Starting phenix.real_space_refine on Tue Feb 20 18:42:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcz_32430/02_2024/7wcz_32430.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcz_32430/02_2024/7wcz_32430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcz_32430/02_2024/7wcz_32430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcz_32430/02_2024/7wcz_32430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcz_32430/02_2024/7wcz_32430.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wcz_32430/02_2024/7wcz_32430.pdb" } resolution = 3.5 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= 0.005 sd= 0.095 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 130 5.16 5 C 18286 2.51 5 N 4770 2.21 5 O 5493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1": "OE1" <-> "OE2" Residue "a GLU 31": "OE1" <-> "OE2" Residue "a TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "a TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 89": "OD1" <-> "OD2" Residue "a PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 1": "OD1" <-> "OD2" Residue "b ASP 15": "OD1" <-> "OD2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b GLU 61": "OE1" <-> "OE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 128": "OE1" <-> "OE2" Residue "b PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 175": "OD1" <-> "OD2" Residue "b TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 200": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1092": "OE1" <-> "OE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "C ASP 1146": "OD1" <-> "OD2" 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: 28679 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'CIS': 1, 'PTRANS': 52, 'TRANS': 1025} Chain breaks: 6 Chain: "a" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1627 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 200} Chain: "b" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1690 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 8 Chain: "C" Number of atoms: 8454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8454 Classifications: {'peptide': 1079} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 8 Time building chain proxies: 15.09, per 1000 atoms: 0.53 Number of scatterers: 28679 At special positions: 0 Unit cell: (147.555, 160.671, 280.901, 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 130 16.00 O 5493 8.00 N 4770 7.00 C 18286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 96 " distance=2.03 Simple disulfide: pdb=" SG CYS a 144 " - pdb=" SG CYS a 199 " distance=2.03 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 94 " distance=2.03 Simple disulfide: pdb=" SG CYS b 139 " - pdb=" SG CYS b 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.52 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.99 Conformation dependent library (CDL) restraints added in 5.1 seconds 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6872 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 59 sheets defined 20.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.531A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.793A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.553A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.688A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.586A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.561A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.578A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.783A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 3.986A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 65 removed outlier: 3.822A pdb=" N LYS a 65 " --> pdb=" O GLN a 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 62 through 65' Processing helix chain 'a' and resid 87 through 91 removed outlier: 3.880A pdb=" N SER a 91 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 131 removed outlier: 4.348A pdb=" N LEU b 130 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR b 131 " --> pdb=" O SER b 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 126 through 131' Processing helix chain 'b' and resid 188 through 193 removed outlier: 3.535A pdb=" N GLU b 192 " --> pdb=" O LYS b 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.561A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.570A pdb=" N TYR B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 506' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.795A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.316A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 780 removed outlier: 3.528A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.581A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 removed outlier: 3.526A pdb=" N PHE B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.586A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.736A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.516A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1032 removed outlier: 4.028A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.562A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.569A pdb=" N TYR C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 506' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.794A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.316A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 780 removed outlier: 3.527A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.580A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 removed outlier: 3.526A pdb=" N PHE C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.585A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.736A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.517A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.029A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1160 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.184A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.432A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.805A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.200A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 142 removed outlier: 7.635A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.525A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.814A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.845A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.618A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.969A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.562A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.865A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'a' and resid 3 through 6 removed outlier: 3.574A pdb=" N GLN a 3 " --> pdb=" O SER a 25 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL a 18 " --> pdb=" O PHE a 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU a 82 " --> pdb=" O THR a 69 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR a 69 " --> pdb=" O GLU a 82 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA a 92 " --> pdb=" O VAL a 113 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR a 33 " --> pdb=" O ASP a 99 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET a 34 " --> pdb=" O GLY a 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP a 36 " --> pdb=" O ILE a 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP a 57 " --> pdb=" O ASN a 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLU a 10 " --> pdb=" O LEU a 112 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR a 114 " --> pdb=" O GLU a 10 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL a 12 " --> pdb=" O THR a 114 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL a 113 " --> pdb=" O ALA a 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA a 92 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 124 through 128 removed outlier: 4.009A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 124 through 128 removed outlier: 4.009A pdb=" N GLY a 143 " --> pdb=" O LEU a 128 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS a 144 " --> pdb=" O SER a 183 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER a 183 " --> pdb=" O CYS a 144 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY a 148 " --> pdb=" O TYR a 179 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR a 179 " --> pdb=" O GLY a 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 155 through 158 removed outlier: 3.759A pdb=" N VAL a 197 " --> pdb=" O ILE a 214 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.741A pdb=" N THR b 22 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 10 through 12 removed outlier: 6.889A pdb=" N LEU b 11 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU b 39 " --> pdb=" O TYR b 55 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR b 55 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP b 41 " --> pdb=" O LEU b 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 30 through 31 removed outlier: 3.637A pdb=" N LYS b 36 " --> pdb=" O TYR b 31 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 122 through 123 removed outlier: 3.924A pdb=" N PHE b 123 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL b 138 " --> pdb=" O PHE b 123 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR b 178 " --> pdb=" O ASN b 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 158 through 159 removed outlier: 3.872A pdb=" N ASN b 150 " --> pdb=" O THR b 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.166A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.766A pdb=" N PHE B 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.646A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.954A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.814A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.572A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 357 through 361 removed outlier: 3.672A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR B 393 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 423 through 424 removed outlier: 4.014A pdb=" N GLU B 465 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.674A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.846A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.167A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.646A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.954A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.813A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.486A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 357 through 361 removed outlier: 3.672A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 393 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 423 through 424 removed outlier: 4.014A pdb=" N GLU C 465 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.236A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.675A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AG4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG5, first strand: chain 'C' and resid 1094 through 1097 1015 hydrogen bonds defined for protein. 2838 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: 12.41 Time building geometry restraints manager: 11.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.40: 12224 1.40 - 1.65: 16957 1.65 - 1.90: 165 1.90 - 2.15: 1 2.15 - 2.40: 1 Bond restraints: 29348 Sorted by residual: bond pdb=" C SER B 325 " pdb=" N ILE B 326 " ideal model delta sigma weight residual 1.329 2.403 -1.073 1.37e-02 5.33e+03 6.14e+03 bond pdb=" C LEU B 585 " pdb=" N ASP B 586 " ideal model delta sigma weight residual 1.328 2.005 -0.677 1.44e-02 4.82e+03 2.21e+03 bond pdb=" C VAL B 595 " pdb=" N SER B 596 " ideal model delta sigma weight residual 1.330 1.154 0.176 1.45e-02 4.76e+03 1.47e+02 bond pdb=" C THR B 315 " pdb=" N SER B 316 " ideal model delta sigma weight residual 1.331 1.261 0.070 1.39e-02 5.18e+03 2.51e+01 bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.337 1.383 -0.047 1.06e-02 8.90e+03 1.93e+01 ... (remaining 29343 not shown) Histogram of bond angle deviations from ideal: 100.69 - 107.37: 977 107.37 - 114.05: 16322 114.05 - 120.74: 11680 120.74 - 127.42: 10676 127.42 - 134.10: 264 Bond angle restraints: 39919 Sorted by residual: angle pdb=" C LEU B 585 " pdb=" N ASP B 586 " pdb=" CA ASP B 586 " ideal model delta sigma weight residual 122.07 102.28 19.79 2.01e+00 2.48e-01 9.69e+01 angle pdb=" C SER B 325 " pdb=" N ILE B 326 " pdb=" CA ILE B 326 " ideal model delta sigma weight residual 123.11 110.46 12.65 1.36e+00 5.41e-01 8.65e+01 angle pdb=" O SER B 325 " pdb=" C SER B 325 " pdb=" N ILE B 326 " ideal model delta sigma weight residual 123.27 133.71 -10.44 1.18e+00 7.18e-01 7.83e+01 angle pdb=" CA SER B 325 " pdb=" C SER B 325 " pdb=" N ILE B 326 " ideal model delta sigma weight residual 116.37 105.96 10.41 1.19e+00 7.06e-01 7.65e+01 angle pdb=" O LEU B 585 " pdb=" C LEU B 585 " pdb=" N ASP B 586 " ideal model delta sigma weight residual 123.21 132.09 -8.88 1.27e+00 6.20e-01 4.89e+01 ... (remaining 39914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 16818 26.29 - 52.58: 580 52.58 - 78.87: 58 78.87 - 105.16: 10 105.16 - 131.45: 2 Dihedral angle restraints: 17468 sinusoidal: 6788 harmonic: 10680 Sorted by residual: dihedral pdb=" CA CYS C 361 " pdb=" C CYS C 361 " pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta harmonic sigma weight residual 180.00 48.55 131.45 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 48.57 131.43 0 5.00e+00 4.00e-02 6.91e+02 dihedral pdb=" CB CYS b 139 " pdb=" SG CYS b 139 " pdb=" SG CYS b 199 " pdb=" CB CYS b 199 " ideal model delta sinusoidal sigma weight residual 93.00 175.69 -82.69 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 17465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3853 0.066 - 0.131: 605 0.131 - 0.197: 40 0.197 - 0.262: 7 0.262 - 0.328: 1 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CB ILE b 155 " pdb=" CA ILE b 155 " pdb=" CG1 ILE b 155 " pdb=" CG2 ILE b 155 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ALA b 114 " pdb=" N ALA b 114 " pdb=" C ALA b 114 " pdb=" CB ALA b 114 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB THR b 119 " pdb=" CA THR b 119 " pdb=" OG1 THR b 119 " pdb=" CG2 THR b 119 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4503 not shown) Planarity restraints: 5163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 315 " 0.032 2.00e-02 2.50e+03 6.92e-02 4.79e+01 pdb=" C THR B 315 " -0.120 2.00e-02 2.50e+03 pdb=" O THR B 315 " 0.046 2.00e-02 2.50e+03 pdb=" N SER B 316 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 117 " 0.032 2.00e-02 2.50e+03 6.34e-02 4.01e+01 pdb=" C ALA a 117 " -0.110 2.00e-02 2.50e+03 pdb=" O ALA a 117 " 0.042 2.00e-02 2.50e+03 pdb=" N ALA a 118 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG b 113 " -0.031 2.00e-02 2.50e+03 6.16e-02 3.80e+01 pdb=" C ARG b 113 " 0.107 2.00e-02 2.50e+03 pdb=" O ARG b 113 " -0.041 2.00e-02 2.50e+03 pdb=" N ALA b 114 " -0.035 2.00e-02 2.50e+03 ... (remaining 5160 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 254 2.64 - 3.21: 22770 3.21 - 3.77: 42266 3.77 - 4.34: 59444 4.34 - 4.90: 97579 Nonbonded interactions: 222313 Sorted by model distance: nonbonded pdb=" NE2 GLN B 787 " pdb=" OD1 ASN C 703 " model vdw 2.076 2.520 nonbonded pdb=" NE2 GLN B 787 " pdb=" O VAL C 701 " model vdw 2.126 2.520 nonbonded pdb=" NE2 GLN A 787 " pdb=" OD1 ASN B 703 " model vdw 2.140 2.520 nonbonded pdb=" NE2 GLN A 787 " pdb=" O VAL B 701 " model vdw 2.161 2.520 nonbonded pdb=" NE2 GLN A 895 " pdb=" OD1 ASN B1074 " model vdw 2.214 2.520 ... (remaining 222308 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.560 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 75.200 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.150 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 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 : 0.008 1.073 29348 Z= 0.622 Angle : 0.697 19.787 39919 Z= 0.421 Chirality : 0.047 0.328 4506 Planarity : 0.006 0.069 5163 Dihedral : 12.674 131.451 10479 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.12 % Allowed : 4.24 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.11), residues: 3616 helix: -4.64 (0.05), residues: 654 sheet: -0.25 (0.16), residues: 827 loop : -2.18 (0.11), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 56 HIS 0.002 0.000 HIS B 146 PHE 0.014 0.001 PHE C 490 TYR 0.017 0.001 TYR A 380 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7232 Ramachandran restraints generated. 3616 Oldfield, 0 Emsley, 3616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 782 time to evaluate : 3.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 PHE cc_start: 0.7212 (p90) cc_final: 0.6798 (p90) REVERT: A 985 ASP cc_start: 0.7725 (m-30) cc_final: 0.6699 (m-30) REVERT: A 1081 ILE cc_start: 0.8752 (mm) cc_final: 0.8527 (mm) REVERT: a 139 MET cc_start: 0.1435 (ppp) cc_final: 0.0361 (mpp) REVERT: b 30 LEU cc_start: 0.6263 (tt) cc_final: 0.5823 (tp) REVERT: b 31 TYR cc_start: -0.2336 (t80) cc_final: -0.2716 (t80) REVERT: b 56 TRP cc_start: 0.3300 (m100) cc_final: 0.2500 (m100) REVERT: b 98 TYR cc_start: 0.3419 (t80) cc_final: 0.2532 (t80) REVERT: b 174 LYS cc_start: 0.3687 (mmtt) cc_final: 0.3464 (ptmm) REVERT: B 326 ILE cc_start: 0.4591 (mm) cc_final: 0.4295 (mt) REVERT: B 902 MET cc_start: 0.7935 (mmm) cc_final: 0.7714 (mmt) REVERT: B 933 LYS cc_start: 0.8673 (mttt) cc_final: 0.8366 (pttp) REVERT: C 316 SER cc_start: 0.8278 (p) cc_final: 0.8034 (p) REVERT: C 468 ILE cc_start: 0.4870 (pt) cc_final: 0.4586 (pt) REVERT: C 585 LEU cc_start: 0.5332 (mt) cc_final: 0.4939 (mt) REVERT: C 791 THR cc_start: 0.7130 (m) cc_final: 0.6856 (p) REVERT: C 902 MET cc_start: 0.8255 (mmm) cc_final: 0.8029 (mmt) REVERT: C 978 ASN cc_start: 0.8671 (m-40) cc_final: 0.8320 (p0) outliers start: 4 outliers final: 1 residues processed: 786 average time/residue: 0.4150 time to fit residues: 505.8253 Evaluate side-chains 354 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.3980 chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 284 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 211 optimal weight: 0.9990 chunk 329 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 149 ASN A 448 ASN A 450 ASN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 703 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1106 GLN a 62 GLN b 171 GLN b 195 ASN b 217 ASN B 164 ASN B 414 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 856 ASN B 914 ASN B 935 GLN B 955 ASN B1048 HIS B1106 GLN C 49 HIS C 185 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 914 ASN C1010 GLN C1048 HIS C1101 HIS C1106 GLN C1119 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29348 Z= 0.206 Angle : 0.588 9.775 39919 Z= 0.316 Chirality : 0.045 0.175 4506 Planarity : 0.005 0.062 5163 Dihedral : 4.502 54.002 3925 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.49 % Allowed : 12.86 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.65 (0.12), residues: 3620 helix: -1.11 (0.16), residues: 681 sheet: 0.35 (0.17), residues: 814 loop : -1.74 (0.11), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.005 0.001 HIS C 49 PHE 0.028 0.002 PHE A 135 TYR 0.020 0.002 TYR B 160 ARG 0.012 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 394 time to evaluate : 3.055 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 541 PHE cc_start: 0.7113 (p90) cc_final: 0.6886 (p90) REVERT: A 608 VAL cc_start: 0.7667 (t) cc_final: 0.7431 (p) REVERT: A 697 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6733 (mtt) REVERT: a 19 LYS cc_start: 0.5797 (mttt) cc_final: 0.5533 (ttpp) REVERT: a 139 MET cc_start: 0.1437 (ppp) cc_final: 0.0211 (mpp) REVERT: b 30 LEU cc_start: 0.5811 (tt) cc_final: 0.5431 (tt) REVERT: b 98 TYR cc_start: 0.3803 (t80) cc_final: 0.2667 (t80) REVERT: b 174 LYS cc_start: 0.3317 (mmtt) cc_final: 0.3075 (ptmm) REVERT: B 153 MET cc_start: 0.0977 (pmm) cc_final: 0.0231 (pmm) REVERT: B 158 ARG cc_start: 0.5118 (OUTLIER) cc_final: 0.4905 (mmm160) REVERT: B 309 GLU cc_start: 0.7647 (pt0) cc_final: 0.7305 (pt0) REVERT: B 902 MET cc_start: 0.8399 (mmm) cc_final: 0.8195 (mmt) REVERT: C 228 ASP cc_start: 0.6579 (t0) cc_final: 0.6262 (t0) REVERT: C 791 THR cc_start: 0.7336 (m) cc_final: 0.7087 (p) REVERT: C 938 LEU cc_start: 0.8494 (mt) cc_final: 0.8242 (mt) REVERT: C 978 ASN cc_start: 0.8697 (m-40) cc_final: 0.8204 (t0) REVERT: C 1014 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7364 (mtt180) outliers start: 80 outliers final: 43 residues processed: 458 average time/residue: 0.3791 time to fit residues: 281.6795 Evaluate side-chains 325 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 51 ILE Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 274 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 330 optimal weight: 0.7980 chunk 356 optimal weight: 0.9980 chunk 294 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 655 HIS A 690 GLN A 703 ASN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 39 GLN ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 95 GLN b 217 ASN B 185 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1119 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 919 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29348 Z= 0.289 Angle : 0.629 10.925 39919 Z= 0.336 Chirality : 0.046 0.194 4506 Planarity : 0.005 0.061 5163 Dihedral : 4.769 40.551 3925 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.77 % Allowed : 15.70 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.00 (0.13), residues: 3620 helix: 0.54 (0.19), residues: 711 sheet: 0.29 (0.17), residues: 848 loop : -1.58 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 158 HIS 0.009 0.001 HIS A 519 PHE 0.028 0.002 PHE A 643 TYR 0.018 0.002 TYR A 380 ARG 0.007 0.001 ARG C 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 320 time to evaluate : 3.087 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 608 VAL cc_start: 0.8171 (t) cc_final: 0.7813 (p) REVERT: A 900 MET cc_start: 0.7879 (mtm) cc_final: 0.7475 (mtp) REVERT: a 139 MET cc_start: 0.1727 (ppp) cc_final: 0.0389 (mpp) REVERT: b 30 LEU cc_start: 0.5905 (tt) cc_final: 0.5397 (tt) REVERT: b 98 TYR cc_start: 0.4165 (t80) cc_final: 0.2650 (t80) REVERT: B 153 MET cc_start: 0.0964 (pmm) cc_final: 0.0560 (pmm) REVERT: B 740 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6612 (mtt) REVERT: B 904 TYR cc_start: 0.6630 (t80) cc_final: 0.6375 (t80) REVERT: C 480 CYS cc_start: 0.4189 (OUTLIER) cc_final: 0.3575 (t) REVERT: C 737 ASP cc_start: 0.8155 (t0) cc_final: 0.7889 (t0) REVERT: C 938 LEU cc_start: 0.8535 (mt) cc_final: 0.8304 (mt) REVERT: C 974 SER cc_start: 0.8856 (t) cc_final: 0.8376 (p) REVERT: C 978 ASN cc_start: 0.8635 (m-40) cc_final: 0.8360 (t0) REVERT: C 1156 PHE cc_start: -0.2197 (m-80) cc_final: -0.2525 (m-80) outliers start: 121 outliers final: 73 residues processed: 412 average time/residue: 0.3449 time to fit residues: 240.4471 Evaluate side-chains 333 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 258 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 197 VAL Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 chunk 331 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 314 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 95 GLN B 185 ASN B 563 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 506 GLN C 655 HIS ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 969 ASN C1002 GLN C1005 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29348 Z= 0.180 Angle : 0.525 6.778 39919 Z= 0.279 Chirality : 0.044 0.174 4506 Planarity : 0.004 0.059 5163 Dihedral : 4.414 39.632 3924 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.18 % Allowed : 17.78 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3620 helix: 1.14 (0.20), residues: 715 sheet: 0.45 (0.17), residues: 843 loop : -1.39 (0.12), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 158 HIS 0.004 0.001 HIS A 519 PHE 0.022 0.001 PHE A 135 TYR 0.020 0.001 TYR A 380 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 268 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.2500 (tmm) cc_final: 0.2226 (tmm) REVERT: A 541 PHE cc_start: 0.7081 (p90) cc_final: 0.6694 (p90) REVERT: A 608 VAL cc_start: 0.7920 (t) cc_final: 0.7598 (p) REVERT: A 661 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 737 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6713 (t70) REVERT: A 900 MET cc_start: 0.7890 (mtm) cc_final: 0.7444 (mtp) REVERT: a 139 MET cc_start: 0.2180 (ppp) cc_final: 0.0660 (mpp) REVERT: b 30 LEU cc_start: 0.5741 (tt) cc_final: 0.5220 (tt) REVERT: b 98 TYR cc_start: 0.4028 (t80) cc_final: 0.2514 (t80) REVERT: B 153 MET cc_start: 0.0765 (pmm) cc_final: 0.0417 (pmm) REVERT: B 904 TYR cc_start: 0.6663 (t80) cc_final: 0.6387 (t80) REVERT: C 480 CYS cc_start: 0.4157 (OUTLIER) cc_final: 0.3777 (t) REVERT: C 737 ASP cc_start: 0.8210 (t0) cc_final: 0.7916 (t0) REVERT: C 974 SER cc_start: 0.8900 (t) cc_final: 0.8264 (p) REVERT: C 978 ASN cc_start: 0.8734 (m-40) cc_final: 0.8303 (t0) REVERT: C 1014 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7427 (mtt-85) outliers start: 102 outliers final: 68 residues processed: 352 average time/residue: 0.3486 time to fit residues: 209.5201 Evaluate side-chains 302 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 299 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 314 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 207 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 872 GLN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 95 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 690 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 23 GLN ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 29348 Z= 0.314 Angle : 0.638 12.275 39919 Z= 0.339 Chirality : 0.046 0.214 4506 Planarity : 0.005 0.063 5163 Dihedral : 4.942 40.333 3924 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.05 % Allowed : 17.94 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % 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: -0.76 (0.13), residues: 3620 helix: 0.95 (0.20), residues: 726 sheet: 0.26 (0.17), residues: 863 loop : -1.44 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 886 HIS 0.009 0.002 HIS A 146 PHE 0.030 0.002 PHE A 429 TYR 0.031 0.002 TYR A 380 ARG 0.007 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 255 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 608 VAL cc_start: 0.8133 (t) cc_final: 0.7825 (p) REVERT: A 759 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7818 (t80) REVERT: A 900 MET cc_start: 0.8099 (mtm) cc_final: 0.7764 (mtp) REVERT: a 107 TRP cc_start: 0.1841 (OUTLIER) cc_final: 0.1625 (m100) REVERT: a 139 MET cc_start: 0.1598 (ppp) cc_final: 0.0433 (mpp) REVERT: B 102 ARG cc_start: 0.3904 (OUTLIER) cc_final: 0.1272 (mpt180) REVERT: B 559 PHE cc_start: 0.5588 (OUTLIER) cc_final: 0.3913 (m-80) REVERT: B 900 MET cc_start: 0.8447 (mtm) cc_final: 0.8108 (mtm) REVERT: C 480 CYS cc_start: 0.3398 (OUTLIER) cc_final: 0.3159 (t) REVERT: C 737 ASP cc_start: 0.8373 (t0) cc_final: 0.8121 (t0) REVERT: C 740 MET cc_start: 0.7500 (ttt) cc_final: 0.6880 (ttt) REVERT: C 974 SER cc_start: 0.8973 (t) cc_final: 0.8445 (p) REVERT: C 978 ASN cc_start: 0.8780 (m-40) cc_final: 0.8462 (t0) REVERT: C 988 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8628 (mm-30) REVERT: C 1010 GLN cc_start: 0.8273 (tm-30) cc_final: 0.8033 (tm-30) outliers start: 130 outliers final: 84 residues processed: 367 average time/residue: 0.3359 time to fit residues: 211.8285 Evaluate side-chains 314 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 225 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 107 TRP Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 181 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 206 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 291 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 49 HIS A 137 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 690 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1106 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29348 Z= 0.286 Angle : 0.600 12.248 39919 Z= 0.317 Chirality : 0.045 0.178 4506 Planarity : 0.004 0.064 5163 Dihedral : 4.903 38.593 3924 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.14 % Allowed : 19.40 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % 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: -0.71 (0.13), residues: 3620 helix: 1.16 (0.20), residues: 724 sheet: 0.21 (0.17), residues: 865 loop : -1.45 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 886 HIS 0.006 0.001 HIS C1064 PHE 0.036 0.002 PHE C1148 TYR 0.021 0.002 TYR B 160 ARG 0.007 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 252 time to evaluate : 3.499 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 177 MET cc_start: 0.2985 (tmm) cc_final: 0.2611 (tmm) REVERT: A 608 VAL cc_start: 0.8130 (t) cc_final: 0.7857 (p) REVERT: A 900 MET cc_start: 0.8044 (mtm) cc_final: 0.7708 (mtp) REVERT: A 920 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: a 139 MET cc_start: 0.1348 (ppp) cc_final: 0.0244 (mpp) REVERT: B 177 MET cc_start: 0.0947 (OUTLIER) cc_final: 0.0107 (tpt) REVERT: B 238 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.5438 (p90) REVERT: B 258 TRP cc_start: 0.3197 (m100) cc_final: 0.2985 (m100) REVERT: B 559 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.3776 (m-80) REVERT: B 762 GLN cc_start: 0.7894 (mt0) cc_final: 0.7521 (mt0) REVERT: B 1150 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6481 (tt0) REVERT: C 737 ASP cc_start: 0.8370 (t0) cc_final: 0.8098 (t0) REVERT: C 968 SER cc_start: 0.9308 (m) cc_final: 0.9070 (p) REVERT: C 969 ASN cc_start: 0.8182 (m110) cc_final: 0.7449 (t0) REVERT: C 974 SER cc_start: 0.8913 (t) cc_final: 0.8164 (p) REVERT: C 978 ASN cc_start: 0.8860 (m-40) cc_final: 0.8437 (t0) REVERT: C 1010 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7845 (tm-30) outliers start: 133 outliers final: 97 residues processed: 361 average time/residue: 0.3493 time to fit residues: 214.9421 Evaluate side-chains 333 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 232 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 920 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 83 PHE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 349 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 213 optimal weight: 0.0570 chunk 161 optimal weight: 0.0670 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1159 HIS C 207 HIS ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29348 Z= 0.170 Angle : 0.542 14.161 39919 Z= 0.284 Chirality : 0.044 0.180 4506 Planarity : 0.004 0.058 5163 Dihedral : 4.567 37.278 3924 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.39 % Allowed : 20.65 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3620 helix: 1.51 (0.20), residues: 724 sheet: 0.30 (0.17), residues: 863 loop : -1.34 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 886 HIS 0.004 0.001 HIS C 207 PHE 0.035 0.001 PHE C 643 TYR 0.029 0.001 TYR a 179 ARG 0.004 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 266 time to evaluate : 3.061 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 191 GLU cc_start: 0.5954 (mt-10) cc_final: 0.5625 (mt-10) REVERT: A 608 VAL cc_start: 0.8049 (t) cc_final: 0.7790 (p) REVERT: A 900 MET cc_start: 0.7979 (mtm) cc_final: 0.7654 (mtp) REVERT: A 955 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7772 (t0) REVERT: a 139 MET cc_start: 0.1315 (ppp) cc_final: 0.0253 (mpp) REVERT: a 179 TYR cc_start: 0.4643 (OUTLIER) cc_final: 0.4137 (t80) REVERT: B 102 ARG cc_start: 0.4015 (OUTLIER) cc_final: 0.1417 (mtt180) REVERT: B 203 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7434 (mp) REVERT: B 377 PHE cc_start: 0.2100 (OUTLIER) cc_final: 0.1699 (m-80) REVERT: B 559 PHE cc_start: 0.5822 (OUTLIER) cc_final: 0.4112 (m-80) REVERT: B 762 GLN cc_start: 0.7819 (mt0) cc_final: 0.7469 (mt0) REVERT: B 900 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: B 929 SER cc_start: 0.8279 (m) cc_final: 0.7984 (t) REVERT: C 968 SER cc_start: 0.9305 (m) cc_final: 0.9053 (p) REVERT: C 974 SER cc_start: 0.8889 (t) cc_final: 0.8165 (p) REVERT: C 978 ASN cc_start: 0.8914 (m-40) cc_final: 0.8437 (t0) REVERT: C 1031 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7379 (mp0) outliers start: 109 outliers final: 80 residues processed: 354 average time/residue: 0.3759 time to fit residues: 226.2225 Evaluate side-chains 325 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 237 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 197 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 222 optimal weight: 0.0050 chunk 238 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 275 optimal weight: 0.1980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.6546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 29348 Z= 0.149 Angle : 0.526 10.986 39919 Z= 0.274 Chirality : 0.043 0.155 4506 Planarity : 0.004 0.084 5163 Dihedral : 4.395 36.885 3924 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.02 % Allowed : 21.52 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3620 helix: 1.82 (0.21), residues: 704 sheet: 0.45 (0.17), residues: 844 loop : -1.25 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 258 HIS 0.003 0.001 HIS A1083 PHE 0.034 0.001 PHE C 643 TYR 0.025 0.001 TYR C 160 ARG 0.004 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 251 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.5902 (mt-10) cc_final: 0.5561 (mt-10) REVERT: A 608 VAL cc_start: 0.8008 (t) cc_final: 0.7769 (p) REVERT: A 900 MET cc_start: 0.7908 (mtm) cc_final: 0.7537 (mtp) REVERT: A 955 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7679 (t0) REVERT: a 107 TRP cc_start: 0.1789 (m-90) cc_final: 0.1544 (m-90) REVERT: a 139 MET cc_start: 0.1053 (ppp) cc_final: 0.0107 (mpp) REVERT: a 179 TYR cc_start: 0.4509 (OUTLIER) cc_final: 0.3850 (t80) REVERT: B 102 ARG cc_start: 0.3949 (OUTLIER) cc_final: 0.1378 (mtt180) REVERT: B 238 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5462 (p90) REVERT: B 559 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.4195 (m-80) REVERT: B 740 MET cc_start: 0.7351 (mpp) cc_final: 0.7142 (mpp) REVERT: B 762 GLN cc_start: 0.7768 (mt0) cc_final: 0.7429 (mt0) REVERT: B 900 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7967 (mtm) REVERT: B 929 SER cc_start: 0.8267 (m) cc_final: 0.7950 (t) REVERT: B 934 ILE cc_start: 0.8812 (tt) cc_final: 0.8544 (tt) REVERT: C 968 SER cc_start: 0.9308 (m) cc_final: 0.8998 (p) REVERT: C 974 SER cc_start: 0.8757 (t) cc_final: 0.8208 (p) REVERT: C 978 ASN cc_start: 0.8889 (m-40) cc_final: 0.8474 (t0) REVERT: C 1031 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7443 (mp0) outliers start: 97 outliers final: 71 residues processed: 328 average time/residue: 0.3517 time to fit residues: 193.2409 Evaluate side-chains 314 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 236 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 4.9990 chunk 335 optimal weight: 0.6980 chunk 305 optimal weight: 0.3980 chunk 326 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 294 optimal weight: 0.0970 chunk 308 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29348 Z= 0.150 Angle : 0.528 11.123 39919 Z= 0.274 Chirality : 0.043 0.152 4506 Planarity : 0.004 0.085 5163 Dihedral : 4.323 36.015 3924 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.68 % Allowed : 21.74 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3620 helix: 1.83 (0.20), residues: 718 sheet: 0.50 (0.17), residues: 844 loop : -1.22 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 258 HIS 0.002 0.001 HIS A1083 PHE 0.053 0.001 PHE A 643 TYR 0.021 0.001 TYR C 160 ARG 0.017 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 251 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3611 (tmm) cc_final: 0.3355 (tmm) REVERT: A 191 GLU cc_start: 0.5891 (mt-10) cc_final: 0.5529 (mt-10) REVERT: A 608 VAL cc_start: 0.7948 (t) cc_final: 0.7734 (p) REVERT: A 900 MET cc_start: 0.7879 (mtm) cc_final: 0.7504 (mtp) REVERT: A 955 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7758 (t0) REVERT: a 107 TRP cc_start: 0.1801 (m-90) cc_final: 0.1540 (m-10) REVERT: a 139 MET cc_start: 0.1249 (ppp) cc_final: 0.0054 (mpp) REVERT: a 179 TYR cc_start: 0.4462 (OUTLIER) cc_final: 0.3795 (t80) REVERT: B 203 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7395 (mp) REVERT: B 238 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.5536 (p90) REVERT: B 559 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.4231 (m-80) REVERT: B 762 GLN cc_start: 0.7796 (mt0) cc_final: 0.7478 (mt0) REVERT: B 900 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7924 (mtm) REVERT: B 934 ILE cc_start: 0.8767 (tt) cc_final: 0.8517 (tt) REVERT: C 740 MET cc_start: 0.7492 (ttt) cc_final: 0.7106 (ttt) REVERT: C 968 SER cc_start: 0.9312 (m) cc_final: 0.9019 (p) REVERT: C 974 SER cc_start: 0.8799 (t) cc_final: 0.8239 (p) REVERT: C 978 ASN cc_start: 0.8946 (m-40) cc_final: 0.8528 (t0) REVERT: C 1031 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7452 (mp0) outliers start: 86 outliers final: 72 residues processed: 322 average time/residue: 0.3489 time to fit residues: 189.6898 Evaluate side-chains 316 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 237 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 197 VAL Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 0.4980 chunk 344 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 361 optimal weight: 0.2980 chunk 332 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 222 optimal weight: 0.0010 chunk 176 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29348 Z= 0.140 Angle : 0.522 11.541 39919 Z= 0.271 Chirality : 0.043 0.160 4506 Planarity : 0.004 0.086 5163 Dihedral : 4.248 35.975 3924 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.43 % Allowed : 21.99 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3620 helix: 1.94 (0.20), residues: 718 sheet: 0.53 (0.17), residues: 846 loop : -1.18 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 886 HIS 0.003 0.001 HIS A1083 PHE 0.041 0.001 PHE A 643 TYR 0.023 0.001 TYR C 160 ARG 0.004 0.000 ARG C 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7240 Ramachandran restraints generated. 3620 Oldfield, 0 Emsley, 3620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 255 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3170 (tmm) cc_final: 0.2897 (tmm) REVERT: A 823 PHE cc_start: 0.7987 (t80) cc_final: 0.7660 (m-80) REVERT: A 900 MET cc_start: 0.7865 (mtm) cc_final: 0.7486 (mtp) REVERT: A 955 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7672 (t0) REVERT: a 107 TRP cc_start: 0.1830 (m-90) cc_final: 0.1568 (m-10) REVERT: a 139 MET cc_start: 0.1196 (ppp) cc_final: 0.0003 (mpp) REVERT: a 179 TYR cc_start: 0.4452 (OUTLIER) cc_final: 0.3804 (t80) REVERT: b 98 TYR cc_start: 0.4210 (t80) cc_final: 0.2599 (t80) REVERT: B 203 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7389 (mp) REVERT: B 238 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5507 (p90) REVERT: B 581 THR cc_start: 0.5993 (p) cc_final: 0.5775 (p) REVERT: B 762 GLN cc_start: 0.7736 (mt0) cc_final: 0.7421 (mt0) REVERT: B 900 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7891 (mtm) REVERT: B 934 ILE cc_start: 0.8684 (tt) cc_final: 0.8449 (tt) REVERT: C 740 MET cc_start: 0.7418 (ttt) cc_final: 0.7203 (ttt) REVERT: C 968 SER cc_start: 0.9266 (m) cc_final: 0.9005 (p) REVERT: C 974 SER cc_start: 0.8817 (t) cc_final: 0.8246 (p) REVERT: C 978 ASN cc_start: 0.8907 (m-40) cc_final: 0.8501 (t0) REVERT: C 1014 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7454 (mtt180) REVERT: C 1031 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7443 (mp0) outliers start: 78 outliers final: 67 residues processed: 317 average time/residue: 0.3566 time to fit residues: 191.8769 Evaluate side-chains 312 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 239 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 136 THR Chi-restraints excluded: chain a residue 157 THR Chi-restraints excluded: chain a residue 163 LEU Chi-restraints excluded: chain a residue 179 TYR Chi-restraints excluded: chain a residue 210 VAL Chi-restraints excluded: chain b residue 28 SER Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 93 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 543 PHE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 0.5980 chunk 306 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 288 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 474 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.161491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123148 restraints weight = 75762.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.125972 restraints weight = 41685.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.126602 restraints weight = 21244.176| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29348 Z= 0.335 Angle : 0.663 16.622 39919 Z= 0.349 Chirality : 0.046 0.162 4506 Planarity : 0.005 0.089 5163 Dihedral : 4.942 37.369 3924 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.80 % Allowed : 21.74 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3620 helix: 1.43 (0.20), residues: 716 sheet: 0.32 (0.17), residues: 838 loop : -1.45 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 107 HIS 0.007 0.001 HIS C1064 PHE 0.033 0.002 PHE A 643 TYR 0.059 0.002 TYR C 160 ARG 0.009 0.001 ARG B 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6091.83 seconds wall clock time: 111 minutes 55.69 seconds (6715.69 seconds total)