Starting phenix.real_space_refine on Sun Feb 18 13:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7k_23215/02_2024/7l7k_23215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7k_23215/02_2024/7l7k_23215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7k_23215/02_2024/7l7k_23215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7k_23215/02_2024/7l7k_23215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7k_23215/02_2024/7l7k_23215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l7k_23215/02_2024/7l7k_23215.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 102 5.16 5 C 14136 2.51 5 N 3675 2.21 5 O 4211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ASP 796": "OD1" <-> "OD2" Residue "B ASP 808": "OD1" <-> "OD2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B ASP 979": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1084": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B ASP 1127": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 294": "OD1" <-> "OD2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" 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 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1084": "OD1" <-> "OD2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A ASP 737": "OD1" <-> "OD2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A ASP 808": "OD1" <-> "OD2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22124 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7370 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 172 Chain: "C" Number of atoms: 7384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7384 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 47, 'TRANS': 925} Chain breaks: 13 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 170 Chain: "A" Number of atoms: 7370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 973, 7370 Classifications: {'peptide': 973} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 48, 'TRANS': 924} Chain breaks: 13 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 172 Time building chain proxies: 10.82, per 1000 atoms: 0.49 Number of scatterers: 22124 At special positions: 0 Unit cell: (133.56, 127.68, 173.04, 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 102 16.00 O 4211 8.00 N 3675 7.00 C 14136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 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 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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 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 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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: 7.21 Conformation dependent library (CDL) restraints added in 4.0 seconds 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5496 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 43 sheets defined 24.3% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'B' and resid 296 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.873A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.923A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.779A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.865A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.857A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.693A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.635A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.302A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.813A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.619A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 4.109A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.762A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.649A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.158A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.616A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.622A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.199A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.754A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.041A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.178A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.654A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 439 through 442 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 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 783 removed outlier: 3.794A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.512A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.699A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.874A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.678A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.548A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.253A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.807A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.606A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1146 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.797A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.248A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.977A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.522A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 128 Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.644A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 323 through 326 removed outlier: 6.671A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'B' and resid 665 through 667 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.459A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TRP B1102 " --> pdb=" O GLN B1113 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN B1113 " --> pdb=" O TRP B1102 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B1104 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU B1111 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B1106 " --> pdb=" O PHE B1109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.226A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 9.962A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 169 through 172 Processing sheet with id=AC1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.578A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 326 through 328 removed outlier: 4.987A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.697A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE C 515 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N CYS C 432 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS C 378 " --> pdb=" O CYS C 432 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.945A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.161A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 665 through 667 removed outlier: 6.642A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.423A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.423A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.637A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'A' and resid 29 through 30 removed outlier: 6.046A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.981A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AD6, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.740A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.643A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AD9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.184A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.028A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.428A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.428A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.586A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.184A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) 906 hydrogen bonds defined for protein. 2472 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: 9.38 Time building geometry restraints manager: 8.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7164 1.35 - 1.48: 5781 1.48 - 1.60: 9523 1.60 - 1.73: 0 1.73 - 1.86: 126 Bond restraints: 22594 Sorted by residual: bond pdb=" C PHE B 329 " pdb=" N PRO B 330 " ideal model delta sigma weight residual 1.331 1.352 -0.020 1.21e-02 6.83e+03 2.80e+00 bond pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 1.808 1.856 -0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CA GLN B 804 " pdb=" C GLN B 804 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.80e-02 3.09e+03 1.82e+00 bond pdb=" N PRO C 272 " pdb=" CA PRO C 272 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.37e+00 bond pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 1.808 1.771 0.037 3.30e-02 9.18e+02 1.23e+00 ... (remaining 22589 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.16: 565 106.16 - 113.14: 12185 113.14 - 120.12: 7693 120.12 - 127.10: 10169 127.10 - 134.08: 183 Bond angle restraints: 30795 Sorted by residual: angle pdb=" N ILE C 805 " pdb=" CA ILE C 805 " pdb=" C ILE C 805 " ideal model delta sigma weight residual 113.71 109.64 4.07 9.50e-01 1.11e+00 1.84e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 111.62 108.98 2.64 7.90e-01 1.60e+00 1.12e+01 angle pdb=" N ILE B 805 " pdb=" CA ILE B 805 " pdb=" C ILE B 805 " ideal model delta sigma weight residual 112.12 109.47 2.65 8.40e-01 1.42e+00 9.99e+00 angle pdb=" N GLY B 404 " pdb=" CA GLY B 404 " pdb=" C GLY B 404 " ideal model delta sigma weight residual 114.66 110.98 3.68 1.24e+00 6.50e-01 8.82e+00 angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" O GLY A 89 " ideal model delta sigma weight residual 122.29 119.94 2.35 8.10e-01 1.52e+00 8.44e+00 ... (remaining 30790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 11829 17.81 - 35.62: 1235 35.62 - 53.43: 275 53.43 - 71.24: 62 71.24 - 89.05: 26 Dihedral angle restraints: 13427 sinusoidal: 4943 harmonic: 8484 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -30.12 -55.88 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -33.04 -52.96 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -41.26 -44.74 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 13424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2356 0.038 - 0.076: 862 0.076 - 0.113: 318 0.113 - 0.151: 56 0.151 - 0.189: 8 Chirality restraints: 3600 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA CYS C 617 " pdb=" N CYS C 617 " pdb=" C CYS C 617 " pdb=" CB CYS C 617 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 3597 not shown) Planarity restraints: 3984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1056 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.26e+00 pdb=" N PRO C1057 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C1057 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1057 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1056 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B1057 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B1057 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1057 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1056 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A1057 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " -0.026 5.00e-02 4.00e+02 ... (remaining 3981 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1069 2.72 - 3.26: 21376 3.26 - 3.81: 33473 3.81 - 4.35: 41055 4.35 - 4.90: 72081 Nonbonded interactions: 169054 Sorted by model distance: nonbonded pdb=" OG1 THR C1006 " pdb=" OE1 GLN A1005 " model vdw 2.170 2.440 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.171 2.440 nonbonded pdb=" OE1 GLN B1005 " pdb=" OG1 THR A1006 " model vdw 2.178 2.440 nonbonded pdb=" OG1 THR B1006 " pdb=" OE1 GLN C1005 " model vdw 2.181 2.440 nonbonded pdb=" OD1 ASN B 978 " pdb=" OG1 THR A 547 " model vdw 2.185 2.440 ... (remaining 169049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 189 or (resid 190 and (name N or name CA or name C or name O \ or name CB )) or resid 191 through 471 or resid 487 through 498 or resid 503 th \ rough 620 or resid 641 through 1146)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 189 or (resid 190 and (name N or name CA or name C or name O \ or name CB )) or resid 191 through 471 or resid 487 through 498 or resid 503 th \ rough 620 or resid 641 through 1146)) selection = (chain 'C' and (resid 27 through 66 or resid 81 through 95 or (resid 99 through \ 100 and (name N or name CA or name C or name O or name CB )) or resid 101 throug \ h 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 209 or resid 217 through 243 or resid 264 through 344 or (resi \ d 345 through 346 and (name N or name CA or name C or name O or name CB )) or re \ sid 347 through 1146)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 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: 20.210 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 56.810 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.003 0.048 22594 Z= 0.217 Angle : 0.616 12.745 30795 Z= 0.347 Chirality : 0.045 0.189 3600 Planarity : 0.004 0.063 3984 Dihedral : 15.728 89.050 7826 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 7.06 % Allowed : 18.78 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.13), residues: 2835 helix: -1.33 (0.17), residues: 633 sheet: -1.89 (0.18), residues: 632 loop : -3.53 (0.12), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 353 HIS 0.003 0.001 HIS A 207 PHE 0.015 0.001 PHE B 541 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 217 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6857 (m-30) REVERT: C 1034 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8504 (mp) REVERT: C 1130 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8861 (tp) outliers start: 168 outliers final: 123 residues processed: 369 average time/residue: 0.3247 time to fit residues: 187.3432 Evaluate side-chains 274 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 148 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 122 optimal weight: 0.0030 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 88 optimal weight: 0.0470 chunk 138 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 264 optimal weight: 3.9990 overall best weight: 2.0094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 122 ASN B 134 GLN B 280 ASN B 536 ASN B 544 ASN B 641 ASN B 644 GLN B 755 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B 965 GLN B 969 ASN B1002 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 66 HIS C 125 ASN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 536 ASN C 644 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 755 GLN C 901 GLN C 919 ASN C 965 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1101 HIS C1106 GLN A 61 ASN A 280 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 542 ASN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 755 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 954 GLN A 965 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22594 Z= 0.268 Angle : 0.602 14.274 30795 Z= 0.310 Chirality : 0.046 0.172 3600 Planarity : 0.005 0.058 3984 Dihedral : 8.885 59.913 3250 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 7.98 % Allowed : 20.97 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 2835 helix: 0.12 (0.21), residues: 616 sheet: -1.50 (0.18), residues: 644 loop : -3.10 (0.12), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS A 207 PHE 0.013 0.001 PHE C 898 TYR 0.021 0.001 TYR C1067 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 155 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7143 (m-80) cc_final: 0.6881 (m-80) REVERT: B 658 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7070 (p0) REVERT: B 697 MET cc_start: 0.6013 (ttp) cc_final: 0.5744 (ptm) REVERT: B 779 GLN cc_start: 0.7175 (tp40) cc_final: 0.6915 (tp40) REVERT: B 990 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6083 (mt-10) REVERT: C 418 ILE cc_start: 0.6045 (mm) cc_final: 0.5636 (mm) REVERT: C 611 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8281 (tp) REVERT: C 1106 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7934 (pt0) outliers start: 190 outliers final: 137 residues processed: 326 average time/residue: 0.2959 time to fit residues: 157.2641 Evaluate side-chains 282 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 141 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 980 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 219 optimal weight: 0.0870 chunk 179 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 235 optimal weight: 20.0000 chunk 262 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 ASN B 563 GLN B 641 ASN B 901 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22594 Z= 0.190 Angle : 0.555 14.025 30795 Z= 0.284 Chirality : 0.044 0.166 3600 Planarity : 0.004 0.052 3984 Dihedral : 7.719 59.441 3178 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 7.44 % Allowed : 21.85 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2835 helix: 0.78 (0.22), residues: 616 sheet: -1.16 (0.19), residues: 638 loop : -2.73 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 104 HIS 0.003 0.001 HIS B 207 PHE 0.012 0.001 PHE B 400 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 157 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ARG cc_start: 0.4709 (OUTLIER) cc_final: 0.4481 (tpm170) REVERT: B 269 TYR cc_start: 0.7071 (m-80) cc_final: 0.6848 (m-80) REVERT: B 611 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8109 (tp) REVERT: C 132 GLU cc_start: 0.4976 (OUTLIER) cc_final: 0.4744 (pm20) REVERT: C 418 ILE cc_start: 0.5961 (mm) cc_final: 0.5552 (mm) REVERT: A 430 THR cc_start: 0.3938 (OUTLIER) cc_final: 0.3642 (t) outliers start: 177 outliers final: 129 residues processed: 319 average time/residue: 0.2947 time to fit residues: 154.9461 Evaluate side-chains 270 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 137 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 177 optimal weight: 0.0270 chunk 265 optimal weight: 1.9990 chunk 281 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 280 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 703 ASN B 787 GLN B 969 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN A 61 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22594 Z= 0.307 Angle : 0.613 16.555 30795 Z= 0.312 Chirality : 0.046 0.178 3600 Planarity : 0.004 0.054 3984 Dihedral : 7.592 59.363 3167 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 9.45 % Allowed : 21.18 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 2835 helix: 0.77 (0.22), residues: 616 sheet: -0.96 (0.20), residues: 612 loop : -2.63 (0.13), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.004 0.001 HIS A 66 PHE 0.014 0.002 PHE C 898 TYR 0.021 0.002 TYR C1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 138 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 PHE cc_start: 0.4788 (OUTLIER) cc_final: 0.4511 (p90) REVERT: B 269 TYR cc_start: 0.7144 (m-80) cc_final: 0.6893 (m-80) REVERT: B 611 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8153 (tp) REVERT: B 613 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: C 132 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.4665 (pm20) REVERT: C 387 LEU cc_start: 0.8026 (mp) cc_final: 0.7736 (mt) REVERT: C 418 ILE cc_start: 0.6028 (mm) cc_final: 0.5667 (mm) REVERT: C 611 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8309 (tp) REVERT: C 854 LYS cc_start: 0.5595 (OUTLIER) cc_final: 0.4805 (tmtt) REVERT: A 430 THR cc_start: 0.4032 (OUTLIER) cc_final: 0.3656 (t) REVERT: A 613 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: A 1072 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7481 (pt0) outliers start: 225 outliers final: 169 residues processed: 346 average time/residue: 0.2989 time to fit residues: 171.1169 Evaluate side-chains 309 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 131 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 952 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.0370 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 209 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 280 ASN B 641 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN A 388 ASN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22594 Z= 0.198 Angle : 0.562 15.212 30795 Z= 0.287 Chirality : 0.044 0.161 3600 Planarity : 0.004 0.053 3984 Dihedral : 7.244 58.346 3164 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 7.56 % Allowed : 23.32 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 2835 helix: 1.08 (0.22), residues: 616 sheet: -0.75 (0.20), residues: 622 loop : -2.43 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 104 HIS 0.003 0.001 HIS A 207 PHE 0.011 0.001 PHE C 490 TYR 0.033 0.001 TYR C1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 147 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7073 (m-80) cc_final: 0.6865 (m-80) REVERT: B 611 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8360 (tp) REVERT: B 613 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7748 (mt0) REVERT: B 1106 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7689 (pt0) REVERT: C 86 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.6690 (t80) REVERT: C 387 LEU cc_start: 0.8027 (mp) cc_final: 0.7789 (mt) REVERT: C 418 ILE cc_start: 0.6017 (mm) cc_final: 0.5660 (mm) REVERT: C 611 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8284 (tp) REVERT: A 430 THR cc_start: 0.3990 (OUTLIER) cc_final: 0.3668 (t) REVERT: A 613 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: A 957 GLN cc_start: 0.7717 (tp40) cc_final: 0.7441 (mm110) outliers start: 180 outliers final: 137 residues processed: 310 average time/residue: 0.2917 time to fit residues: 148.9783 Evaluate side-chains 274 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 130 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 280 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22594 Z= 0.205 Angle : 0.554 14.477 30795 Z= 0.283 Chirality : 0.044 0.155 3600 Planarity : 0.004 0.058 3984 Dihedral : 6.947 58.146 3151 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 7.69 % Allowed : 23.87 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 2835 helix: 1.24 (0.22), residues: 616 sheet: -0.62 (0.20), residues: 622 loop : -2.33 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 104 HIS 0.003 0.001 HIS A 66 PHE 0.025 0.001 PHE B 92 TYR 0.027 0.001 TYR C1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 134 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7070 (m-80) cc_final: 0.6861 (m-80) REVERT: B 611 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8323 (tp) REVERT: B 613 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: C 86 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.6741 (t80) REVERT: C 387 LEU cc_start: 0.7959 (mp) cc_final: 0.7755 (mt) REVERT: C 418 ILE cc_start: 0.6051 (mm) cc_final: 0.5707 (mm) REVERT: C 611 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8299 (tp) REVERT: C 854 LYS cc_start: 0.5536 (OUTLIER) cc_final: 0.4742 (tmtt) REVERT: A 430 THR cc_start: 0.3999 (OUTLIER) cc_final: 0.3656 (t) REVERT: A 613 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: A 957 GLN cc_start: 0.7726 (tp40) cc_final: 0.7456 (mm110) outliers start: 183 outliers final: 150 residues processed: 304 average time/residue: 0.2943 time to fit residues: 147.4074 Evaluate side-chains 284 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 127 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 160 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 237 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 280 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 280 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22594 Z= 0.224 Angle : 0.561 14.754 30795 Z= 0.285 Chirality : 0.044 0.156 3600 Planarity : 0.004 0.053 3984 Dihedral : 6.795 57.760 3143 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 7.94 % Allowed : 23.61 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2835 helix: 1.25 (0.22), residues: 616 sheet: -0.57 (0.20), residues: 624 loop : -2.29 (0.14), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 104 HIS 0.003 0.001 HIS A 66 PHE 0.020 0.001 PHE B 92 TYR 0.026 0.001 TYR C1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 130 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7088 (m-80) cc_final: 0.6877 (m-80) REVERT: B 611 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8296 (tp) REVERT: B 613 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: B 1113 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: C 86 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6756 (t80) REVERT: C 387 LEU cc_start: 0.7970 (mp) cc_final: 0.7741 (mt) REVERT: C 418 ILE cc_start: 0.6061 (mm) cc_final: 0.5723 (mm) REVERT: C 611 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8284 (tp) REVERT: C 854 LYS cc_start: 0.5532 (OUTLIER) cc_final: 0.4733 (tmtt) REVERT: C 1034 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 430 THR cc_start: 0.4065 (OUTLIER) cc_final: 0.3705 (t) REVERT: A 558 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6815 (ttmt) REVERT: A 613 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: A 957 GLN cc_start: 0.7734 (tp40) cc_final: 0.7468 (mm110) outliers start: 189 outliers final: 161 residues processed: 307 average time/residue: 0.2893 time to fit residues: 145.8055 Evaluate side-chains 300 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 129 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 178 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22594 Z= 0.212 Angle : 0.558 14.422 30795 Z= 0.284 Chirality : 0.044 0.173 3600 Planarity : 0.004 0.053 3984 Dihedral : 6.712 57.785 3140 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 7.52 % Allowed : 24.16 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 2835 helix: 1.34 (0.22), residues: 615 sheet: -0.48 (0.20), residues: 624 loop : -2.25 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 104 HIS 0.003 0.001 HIS A 66 PHE 0.030 0.001 PHE B 238 TYR 0.025 0.001 TYR C1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 137 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 TYR cc_start: 0.7084 (m-80) cc_final: 0.6871 (m-80) REVERT: B 613 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7782 (mt0) REVERT: B 1113 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7496 (mt0) REVERT: C 86 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6747 (t80) REVERT: C 387 LEU cc_start: 0.7955 (mp) cc_final: 0.7719 (mt) REVERT: C 418 ILE cc_start: 0.6062 (mm) cc_final: 0.5730 (mm) REVERT: C 611 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8312 (tp) REVERT: C 854 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.4726 (tmtt) REVERT: C 1034 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 430 THR cc_start: 0.4029 (OUTLIER) cc_final: 0.3678 (t) REVERT: A 495 TYR cc_start: 0.3929 (m-80) cc_final: 0.3572 (t80) REVERT: A 558 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6787 (ttmt) REVERT: A 613 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: A 957 GLN cc_start: 0.7678 (tp40) cc_final: 0.7418 (mm110) outliers start: 179 outliers final: 158 residues processed: 304 average time/residue: 0.2983 time to fit residues: 148.8380 Evaluate side-chains 294 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 127 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.6980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B1010 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22594 Z= 0.183 Angle : 0.540 13.475 30795 Z= 0.274 Chirality : 0.043 0.155 3600 Planarity : 0.004 0.055 3984 Dihedral : 6.501 58.111 3135 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.10 % Allowed : 24.92 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2835 helix: 1.48 (0.22), residues: 615 sheet: -0.38 (0.20), residues: 624 loop : -2.14 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 104 HIS 0.003 0.001 HIS B 207 PHE 0.028 0.001 PHE B 238 TYR 0.024 0.001 TYR C1067 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 131 time to evaluate : 2.634 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: B 613 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: B 1113 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: C 86 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6744 (t80) REVERT: C 418 ILE cc_start: 0.6141 (mm) cc_final: 0.5789 (mm) REVERT: C 611 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8365 (tp) REVERT: C 854 LYS cc_start: 0.5506 (OUTLIER) cc_final: 0.4710 (tmtt) REVERT: C 1034 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 430 THR cc_start: 0.4052 (OUTLIER) cc_final: 0.3712 (t) REVERT: A 495 TYR cc_start: 0.3959 (m-80) cc_final: 0.3596 (t80) REVERT: A 558 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6772 (ttmt) REVERT: A 613 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: A 957 GLN cc_start: 0.7647 (tp40) cc_final: 0.7389 (mm110) outliers start: 169 outliers final: 143 residues processed: 287 average time/residue: 0.3016 time to fit residues: 141.0355 Evaluate side-chains 278 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 126 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 875 SER Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 967 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 442 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.7980 chunk 276 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 192 optimal weight: 0.0370 chunk 289 optimal weight: 0.0570 chunk 266 optimal weight: 0.6980 chunk 230 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 388 ASN B 542 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22594 Z= 0.135 Angle : 0.513 10.245 30795 Z= 0.264 Chirality : 0.042 0.163 3600 Planarity : 0.004 0.059 3984 Dihedral : 6.089 59.561 3130 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.95 % Allowed : 27.82 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2835 helix: 1.79 (0.22), residues: 624 sheet: -0.11 (0.21), residues: 586 loop : -1.95 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 104 HIS 0.003 0.000 HIS B 207 PHE 0.027 0.001 PHE B 238 TYR 0.020 0.001 TYR C1067 ARG 0.006 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5670 Ramachandran restraints generated. 2835 Oldfield, 0 Emsley, 2835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 156 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1113 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7471 (mt0) REVERT: C 86 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6910 (t80) REVERT: C 418 ILE cc_start: 0.6207 (mm) cc_final: 0.5796 (mm) REVERT: C 854 LYS cc_start: 0.5488 (OUTLIER) cc_final: 0.4752 (tmtt) REVERT: A 430 THR cc_start: 0.3522 (OUTLIER) cc_final: 0.3253 (t) REVERT: A 495 TYR cc_start: 0.3874 (m-80) cc_final: 0.3580 (t80) REVERT: A 734 THR cc_start: 0.8113 (m) cc_final: 0.7783 (p) outliers start: 94 outliers final: 78 residues processed: 242 average time/residue: 0.3262 time to fit residues: 127.1496 Evaluate side-chains 220 residues out of total 2560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 138 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 654 GLU Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1058 HIS Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1058 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 231 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 542 ASN B 914 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.152091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.126215 restraints weight = 38524.697| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.08 r_work: 0.3402 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22594 Z= 0.180 Angle : 0.541 14.854 30795 Z= 0.274 Chirality : 0.043 0.176 3600 Planarity : 0.004 0.060 3984 Dihedral : 5.985 59.851 3117 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.03 % Allowed : 27.69 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2835 helix: 1.74 (0.22), residues: 625 sheet: -0.06 (0.21), residues: 598 loop : -1.94 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 104 HIS 0.003 0.001 HIS B 207 PHE 0.032 0.001 PHE A 201 TYR 0.024 0.001 TYR C1067 ARG 0.006 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4618.93 seconds wall clock time: 84 minutes 55.73 seconds (5095.73 seconds total)