6635 (pp) REVERT: C 1012 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 1186 TYR cc_start: 0.5278 (m-80) cc_final: 0.4904 (m-80) REVERT: D 24 ARG cc_start: 0.7888 (mmp-170) cc_final: 0.7481 (mmp-170) REVERT: D 138 ASN cc_start: 0.6252 (m110) cc_final: 0.5905 (t0) REVERT: E 32 TYR cc_start: 0.8040 (m-80) cc_final: 0.7772 (m-80) REVERT: E 154 LYS cc_start: 0.5622 (tptt) cc_final: 0.5382 (tptt) REVERT: E 157 PHE cc_start: 0.6129 (m-80) cc_final: 0.5837 (m-80) REVERT: G 81 MET cc_start: 0.7983 (tmm) cc_final: 0.7782 (tmm) REVERT: H 1 ASP cc_start: 0.6955 (t0) cc_final: 0.6336 (m-30) REVERT: H 81 GLU cc_start: 0.7572 (pp20) cc_final: 0.7301 (pp20) REVERT: H 137 ASN cc_start: 0.5368 (m-40) cc_final: 0.5026 (t0) REVERT: I 73 ASP cc_start: 0.7803 (t0) cc_final: 0.7416 (t0) outliers start: 88 outliers final: 37 residues processed: 277 average time/residue: 1.2446 time to fit residues: 434.2945 Evaluate side-chains 233 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1173 ILE Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 649 TYR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 379 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 338 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 388 optimal weight: 7.9990 chunk 314 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 overall best weight: 1.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN B 167 HIS ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN H 6 GLN I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37207 Z= 0.231 Angle : 0.671 12.692 50616 Z= 0.349 Chirality : 0.045 0.238 5700 Planarity : 0.005 0.075 6520 Dihedral : 5.911 64.145 5119 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.08 % Favored : 90.56 % Rotamer: Outliers : 2.46 % Allowed : 13.94 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4674 helix: 1.26 (0.20), residues: 732 sheet: -0.20 (0.15), residues: 1306 loop : -1.69 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1184 HIS 0.009 0.001 HIS A1138 PHE 0.031 0.002 PHE C1172 TYR 0.025 0.002 TYR B 77 ARG 0.011 0.000 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 198 time to evaluate : 4.103 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 193 ASN cc_start: 0.8420 (m-40) cc_final: 0.8073 (p0) REVERT: A 295 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 734 SER cc_start: 0.6119 (m) cc_final: 0.5843 (t) REVERT: A 928 TYR cc_start: 0.5036 (OUTLIER) cc_final: 0.4663 (m-80) REVERT: A 1117 CYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7876 (m) REVERT: A 1169 ASN cc_start: 0.4786 (p0) cc_final: 0.4576 (p0) REVERT: B 563 MET cc_start: 0.6036 (mtp) cc_final: 0.5633 (mtt) REVERT: B 642 TYR cc_start: 0.4354 (OUTLIER) cc_final: 0.4021 (p90) REVERT: B 764 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.5036 (p90) REVERT: C 241 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.5596 (p90) REVERT: C 243 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.6553 (p90) REVERT: C 759 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6789 (pp) REVERT: C 1008 MET cc_start: 0.8160 (tmm) cc_final: 0.7881 (tmm) REVERT: C 1012 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8176 (m-80) REVERT: C 1113 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7876 (tpt90) REVERT: D 138 ASN cc_start: 0.6307 (m110) cc_final: 0.6007 (t0) REVERT: E 154 LYS cc_start: 0.5447 (tptt) cc_final: 0.5074 (tptt) REVERT: G 81 MET cc_start: 0.7977 (tmm) cc_final: 0.7674 (tmt) REVERT: H 1 ASP cc_start: 0.7016 (t0) cc_final: 0.6423 (m-30) REVERT: H 81 GLU cc_start: 0.7427 (pp20) cc_final: 0.7203 (pp20) REVERT: H 125 LEU cc_start: 0.3176 (OUTLIER) cc_final: 0.2828 (tp) REVERT: H 137 ASN cc_start: 0.5425 (m-40) cc_final: 0.5074 (t0) REVERT: I 73 ASP cc_start: 0.7749 (t0) cc_final: 0.7275 (t0) outliers start: 99 outliers final: 45 residues processed: 277 average time/residue: 1.2688 time to fit residues: 440.5905 Evaluate side-chains 247 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 191 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1181 VAL Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 782 ILE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1113 ARG Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 153 optimal weight: 9.9990 chunk 409 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 455 optimal weight: 7.9990 chunk 378 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 733 GLN A1160 ASN ** A1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 ASN C1145 ASN D 160 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN F 166 GLN G 3 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 37207 Z= 0.487 Angle : 0.826 14.070 50616 Z= 0.436 Chirality : 0.052 0.277 5700 Planarity : 0.006 0.078 6520 Dihedral : 6.735 61.455 5119 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.30 % Favored : 89.23 % Rotamer: Outliers : 3.18 % Allowed : 14.50 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.29 % 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: -1.43 (0.12), residues: 4674 helix: 0.81 (0.20), residues: 742 sheet: -0.34 (0.14), residues: 1304 loop : -1.86 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1184 HIS 0.013 0.002 HIS A1138 PHE 0.047 0.003 PHE C1172 TYR 0.044 0.003 TYR C1192 ARG 0.017 0.001 ARG B1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 203 time to evaluate : 4.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8446 (m-40) cc_final: 0.8052 (p0) REVERT: A 295 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 764 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.5953 (p90) REVERT: A 928 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.5013 (m-80) REVERT: B 398 ASN cc_start: 0.8591 (m-40) cc_final: 0.8027 (t0) REVERT: B 563 MET cc_start: 0.6055 (mtp) cc_final: 0.5680 (mtt) REVERT: B 642 TYR cc_start: 0.4573 (OUTLIER) cc_final: 0.3963 (p90) REVERT: B 764 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.6728 (p90) REVERT: C 563 MET cc_start: 0.3356 (mmm) cc_final: 0.2552 (tpt) REVERT: C 726 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5579 (t70) REVERT: C 1186 TYR cc_start: 0.5653 (m-80) cc_final: 0.5402 (m-80) REVERT: D 116 PHE cc_start: 0.3293 (m-10) cc_final: 0.2968 (m-10) REVERT: D 138 ASN cc_start: 0.6355 (m110) cc_final: 0.6055 (t0) REVERT: H 1 ASP cc_start: 0.7132 (t0) cc_final: 0.6578 (m-30) REVERT: H 81 GLU cc_start: 0.7674 (pp20) cc_final: 0.7446 (pp20) REVERT: H 137 ASN cc_start: 0.5568 (m-40) cc_final: 0.5312 (t0) REVERT: I 73 ASP cc_start: 0.7789 (t0) cc_final: 0.7261 (t0) outliers start: 128 outliers final: 60 residues processed: 302 average time/residue: 1.2087 time to fit residues: 460.0634 Evaluate side-chains 251 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 185 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 642 TYR Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 925 CYS Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1187 THR Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 726 ASP Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 933 LYS Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1155 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 439 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 259 optimal weight: 0.5980 chunk 332 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 383 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 453 optimal weight: 4.9990 chunk 284 optimal weight: 20.0000 chunk 276 optimal weight: 30.0000 chunk 209 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1145 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37207 Z= 0.175 Angle : 0.673 14.296 50616 Z= 0.348 Chirality : 0.045 0.290 5700 Planarity : 0.005 0.080 6520 Dihedral : 5.980 64.656 5117 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.56 % Favored : 91.14 % Rotamer: Outliers : 2.04 % Allowed : 16.15 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.13 % 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: -1.19 (0.12), residues: 4674 helix: 1.18 (0.20), residues: 737 sheet: -0.17 (0.15), residues: 1253 loop : -1.74 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 553 HIS 0.006 0.001 HIS C1122 PHE 0.027 0.002 PHE C1172 TYR 0.021 0.001 TYR B 641 ARG 0.013 0.001 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 199 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8242 (m-40) cc_final: 0.7870 (p0) REVERT: A 251 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8870 (tp) REVERT: A 764 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5690 (p90) REVERT: A 928 TYR cc_start: 0.5193 (OUTLIER) cc_final: 0.4731 (m-80) REVERT: A 1117 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7607 (m) REVERT: B 398 ASN cc_start: 0.8567 (m-40) cc_final: 0.7959 (t0) REVERT: B 553 TRP cc_start: 0.5098 (t-100) cc_final: 0.4045 (m100) REVERT: B 764 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.5394 (p90) REVERT: C 243 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.5716 (p90) REVERT: C 563 MET cc_start: 0.3387 (mmm) cc_final: 0.2699 (tpt) REVERT: C 928 TYR cc_start: 0.4204 (m-10) cc_final: 0.3962 (m-10) REVERT: C 1012 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8236 (m-10) REVERT: D 4 MET cc_start: 0.5930 (mtm) cc_final: 0.5557 (mtm) REVERT: D 138 ASN cc_start: 0.6510 (m110) cc_final: 0.6278 (t0) REVERT: E 154 LYS cc_start: 0.5647 (tptt) cc_final: 0.5239 (tptt) REVERT: E 155 ASP cc_start: 0.5589 (t0) cc_final: 0.5182 (t70) REVERT: H 1 ASP cc_start: 0.7059 (t0) cc_final: 0.6385 (p0) REVERT: H 81 GLU cc_start: 0.7837 (pp20) cc_final: 0.7627 (pp20) REVERT: H 125 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4272 (tp) REVERT: H 137 ASN cc_start: 0.5381 (m-40) cc_final: 0.5123 (t0) REVERT: I 73 ASP cc_start: 0.7705 (t0) cc_final: 0.7212 (t0) outliers start: 82 outliers final: 40 residues processed: 267 average time/residue: 1.2637 time to fit residues: 420.8106 Evaluate side-chains 232 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 241 TYR Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 161 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 280 optimal weight: 0.0270 chunk 181 optimal weight: 3.9990 chunk 271 optimal weight: 50.0000 chunk 136 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 356 optimal weight: 40.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A1160 ASN ** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 37207 Z= 0.319 Angle : 0.731 13.519 50616 Z= 0.380 Chirality : 0.047 0.299 5700 Planarity : 0.005 0.082 6520 Dihedral : 6.151 63.048 5115 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.44 % Favored : 90.19 % Rotamer: Outliers : 2.22 % Allowed : 16.74 % Favored : 81.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.27 % 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 (0.12), residues: 4674 helix: 1.18 (0.20), residues: 731 sheet: -0.30 (0.15), residues: 1287 loop : -1.76 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 553 HIS 0.014 0.002 HIS C 91 PHE 0.031 0.002 PHE C1172 TYR 0.030 0.002 TYR B 77 ARG 0.015 0.001 ARG C1179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 186 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASN cc_start: 0.8327 (m-40) cc_final: 0.7952 (p0) REVERT: A 295 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 764 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.5475 (p90) REVERT: A 928 TYR cc_start: 0.5471 (OUTLIER) cc_final: 0.4999 (m-80) REVERT: B 398 ASN cc_start: 0.8793 (m-40) cc_final: 0.8057 (t0) REVERT: B 399 PHE cc_start: 0.7565 (p90) cc_final: 0.7226 (p90) REVERT: B 764 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6256 (p90) REVERT: C 91 HIS cc_start: 0.5988 (t70) cc_final: 0.5763 (t-90) REVERT: C 563 MET cc_start: 0.3198 (mmm) cc_final: 0.1514 (tpt) REVERT: C 928 TYR cc_start: 0.4579 (m-10) cc_final: 0.4347 (m-10) REVERT: C 1012 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: D 4 MET cc_start: 0.5959 (mtm) cc_final: 0.5718 (mtm) REVERT: G 159 GLU cc_start: 0.6405 (tp30) cc_final: 0.6117 (mm-30) REVERT: H 1 ASP cc_start: 0.7039 (t0) cc_final: 0.6400 (p0) REVERT: H 81 GLU cc_start: 0.7895 (pp20) cc_final: 0.7666 (pp20) REVERT: H 125 LEU cc_start: 0.4467 (OUTLIER) cc_final: 0.3856 (tp) REVERT: I 73 ASP cc_start: 0.7703 (t0) cc_final: 0.7214 (t0) REVERT: I 101 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8676 (p) outliers start: 89 outliers final: 56 residues processed: 260 average time/residue: 1.2150 time to fit residues: 398.2465 Evaluate side-chains 239 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 176 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain B residue 77 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 412 optimal weight: 2.9990 chunk 434 optimal weight: 10.0000 chunk 396 optimal weight: 50.0000 chunk 423 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 382 optimal weight: 8.9990 chunk 400 optimal weight: 20.0000 chunk 421 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 GLN A1160 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37207 Z= 0.290 Angle : 0.718 13.239 50616 Z= 0.372 Chirality : 0.047 0.281 5700 Planarity : 0.005 0.083 6520 Dihedral : 6.113 63.309 5113 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.00 % Favored : 89.68 % Rotamer: Outliers : 1.97 % Allowed : 17.38 % Favored : 80.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.25 % 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: -1.26 (0.12), residues: 4674 helix: 1.19 (0.20), residues: 731 sheet: -0.31 (0.15), residues: 1287 loop : -1.77 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 148 HIS 0.013 0.001 HIS C 91 PHE 0.031 0.002 PHE F 209 TYR 0.028 0.002 TYR B 77 ARG 0.010 0.001 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 185 time to evaluate : 4.087 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: A 193 ASN cc_start: 0.8284 (m-40) cc_final: 0.7920 (p0) REVERT: A 295 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8632 (mp) REVERT: A 764 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.5361 (p90) REVERT: A 928 TYR cc_start: 0.5434 (OUTLIER) cc_final: 0.4957 (m-80) REVERT: A 1169 ASN cc_start: 0.4604 (p0) cc_final: 0.4376 (p0) REVERT: B 397 TYR cc_start: 0.8265 (p90) cc_final: 0.8001 (p90) REVERT: B 398 ASN cc_start: 0.8827 (m-40) cc_final: 0.8103 (t0) REVERT: B 399 PHE cc_start: 0.7592 (p90) cc_final: 0.7253 (p90) REVERT: B 764 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.6599 (p90) REVERT: C 563 MET cc_start: 0.3217 (mmm) cc_final: 0.1534 (tpt) REVERT: C 928 TYR cc_start: 0.4678 (m-10) cc_final: 0.4428 (m-10) REVERT: C 1012 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: D 4 MET cc_start: 0.6033 (mtm) cc_final: 0.5725 (mtm) REVERT: E 154 LYS cc_start: 0.5499 (tptt) cc_final: 0.4925 (tmtt) REVERT: G 159 GLU cc_start: 0.6540 (tp30) cc_final: 0.6296 (mm-30) REVERT: H 1 ASP cc_start: 0.7045 (t0) cc_final: 0.6409 (p0) REVERT: H 81 GLU cc_start: 0.8011 (pp20) cc_final: 0.7767 (pp20) REVERT: H 125 LEU cc_start: 0.4479 (OUTLIER) cc_final: 0.3853 (tp) REVERT: I 73 ASP cc_start: 0.7692 (t0) cc_final: 0.7190 (t0) outliers start: 79 outliers final: 57 residues processed: 253 average time/residue: 1.2598 time to fit residues: 402.1444 Evaluate side-chains 243 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 180 time to evaluate : 3.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1204 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 277 optimal weight: 7.9990 chunk 447 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 469 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 229 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 37207 Z= 0.246 Angle : 0.707 13.754 50616 Z= 0.364 Chirality : 0.046 0.280 5700 Planarity : 0.005 0.081 6520 Dihedral : 6.012 63.502 5113 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.78 % Favored : 89.90 % Rotamer: Outliers : 1.90 % Allowed : 17.51 % Favored : 80.60 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.21 (0.12), residues: 4674 helix: 1.21 (0.20), residues: 740 sheet: -0.28 (0.15), residues: 1297 loop : -1.74 (0.12), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 148 HIS 0.009 0.001 HIS C1138 PHE 0.025 0.002 PHE C1172 TYR 0.026 0.002 TYR B 77 ARG 0.009 0.000 ARG D 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9348 Ramachandran restraints generated. 4674 Oldfield, 0 Emsley, 4674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 189 time to evaluate : 3.958 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: A 193 ASN cc_start: 0.8216 (m-40) cc_final: 0.7861 (p0) REVERT: A 295 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 928 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.4917 (m-80) REVERT: B 397 TYR cc_start: 0.8276 (p90) cc_final: 0.7970 (p90) REVERT: B 398 ASN cc_start: 0.8797 (m-40) cc_final: 0.8103 (t0) REVERT: B 399 PHE cc_start: 0.7661 (p90) cc_final: 0.7310 (p90) REVERT: B 764 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.6752 (p90) REVERT: B 1012 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7437 (t80) REVERT: C 563 MET cc_start: 0.3186 (mmm) cc_final: 0.1567 (tpt) REVERT: C 928 TYR cc_start: 0.4738 (m-10) cc_final: 0.4484 (m-10) REVERT: C 1012 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: D 4 MET cc_start: 0.5993 (mtm) cc_final: 0.5678 (mtm) REVERT: D 24 ARG cc_start: 0.7774 (mmp-170) cc_final: 0.7362 (mmp-170) REVERT: G 82 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7617 (tp30) REVERT: G 159 GLU cc_start: 0.6538 (tp30) cc_final: 0.6278 (mm-30) REVERT: H 1 ASP cc_start: 0.7033 (t0) cc_final: 0.6393 (p0) REVERT: H 81 GLU cc_start: 0.7981 (pp20) cc_final: 0.7729 (pp20) REVERT: H 125 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.3966 (tp) REVERT: I 73 ASP cc_start: 0.7680 (t0) cc_final: 0.7191 (t0) REVERT: I 101 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8654 (p) outliers start: 76 outliers final: 57 residues processed: 253 average time/residue: 1.3654 time to fit residues: 430.2705 Evaluate side-chains 245 residues out of total 4061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 181 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 928 TYR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1051 ILE Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain A residue 1117 CYS Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1160 ASN Chi-restraints excluded: chain A residue 1162 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 609 TYR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 PHE Chi-restraints excluded: chain B residue 865 PHE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1012 PHE Chi-restraints excluded: chain B residue 1116 PHE Chi-restraints excluded: chain B residue 1183 GLU Chi-restraints excluded: chain B residue 1184 TRP Chi-restraints excluded: chain B residue 1200 LEU Chi-restraints excluded: chain B residue 1204 TYR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 243 TYR Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 620 CYS Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 641 TYR Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 766 HIS Chi-restraints excluded: chain C residue 1012 PHE Chi-restraints excluded: chain C residue 1047 ILE Chi-restraints excluded: chain C residue 1117 CYS Chi-restraints excluded: chain C residue 1153 TYR Chi-restraints excluded: chain C residue 1204 TYR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 471 random chunks: chunk 296 optimal weight: 8.9990 chunk 398 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 374 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 ASN A1160 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 785 ASN ** B 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1145 ASN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.113759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.081976 restraints weight = 172907.678| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 4.57 r_work: 0.3267 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37207 Z= 0.210 Angle : 0.689 13.187 50616 Z= 0.354 Chirality : 0.045 0.281 5700 Planarity : 0.005 0.083 6520 Dihedral : 5.874 63.814 5113 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.63 % Favored : 90.13 % Rotamer: Outliers : 1.80 % Allowed : 17.83 % Favored : 80.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4674 helix: 1.28 (0.20), residues: 740 sheet: -0.30 (0.14), residues: 1353 loop : -1.70 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 148 HIS 0.007 0.001 HIS A1138 PHE 0.022 0.001 PHE F 209 TYR 0.035 0.001 TYR B 928 ARG 0.011 0.000 ARG H 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10682.95 seconds wall clock time: 192 minutes 59.22 seconds (11579.22 seconds total)