Starting phenix.real_space_refine on Wed Feb 21 12:38:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndc_12283/02_2024/7ndc_12283.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndc_12283/02_2024/7ndc_12283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndc_12283/02_2024/7ndc_12283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndc_12283/02_2024/7ndc_12283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndc_12283/02_2024/7ndc_12283.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndc_12283/02_2024/7ndc_12283.pdb" } resolution = 4.1 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= 0.002 sd= 0.021 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 135 5.16 5 C 19449 2.51 5 N 5079 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30645 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.79, per 1000 atoms: 0.55 Number of scatterers: 30645 At special positions: 0 Unit cell: (168.92, 183.68, 188.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 5982 8.00 N 5079 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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 D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 12.21 Conformation dependent library (CDL) restraints added in 6.1 seconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 60 sheets defined 22.6% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.783A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.409A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.634A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 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: 3.656A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.782A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.409A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.634A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.657A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.782A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.409A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.656A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.594A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 29 through 32 removed outlier: 3.993A pdb=" N ASN E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.593A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.994A pdb=" N ASN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.593A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.993A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.541A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.931A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.622A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.671A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.185A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.411A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.422A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.540A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.671A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.185A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.441A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.420A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.540A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.622A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.816A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.422A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.518A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AF4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.517A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.517A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 1265 hydrogen bonds defined for protein. 3381 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: 15.82 Time building geometry restraints manager: 13.13 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: 9804 1.35 - 1.47: 7981 1.47 - 1.59: 13373 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 31332 Sorted by residual: bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 31327 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 917 106.87 - 113.65: 17275 113.65 - 120.43: 11178 120.43 - 127.20: 12960 127.20 - 133.98: 276 Bond angle restraints: 42606 Sorted by residual: angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA PRO C 527 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 106.20 5.80 1.40e+00 5.10e-01 1.71e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.28 -3.58 1.22e+00 6.72e-01 8.60e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.23 -3.53 1.22e+00 6.72e-01 8.35e+00 ... (remaining 42601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 18113 17.44 - 34.88: 879 34.88 - 52.31: 229 52.31 - 69.75: 75 69.75 - 87.19: 27 Dihedral angle restraints: 19323 sinusoidal: 8157 harmonic: 11166 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.16 79.16 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 19320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4004 0.054 - 0.108: 814 0.108 - 0.161: 108 0.161 - 0.215: 6 0.215 - 0.269: 3 Chirality restraints: 4935 Sorted by residual: chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4932 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO A 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO B 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO C 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.068 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 509 2.67 - 3.23: 28194 3.23 - 3.79: 46148 3.79 - 4.34: 63992 4.34 - 4.90: 106438 Nonbonded interactions: 245281 Sorted by model distance: nonbonded pdb=" NZ LYS B 147 " pdb=" OD1 ASN H 57 " model vdw 2.118 2.520 nonbonded pdb=" OE2 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.167 2.440 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.195 2.440 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.237 2.440 ... (remaining 245276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.030 Extract box with map and model: 6.430 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 85.600 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.390 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.086 31332 Z= 0.212 Angle : 0.560 6.713 42606 Z= 0.295 Chirality : 0.044 0.269 4935 Planarity : 0.005 0.127 5451 Dihedral : 11.857 87.188 12021 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.37 % Allowed : 4.02 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.43 (0.13), residues: 3798 helix: 0.44 (0.18), residues: 744 sheet: 0.23 (0.15), residues: 1020 loop : -0.80 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 258 HIS 0.007 0.001 HIS B1048 PHE 0.009 0.001 PHE C 888 TYR 0.011 0.001 TYR L 37 ARG 0.004 0.000 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 426 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8773 (p90) cc_final: 0.8379 (p90) REVERT: A 285 ILE cc_start: 0.8894 (mt) cc_final: 0.8637 (mt) REVERT: A 380 TYR cc_start: 0.8492 (m-80) cc_final: 0.7960 (m-80) REVERT: A 732 THR cc_start: 0.9242 (m) cc_final: 0.9023 (p) REVERT: A 740 MET cc_start: 0.8509 (ttt) cc_final: 0.8194 (ttm) REVERT: A 990 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8732 (pt0) REVERT: A 1023 ASN cc_start: 0.8816 (m-40) cc_final: 0.8497 (t0) REVERT: B 92 PHE cc_start: 0.8736 (t80) cc_final: 0.6966 (t80) REVERT: B 104 TRP cc_start: 0.7903 (m-90) cc_final: 0.7152 (m-90) REVERT: B 201 PHE cc_start: 0.8946 (t80) cc_final: 0.8265 (t80) REVERT: B 238 PHE cc_start: 0.8734 (p90) cc_final: 0.8456 (p90) REVERT: B 285 ILE cc_start: 0.8854 (mt) cc_final: 0.8556 (mt) REVERT: B 297 SER cc_start: 0.8481 (m) cc_final: 0.8131 (p) REVERT: B 380 TYR cc_start: 0.8442 (m-80) cc_final: 0.7883 (m-80) REVERT: B 402 ILE cc_start: 0.8493 (pt) cc_final: 0.8161 (pt) REVERT: B 610 VAL cc_start: 0.9528 (t) cc_final: 0.9281 (p) REVERT: B 724 THR cc_start: 0.9186 (m) cc_final: 0.8884 (p) REVERT: B 740 MET cc_start: 0.8478 (ttt) cc_final: 0.8243 (ttt) REVERT: B 990 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8493 (pt0) REVERT: B 994 ASP cc_start: 0.8984 (m-30) cc_final: 0.8639 (m-30) REVERT: C 92 PHE cc_start: 0.8560 (t80) cc_final: 0.7163 (t80) REVERT: C 104 TRP cc_start: 0.7968 (m-90) cc_final: 0.7272 (m-90) REVERT: C 285 ILE cc_start: 0.8943 (mt) cc_final: 0.8680 (mt) REVERT: C 297 SER cc_start: 0.8474 (m) cc_final: 0.8195 (p) REVERT: C 380 TYR cc_start: 0.8602 (m-80) cc_final: 0.8323 (m-80) REVERT: C 724 THR cc_start: 0.9326 (m) cc_final: 0.9008 (p) REVERT: C 732 THR cc_start: 0.9144 (m) cc_final: 0.8857 (p) REVERT: C 736 VAL cc_start: 0.9073 (t) cc_final: 0.8867 (t) REVERT: C 740 MET cc_start: 0.8545 (ttt) cc_final: 0.8262 (ttt) REVERT: C 869 MET cc_start: 0.8600 (mtt) cc_final: 0.8143 (mtp) REVERT: C 870 ILE cc_start: 0.9473 (mm) cc_final: 0.9273 (pt) REVERT: C 884 SER cc_start: 0.8742 (p) cc_final: 0.8280 (m) REVERT: C 990 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8959 (pt0) REVERT: C 1023 ASN cc_start: 0.8664 (m-40) cc_final: 0.8359 (t0) REVERT: C 1029 MET cc_start: 0.9060 (tpp) cc_final: 0.8404 (tpp) outliers start: 12 outliers final: 0 residues processed: 438 average time/residue: 0.4146 time to fit residues: 294.6634 Evaluate side-chains 193 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 20.0000 chunk 288 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 298 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 222 optimal weight: 3.9990 chunk 345 optimal weight: 50.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 239 GLN B 321 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 321 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 31332 Z= 0.299 Angle : 0.630 13.388 42606 Z= 0.328 Chirality : 0.045 0.271 4935 Planarity : 0.005 0.131 5451 Dihedral : 6.575 58.007 5289 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.12 % Allowed : 1.86 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.10 (0.13), residues: 3798 helix: 1.15 (0.20), residues: 729 sheet: 0.50 (0.15), residues: 990 loop : -0.50 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 64 HIS 0.009 0.001 HIS D 35 PHE 0.020 0.002 PHE A 175 TYR 0.033 0.002 TYR C 505 ARG 0.009 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 248 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8454 (t80) cc_final: 0.8189 (t80) REVERT: A 238 PHE cc_start: 0.8902 (p90) cc_final: 0.8628 (p90) REVERT: A 369 TYR cc_start: 0.8443 (t80) cc_final: 0.8044 (t80) REVERT: A 377 PHE cc_start: 0.8126 (t80) cc_final: 0.7762 (t80) REVERT: A 380 TYR cc_start: 0.8830 (m-80) cc_final: 0.8272 (m-80) REVERT: A 732 THR cc_start: 0.9231 (m) cc_final: 0.8909 (p) REVERT: A 902 MET cc_start: 0.9441 (mmm) cc_final: 0.9010 (tpp) REVERT: A 936 ASP cc_start: 0.8957 (t0) cc_final: 0.8648 (t0) REVERT: A 968 SER cc_start: 0.9467 (m) cc_final: 0.9187 (p) REVERT: A 990 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8960 (pt0) REVERT: B 92 PHE cc_start: 0.8381 (t80) cc_final: 0.8160 (t80) REVERT: B 238 PHE cc_start: 0.8987 (p90) cc_final: 0.8735 (p90) REVERT: B 297 SER cc_start: 0.8621 (m) cc_final: 0.8281 (p) REVERT: B 380 TYR cc_start: 0.8941 (m-80) cc_final: 0.8222 (m-80) REVERT: B 402 ILE cc_start: 0.8623 (pt) cc_final: 0.8340 (pt) REVERT: B 610 VAL cc_start: 0.9603 (t) cc_final: 0.9241 (p) REVERT: B 731 MET cc_start: 0.8849 (ptm) cc_final: 0.8613 (ptp) REVERT: B 737 ASP cc_start: 0.8574 (t70) cc_final: 0.7878 (p0) REVERT: B 740 MET cc_start: 0.8404 (ttt) cc_final: 0.7819 (ttt) REVERT: B 773 GLU cc_start: 0.8514 (tt0) cc_final: 0.8045 (tm-30) REVERT: B 869 MET cc_start: 0.8715 (mtm) cc_final: 0.8302 (mpp) REVERT: B 936 ASP cc_start: 0.8787 (t0) cc_final: 0.8495 (t0) REVERT: C 92 PHE cc_start: 0.8670 (t80) cc_final: 0.8204 (t80) REVERT: C 104 TRP cc_start: 0.8251 (m-90) cc_final: 0.7986 (m-90) REVERT: C 238 PHE cc_start: 0.8894 (p90) cc_final: 0.8392 (p90) REVERT: C 297 SER cc_start: 0.8610 (m) cc_final: 0.8321 (p) REVERT: C 380 TYR cc_start: 0.8906 (m-80) cc_final: 0.8606 (m-80) REVERT: C 731 MET cc_start: 0.8996 (ptm) cc_final: 0.8771 (ptp) REVERT: C 732 THR cc_start: 0.9132 (m) cc_final: 0.8849 (p) REVERT: C 764 ASN cc_start: 0.8863 (t0) cc_final: 0.8455 (t0) REVERT: C 773 GLU cc_start: 0.8486 (tt0) cc_final: 0.7733 (tm-30) REVERT: C 869 MET cc_start: 0.8849 (mtt) cc_final: 0.8332 (mtp) REVERT: C 936 ASP cc_start: 0.8638 (t0) cc_final: 0.8433 (t0) REVERT: C 1029 MET cc_start: 0.9019 (tpp) cc_final: 0.7923 (tpp) REVERT: C 1050 MET cc_start: 0.8787 (ptp) cc_final: 0.8501 (ptm) REVERT: D 110 MET cc_start: 0.5138 (mmp) cc_final: 0.4264 (mmp) REVERT: F 110 MET cc_start: 0.5359 (mmp) cc_final: 0.4372 (mmp) REVERT: H 110 MET cc_start: 0.5681 (mmp) cc_final: 0.4897 (mmp) outliers start: 4 outliers final: 1 residues processed: 252 average time/residue: 0.3963 time to fit residues: 167.9871 Evaluate side-chains 165 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 287 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 chunk 374 optimal weight: 50.0000 chunk 308 optimal weight: 0.6980 chunk 343 optimal weight: 50.0000 chunk 118 optimal weight: 30.0000 chunk 278 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN A1119 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN C 239 GLN C 901 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 31332 Z= 0.292 Angle : 0.582 10.386 42606 Z= 0.302 Chirality : 0.044 0.230 4935 Planarity : 0.004 0.053 5451 Dihedral : 5.889 53.971 5289 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.15 % Allowed : 1.98 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.14 (0.13), residues: 3798 helix: 1.28 (0.20), residues: 705 sheet: 0.28 (0.15), residues: 993 loop : -0.36 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.008 0.001 HIS A1064 PHE 0.020 0.002 PHE A 135 TYR 0.023 0.001 TYR A1067 ARG 0.018 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7682 (m-90) cc_final: 0.7480 (m-10) REVERT: A 159 VAL cc_start: 0.9052 (t) cc_final: 0.8787 (m) REVERT: A 238 PHE cc_start: 0.8972 (p90) cc_final: 0.8687 (p90) REVERT: A 369 TYR cc_start: 0.8473 (t80) cc_final: 0.8060 (t80) REVERT: A 377 PHE cc_start: 0.8443 (t80) cc_final: 0.8007 (t80) REVERT: A 388 ASN cc_start: 0.8084 (p0) cc_final: 0.7384 (m-40) REVERT: A 732 THR cc_start: 0.9221 (m) cc_final: 0.9003 (p) REVERT: A 869 MET cc_start: 0.8700 (mtp) cc_final: 0.8478 (mtp) REVERT: A 936 ASP cc_start: 0.8943 (t0) cc_final: 0.8610 (t0) REVERT: A 968 SER cc_start: 0.9413 (m) cc_final: 0.9076 (p) REVERT: A 990 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8944 (pt0) REVERT: B 104 TRP cc_start: 0.8429 (m-90) cc_final: 0.7453 (m-10) REVERT: B 238 PHE cc_start: 0.9122 (p90) cc_final: 0.8857 (p90) REVERT: B 297 SER cc_start: 0.8613 (m) cc_final: 0.8264 (p) REVERT: B 380 TYR cc_start: 0.8947 (m-80) cc_final: 0.8588 (m-80) REVERT: B 388 ASN cc_start: 0.7991 (p0) cc_final: 0.7286 (m-40) REVERT: B 402 ILE cc_start: 0.8595 (pt) cc_final: 0.8349 (pt) REVERT: B 414 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8345 (tm-30) REVERT: B 610 VAL cc_start: 0.9632 (t) cc_final: 0.9312 (p) REVERT: B 731 MET cc_start: 0.8887 (ptm) cc_final: 0.8550 (ptp) REVERT: B 773 GLU cc_start: 0.8453 (tt0) cc_final: 0.7950 (tm-30) REVERT: B 819 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8866 (mt-10) REVERT: B 869 MET cc_start: 0.8817 (mtm) cc_final: 0.8475 (mtp) REVERT: B 936 ASP cc_start: 0.8854 (t0) cc_final: 0.8572 (t0) REVERT: C 104 TRP cc_start: 0.8380 (m-90) cc_final: 0.7198 (m-10) REVERT: C 238 PHE cc_start: 0.8985 (p90) cc_final: 0.8748 (p90) REVERT: C 297 SER cc_start: 0.8653 (m) cc_final: 0.8341 (p) REVERT: C 387 LEU cc_start: 0.9486 (mt) cc_final: 0.9261 (mt) REVERT: C 388 ASN cc_start: 0.8840 (p0) cc_final: 0.8369 (m-40) REVERT: C 732 THR cc_start: 0.8804 (m) cc_final: 0.8551 (p) REVERT: C 764 ASN cc_start: 0.9054 (t0) cc_final: 0.8661 (t0) REVERT: C 773 GLU cc_start: 0.8648 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 869 MET cc_start: 0.8919 (mtt) cc_final: 0.8433 (mtp) REVERT: C 1050 MET cc_start: 0.8783 (ptp) cc_final: 0.8420 (ptm) REVERT: D 110 MET cc_start: 0.5683 (mmp) cc_final: 0.4644 (mmp) REVERT: F 110 MET cc_start: 0.5864 (mmp) cc_final: 0.4812 (mmp) REVERT: H 110 MET cc_start: 0.5718 (mmp) cc_final: 0.4869 (mmp) outliers start: 5 outliers final: 0 residues processed: 215 average time/residue: 0.3835 time to fit residues: 140.7875 Evaluate side-chains 161 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 50.0000 chunk 260 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 347 optimal weight: 40.0000 chunk 368 optimal weight: 50.0000 chunk 181 optimal weight: 3.9990 chunk 329 optimal weight: 40.0000 chunk 99 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B1010 GLN C 655 HIS C 675 GLN C1011 GLN F 35 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 31332 Z= 0.416 Angle : 0.669 11.686 42606 Z= 0.344 Chirality : 0.044 0.242 4935 Planarity : 0.004 0.067 5451 Dihedral : 5.729 51.229 5289 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.15 % Allowed : 2.19 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.10 (0.13), residues: 3798 helix: 0.86 (0.20), residues: 696 sheet: 0.26 (0.15), residues: 1008 loop : -0.49 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.008 0.002 HIS A1064 PHE 0.033 0.002 PHE A 906 TYR 0.031 0.002 TYR B1067 ARG 0.005 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7777 (m-90) cc_final: 0.7531 (m-10) REVERT: A 238 PHE cc_start: 0.9141 (p90) cc_final: 0.8805 (p90) REVERT: A 902 MET cc_start: 0.9586 (mmm) cc_final: 0.9339 (mmt) REVERT: A 936 ASP cc_start: 0.8983 (t0) cc_final: 0.8707 (t0) REVERT: A 968 SER cc_start: 0.9423 (m) cc_final: 0.9030 (p) REVERT: A 990 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8961 (pt0) REVERT: A 994 ASP cc_start: 0.8882 (m-30) cc_final: 0.8517 (m-30) REVERT: B 104 TRP cc_start: 0.8616 (m-90) cc_final: 0.7674 (m-10) REVERT: B 238 PHE cc_start: 0.9293 (p90) cc_final: 0.9004 (p90) REVERT: B 297 SER cc_start: 0.8661 (m) cc_final: 0.8301 (p) REVERT: B 388 ASN cc_start: 0.8060 (p0) cc_final: 0.7384 (m-40) REVERT: B 402 ILE cc_start: 0.8897 (pt) cc_final: 0.8651 (pt) REVERT: B 414 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8371 (tm-30) REVERT: B 610 VAL cc_start: 0.9673 (t) cc_final: 0.9384 (p) REVERT: B 731 MET cc_start: 0.8941 (ptm) cc_final: 0.8637 (ptp) REVERT: B 737 ASP cc_start: 0.8583 (t0) cc_final: 0.7569 (p0) REVERT: B 773 GLU cc_start: 0.8448 (tt0) cc_final: 0.7943 (tm-30) REVERT: B 869 MET cc_start: 0.9004 (mtm) cc_final: 0.8665 (mtp) REVERT: B 936 ASP cc_start: 0.8944 (t0) cc_final: 0.8670 (t0) REVERT: C 104 TRP cc_start: 0.8437 (m-90) cc_final: 0.8214 (m-90) REVERT: C 238 PHE cc_start: 0.9141 (p90) cc_final: 0.8895 (p90) REVERT: C 297 SER cc_start: 0.8665 (m) cc_final: 0.8303 (p) REVERT: C 387 LEU cc_start: 0.9536 (mt) cc_final: 0.9274 (mt) REVERT: C 388 ASN cc_start: 0.8866 (p0) cc_final: 0.8398 (m-40) REVERT: C 731 MET cc_start: 0.8971 (ptm) cc_final: 0.8759 (ptp) REVERT: C 740 MET cc_start: 0.8588 (ppp) cc_final: 0.8360 (ppp) REVERT: C 869 MET cc_start: 0.8948 (mtt) cc_final: 0.8558 (mtp) REVERT: C 990 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9071 (pt0) REVERT: C 1029 MET cc_start: 0.8991 (tpp) cc_final: 0.7822 (tpp) REVERT: D 83 MET cc_start: -0.7349 (mmt) cc_final: -0.8550 (mtt) REVERT: D 110 MET cc_start: 0.5380 (mmp) cc_final: 0.4336 (mmp) REVERT: F 83 MET cc_start: -0.7283 (mmt) cc_final: -0.8330 (mtt) REVERT: F 110 MET cc_start: 0.5802 (mmp) cc_final: 0.4780 (mmp) REVERT: H 110 MET cc_start: 0.5880 (mmp) cc_final: 0.4953 (mmp) outliers start: 5 outliers final: 0 residues processed: 197 average time/residue: 0.4003 time to fit residues: 133.0181 Evaluate side-chains 147 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 0.5980 chunk 209 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 274 optimal weight: 0.9990 chunk 151 optimal weight: 30.0000 chunk 314 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 188 optimal weight: 0.6980 chunk 330 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1005 GLN B 901 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31332 Z= 0.172 Angle : 0.520 8.922 42606 Z= 0.271 Chirality : 0.043 0.281 4935 Planarity : 0.003 0.038 5451 Dihedral : 5.090 45.897 5289 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.19 (0.13), residues: 3798 helix: 1.30 (0.20), residues: 684 sheet: 0.44 (0.15), residues: 990 loop : -0.37 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.007 0.001 HIS B1048 PHE 0.021 0.001 PHE A 802 TYR 0.015 0.001 TYR B 904 ARG 0.009 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.9072 (p90) cc_final: 0.8733 (p90) REVERT: A 425 LEU cc_start: 0.9245 (tt) cc_final: 0.9041 (tp) REVERT: A 869 MET cc_start: 0.8702 (mtm) cc_final: 0.8436 (mtp) REVERT: A 902 MET cc_start: 0.9474 (mmm) cc_final: 0.9204 (mmt) REVERT: A 936 ASP cc_start: 0.8982 (t0) cc_final: 0.8663 (t0) REVERT: A 968 SER cc_start: 0.9462 (m) cc_final: 0.9103 (t) REVERT: A 990 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8907 (pt0) REVERT: A 994 ASP cc_start: 0.8797 (m-30) cc_final: 0.8578 (m-30) REVERT: B 104 TRP cc_start: 0.8499 (m-90) cc_final: 0.7576 (m-10) REVERT: B 238 PHE cc_start: 0.9256 (p90) cc_final: 0.8920 (p90) REVERT: B 297 SER cc_start: 0.8524 (m) cc_final: 0.8174 (p) REVERT: B 387 LEU cc_start: 0.9210 (mt) cc_final: 0.8980 (mt) REVERT: B 402 ILE cc_start: 0.8841 (pt) cc_final: 0.8622 (pt) REVERT: B 414 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8419 (tm-30) REVERT: B 610 VAL cc_start: 0.9655 (t) cc_final: 0.9360 (p) REVERT: B 737 ASP cc_start: 0.8399 (t0) cc_final: 0.7497 (p0) REVERT: B 773 GLU cc_start: 0.8042 (tt0) cc_final: 0.7733 (tm-30) REVERT: B 902 MET cc_start: 0.9624 (mmm) cc_final: 0.9215 (mmm) REVERT: B 936 ASP cc_start: 0.8942 (t0) cc_final: 0.8625 (t0) REVERT: B 990 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9027 (pt0) REVERT: C 104 TRP cc_start: 0.8234 (m-90) cc_final: 0.8024 (m-90) REVERT: C 238 PHE cc_start: 0.9075 (p90) cc_final: 0.8655 (p90) REVERT: C 297 SER cc_start: 0.8602 (m) cc_final: 0.8270 (p) REVERT: C 414 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8089 (tm-30) REVERT: C 869 MET cc_start: 0.8792 (mtt) cc_final: 0.8443 (mtp) REVERT: C 900 MET cc_start: 0.8574 (mmm) cc_final: 0.8277 (tpp) REVERT: C 990 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9013 (pt0) REVERT: C 1029 MET cc_start: 0.8949 (tpp) cc_final: 0.7924 (tpp) REVERT: C 1050 MET cc_start: 0.8720 (ptp) cc_final: 0.8390 (ptp) REVERT: D 83 MET cc_start: -0.6950 (mmt) cc_final: -0.8483 (mtt) REVERT: D 110 MET cc_start: 0.5294 (mmp) cc_final: 0.4038 (mmp) REVERT: F 83 MET cc_start: -0.6659 (mmt) cc_final: -0.8310 (mtt) REVERT: F 110 MET cc_start: 0.5763 (mmp) cc_final: 0.4731 (mmp) REVERT: H 110 MET cc_start: 0.6057 (mmp) cc_final: 0.5133 (mmp) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.4114 time to fit residues: 140.1551 Evaluate side-chains 149 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 9.9990 chunk 331 optimal weight: 40.0000 chunk 72 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 368 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 31332 Z= 0.367 Angle : 0.615 11.242 42606 Z= 0.318 Chirality : 0.044 0.286 4935 Planarity : 0.004 0.055 5451 Dihedral : 4.989 38.889 5289 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.04 (0.13), residues: 3798 helix: 0.96 (0.20), residues: 684 sheet: 0.41 (0.16), residues: 963 loop : -0.42 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 104 HIS 0.007 0.001 HIS A1048 PHE 0.024 0.002 PHE C 802 TYR 0.027 0.002 TYR B1067 ARG 0.014 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7959 (m-10) cc_final: 0.7494 (m-10) REVERT: A 238 PHE cc_start: 0.9142 (p90) cc_final: 0.8846 (p90) REVERT: A 869 MET cc_start: 0.8990 (mtm) cc_final: 0.8591 (mtp) REVERT: A 902 MET cc_start: 0.9527 (mmm) cc_final: 0.9308 (tpp) REVERT: A 936 ASP cc_start: 0.8979 (t0) cc_final: 0.8650 (t0) REVERT: A 968 SER cc_start: 0.9457 (m) cc_final: 0.9082 (t) REVERT: B 104 TRP cc_start: 0.8607 (m-90) cc_final: 0.7713 (m-10) REVERT: B 238 PHE cc_start: 0.9326 (p90) cc_final: 0.9007 (p90) REVERT: B 297 SER cc_start: 0.8607 (m) cc_final: 0.8221 (p) REVERT: B 392 PHE cc_start: 0.8494 (m-80) cc_final: 0.8233 (m-80) REVERT: B 402 ILE cc_start: 0.8936 (pt) cc_final: 0.8698 (pt) REVERT: B 414 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8480 (tm-30) REVERT: B 610 VAL cc_start: 0.9675 (t) cc_final: 0.9399 (p) REVERT: B 737 ASP cc_start: 0.8602 (t0) cc_final: 0.7671 (p0) REVERT: B 773 GLU cc_start: 0.7968 (tt0) cc_final: 0.7354 (tm-30) REVERT: B 819 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8957 (mt-10) REVERT: B 902 MET cc_start: 0.9660 (mmm) cc_final: 0.9357 (tpt) REVERT: B 936 ASP cc_start: 0.8985 (t0) cc_final: 0.8704 (t0) REVERT: B 1001 LEU cc_start: 0.9498 (tp) cc_final: 0.9232 (tp) REVERT: C 238 PHE cc_start: 0.9162 (p90) cc_final: 0.8928 (p90) REVERT: C 297 SER cc_start: 0.8679 (m) cc_final: 0.8311 (p) REVERT: C 869 MET cc_start: 0.8994 (mtt) cc_final: 0.8530 (mtp) REVERT: C 990 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9128 (pt0) REVERT: C 1050 MET cc_start: 0.8930 (ptp) cc_final: 0.8400 (ptm) REVERT: D 83 MET cc_start: -0.6761 (mmt) cc_final: -0.8428 (mtt) REVERT: D 110 MET cc_start: 0.5506 (mmp) cc_final: 0.4286 (mmp) REVERT: F 83 MET cc_start: -0.6620 (mmt) cc_final: -0.8390 (mtt) REVERT: F 110 MET cc_start: 0.5784 (mmp) cc_final: 0.4742 (mmp) REVERT: H 110 MET cc_start: 0.6090 (mmp) cc_final: 0.5135 (mmp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.4004 time to fit residues: 122.4575 Evaluate side-chains 137 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 40.0000 chunk 41 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 269 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 310 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 169 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31332 Z= 0.168 Angle : 0.514 11.701 42606 Z= 0.266 Chirality : 0.043 0.223 4935 Planarity : 0.003 0.040 5451 Dihedral : 4.515 30.589 5289 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.22 (0.14), residues: 3798 helix: 1.28 (0.20), residues: 684 sheet: 0.46 (0.16), residues: 993 loop : -0.34 (0.14), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.007 0.001 HIS A1048 PHE 0.018 0.001 PHE C 562 TYR 0.013 0.001 TYR C 369 ARG 0.007 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7704 (m-10) cc_final: 0.7190 (m-10) REVERT: A 201 PHE cc_start: 0.8940 (t80) cc_final: 0.8279 (t80) REVERT: A 238 PHE cc_start: 0.9105 (p90) cc_final: 0.8750 (p90) REVERT: A 936 ASP cc_start: 0.9010 (t0) cc_final: 0.8655 (t0) REVERT: A 968 SER cc_start: 0.9470 (m) cc_final: 0.9101 (t) REVERT: B 104 TRP cc_start: 0.8470 (m-90) cc_final: 0.7585 (m-10) REVERT: B 238 PHE cc_start: 0.9287 (p90) cc_final: 0.8932 (p90) REVERT: B 297 SER cc_start: 0.8430 (m) cc_final: 0.8040 (p) REVERT: B 378 LYS cc_start: 0.9418 (mptt) cc_final: 0.9211 (mmtt) REVERT: B 387 LEU cc_start: 0.9119 (mt) cc_final: 0.8867 (mt) REVERT: B 388 ASN cc_start: 0.8150 (p0) cc_final: 0.7587 (m-40) REVERT: B 392 PHE cc_start: 0.8733 (m-80) cc_final: 0.8387 (m-80) REVERT: B 402 ILE cc_start: 0.8881 (pt) cc_final: 0.8649 (pt) REVERT: B 610 VAL cc_start: 0.9659 (t) cc_final: 0.9374 (p) REVERT: B 737 ASP cc_start: 0.8552 (t0) cc_final: 0.7521 (p0) REVERT: B 773 GLU cc_start: 0.7683 (tt0) cc_final: 0.7200 (tm-30) REVERT: B 869 MET cc_start: 0.8685 (mtm) cc_final: 0.8231 (mpp) REVERT: B 902 MET cc_start: 0.9638 (mmm) cc_final: 0.9393 (tpt) REVERT: B 936 ASP cc_start: 0.8969 (t0) cc_final: 0.8673 (t0) REVERT: B 990 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8988 (pt0) REVERT: B 1001 LEU cc_start: 0.9435 (tp) cc_final: 0.9129 (tp) REVERT: C 238 PHE cc_start: 0.9132 (p90) cc_final: 0.8924 (p90) REVERT: C 297 SER cc_start: 0.8575 (m) cc_final: 0.8230 (p) REVERT: C 387 LEU cc_start: 0.9306 (mt) cc_final: 0.9071 (mt) REVERT: C 388 ASN cc_start: 0.8722 (p0) cc_final: 0.8201 (m-40) REVERT: C 414 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8109 (tm-30) REVERT: C 819 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8794 (mt-10) REVERT: C 869 MET cc_start: 0.8887 (mtt) cc_final: 0.8476 (mtp) REVERT: C 990 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8971 (pt0) REVERT: C 1050 MET cc_start: 0.8708 (ptp) cc_final: 0.8358 (ptp) REVERT: D 83 MET cc_start: -0.6654 (mmt) cc_final: -0.8377 (mtt) REVERT: D 110 MET cc_start: 0.5445 (mmp) cc_final: 0.4210 (mmp) REVERT: F 83 MET cc_start: -0.6534 (mmt) cc_final: -0.8319 (mtt) REVERT: F 110 MET cc_start: 0.5779 (mmp) cc_final: 0.4723 (mmp) REVERT: H 110 MET cc_start: 0.6055 (mmp) cc_final: 0.5085 (mmp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.4159 time to fit residues: 129.6184 Evaluate side-chains 145 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 233 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31332 Z= 0.261 Angle : 0.551 10.454 42606 Z= 0.284 Chirality : 0.043 0.259 4935 Planarity : 0.004 0.039 5451 Dihedral : 4.446 28.155 5289 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.18 (0.14), residues: 3798 helix: 1.20 (0.20), residues: 684 sheet: 0.46 (0.16), residues: 996 loop : -0.36 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.009 0.001 HIS C1048 PHE 0.021 0.001 PHE C 802 TYR 0.019 0.001 TYR C1067 ARG 0.007 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8030 (m-10) cc_final: 0.7428 (m-10) REVERT: A 153 MET cc_start: 0.7492 (ptp) cc_final: 0.7182 (ptp) REVERT: A 201 PHE cc_start: 0.8979 (t80) cc_final: 0.8309 (t80) REVERT: A 238 PHE cc_start: 0.9164 (p90) cc_final: 0.8816 (p90) REVERT: A 902 MET cc_start: 0.9341 (mmm) cc_final: 0.9121 (mmt) REVERT: A 936 ASP cc_start: 0.9045 (t0) cc_final: 0.8699 (t0) REVERT: A 968 SER cc_start: 0.9482 (m) cc_final: 0.9114 (t) REVERT: B 104 TRP cc_start: 0.8535 (m-90) cc_final: 0.7659 (m-10) REVERT: B 238 PHE cc_start: 0.9315 (p90) cc_final: 0.8980 (p90) REVERT: B 297 SER cc_start: 0.8537 (m) cc_final: 0.8152 (p) REVERT: B 387 LEU cc_start: 0.9136 (mt) cc_final: 0.8885 (mt) REVERT: B 388 ASN cc_start: 0.8261 (p0) cc_final: 0.7629 (m-40) REVERT: B 392 PHE cc_start: 0.8769 (m-80) cc_final: 0.8428 (m-80) REVERT: B 610 VAL cc_start: 0.9654 (t) cc_final: 0.9353 (p) REVERT: B 869 MET cc_start: 0.8877 (mtm) cc_final: 0.8322 (mpp) REVERT: B 902 MET cc_start: 0.9602 (mmm) cc_final: 0.9314 (tpt) REVERT: B 936 ASP cc_start: 0.9004 (t0) cc_final: 0.8714 (t0) REVERT: B 968 SER cc_start: 0.9377 (m) cc_final: 0.8993 (t) REVERT: B 990 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8983 (pt0) REVERT: B 1118 ASP cc_start: 0.8258 (m-30) cc_final: 0.8047 (m-30) REVERT: C 238 PHE cc_start: 0.9142 (p90) cc_final: 0.8878 (p90) REVERT: C 297 SER cc_start: 0.8635 (m) cc_final: 0.8260 (p) REVERT: C 387 LEU cc_start: 0.9334 (mt) cc_final: 0.9071 (mt) REVERT: C 388 ASN cc_start: 0.8764 (p0) cc_final: 0.8197 (m-40) REVERT: C 869 MET cc_start: 0.8947 (mtt) cc_final: 0.8536 (mtp) REVERT: C 990 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8973 (pt0) REVERT: C 1050 MET cc_start: 0.8830 (ptp) cc_final: 0.8469 (ptp) REVERT: D 83 MET cc_start: -0.6621 (mmt) cc_final: -0.8345 (mtt) REVERT: D 110 MET cc_start: 0.5461 (mmp) cc_final: 0.4277 (mmp) REVERT: F 83 MET cc_start: -0.6471 (mmt) cc_final: -0.8268 (mtt) REVERT: F 110 MET cc_start: 0.5284 (mmp) cc_final: 0.4323 (mmp) REVERT: H 110 MET cc_start: 0.6013 (mmp) cc_final: 0.5042 (mmp) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4246 time to fit residues: 129.8366 Evaluate side-chains 143 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 20.0000 chunk 351 optimal weight: 20.0000 chunk 320 optimal weight: 50.0000 chunk 342 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 309 optimal weight: 0.2980 chunk 323 optimal weight: 8.9990 chunk 341 optimal weight: 40.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1005 GLN B 99 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 31332 Z= 0.383 Angle : 0.640 10.436 42606 Z= 0.332 Chirality : 0.044 0.241 4935 Planarity : 0.004 0.044 5451 Dihedral : 4.755 26.403 5289 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.01 (0.13), residues: 3798 helix: 0.76 (0.20), residues: 684 sheet: 0.61 (0.17), residues: 897 loop : -0.49 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1102 HIS 0.007 0.002 HIS C1048 PHE 0.032 0.002 PHE C 927 TYR 0.027 0.002 TYR C1067 ARG 0.005 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 3.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8386 (m-10) cc_final: 0.7794 (m-10) REVERT: A 153 MET cc_start: 0.7620 (ptp) cc_final: 0.7389 (ptp) REVERT: A 238 PHE cc_start: 0.9236 (p90) cc_final: 0.8915 (p90) REVERT: A 377 PHE cc_start: 0.9074 (t80) cc_final: 0.8854 (t80) REVERT: A 902 MET cc_start: 0.9373 (mmm) cc_final: 0.9097 (mmt) REVERT: A 936 ASP cc_start: 0.9054 (t0) cc_final: 0.8729 (t0) REVERT: A 968 SER cc_start: 0.9511 (m) cc_final: 0.9164 (t) REVERT: B 104 TRP cc_start: 0.8766 (m-90) cc_final: 0.7785 (m-10) REVERT: B 201 PHE cc_start: 0.9195 (t80) cc_final: 0.8519 (t80) REVERT: B 238 PHE cc_start: 0.9352 (p90) cc_final: 0.9061 (p90) REVERT: B 297 SER cc_start: 0.8519 (m) cc_final: 0.8072 (p) REVERT: B 387 LEU cc_start: 0.9167 (mt) cc_final: 0.8940 (mt) REVERT: B 388 ASN cc_start: 0.8406 (p0) cc_final: 0.7994 (m-40) REVERT: B 392 PHE cc_start: 0.8598 (m-80) cc_final: 0.8384 (m-80) REVERT: B 610 VAL cc_start: 0.9686 (t) cc_final: 0.9417 (p) REVERT: B 869 MET cc_start: 0.8860 (mtm) cc_final: 0.8635 (mtp) REVERT: B 936 ASP cc_start: 0.9045 (t0) cc_final: 0.8771 (t0) REVERT: B 990 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8965 (pt0) REVERT: B 1001 LEU cc_start: 0.9536 (tp) cc_final: 0.9302 (tp) REVERT: B 1019 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8108 (ttm110) REVERT: B 1118 ASP cc_start: 0.8306 (m-30) cc_final: 0.8103 (m-30) REVERT: C 153 MET cc_start: 0.6315 (pmm) cc_final: 0.5838 (ppp) REVERT: C 238 PHE cc_start: 0.9275 (p90) cc_final: 0.9002 (p90) REVERT: C 297 SER cc_start: 0.8649 (m) cc_final: 0.8252 (p) REVERT: C 377 PHE cc_start: 0.9002 (t80) cc_final: 0.8745 (t80) REVERT: C 387 LEU cc_start: 0.9306 (mt) cc_final: 0.8293 (mt) REVERT: C 388 ASN cc_start: 0.8814 (p0) cc_final: 0.8139 (m-40) REVERT: C 869 MET cc_start: 0.8999 (mtt) cc_final: 0.8440 (mmp) REVERT: C 990 GLU cc_start: 0.9332 (mt-10) cc_final: 0.9055 (pt0) REVERT: D 83 MET cc_start: -0.6563 (mmt) cc_final: -0.8304 (mtt) REVERT: D 110 MET cc_start: 0.5564 (mmp) cc_final: 0.4458 (mmp) REVERT: F 83 MET cc_start: -0.6393 (mmt) cc_final: -0.8204 (mtt) REVERT: F 110 MET cc_start: 0.5287 (mmp) cc_final: 0.4335 (mmp) REVERT: H 110 MET cc_start: 0.6075 (mmp) cc_final: 0.5077 (mmp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4203 time to fit residues: 125.0848 Evaluate side-chains 134 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 0.0670 chunk 361 optimal weight: 40.0000 chunk 220 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 379 optimal weight: 40.0000 chunk 349 optimal weight: 50.0000 chunk 302 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31332 Z= 0.239 Angle : 0.564 14.912 42606 Z= 0.293 Chirality : 0.044 0.312 4935 Planarity : 0.004 0.038 5451 Dihedral : 4.574 23.744 5289 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.10 (0.14), residues: 3798 helix: 1.06 (0.20), residues: 681 sheet: 0.50 (0.17), residues: 957 loop : -0.42 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 152 HIS 0.008 0.001 HIS A1048 PHE 0.035 0.001 PHE C 377 TYR 0.018 0.001 TYR A 369 ARG 0.004 0.000 ARG A1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8274 (m-10) cc_final: 0.7670 (m-10) REVERT: A 153 MET cc_start: 0.7505 (ptp) cc_final: 0.7300 (ptp) REVERT: A 238 PHE cc_start: 0.9197 (p90) cc_final: 0.8912 (p90) REVERT: A 902 MET cc_start: 0.9330 (mmm) cc_final: 0.9047 (mmt) REVERT: A 936 ASP cc_start: 0.9047 (t0) cc_final: 0.8710 (t0) REVERT: A 968 SER cc_start: 0.9514 (m) cc_final: 0.9146 (t) REVERT: B 104 TRP cc_start: 0.8688 (m-90) cc_final: 0.7690 (m-10) REVERT: B 118 LEU cc_start: 0.9215 (tt) cc_final: 0.8859 (mt) REVERT: B 135 PHE cc_start: 0.8797 (m-10) cc_final: 0.8525 (m-10) REVERT: B 201 PHE cc_start: 0.9181 (t80) cc_final: 0.8501 (t80) REVERT: B 238 PHE cc_start: 0.9338 (p90) cc_final: 0.8993 (p90) REVERT: B 297 SER cc_start: 0.8430 (m) cc_final: 0.8004 (p) REVERT: B 378 LYS cc_start: 0.9334 (mptt) cc_final: 0.9104 (mmtt) REVERT: B 387 LEU cc_start: 0.9113 (mt) cc_final: 0.8850 (mt) REVERT: B 388 ASN cc_start: 0.8355 (p0) cc_final: 0.7962 (m-40) REVERT: B 392 PHE cc_start: 0.8568 (m-80) cc_final: 0.8330 (m-80) REVERT: B 610 VAL cc_start: 0.9673 (t) cc_final: 0.9394 (p) REVERT: B 737 ASP cc_start: 0.8734 (t0) cc_final: 0.7936 (p0) REVERT: B 740 MET cc_start: 0.8691 (ppp) cc_final: 0.8290 (ppp) REVERT: B 869 MET cc_start: 0.8699 (mtm) cc_final: 0.8244 (mpp) REVERT: B 936 ASP cc_start: 0.9039 (t0) cc_final: 0.8774 (t0) REVERT: B 968 SER cc_start: 0.9476 (m) cc_final: 0.9111 (t) REVERT: B 990 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8947 (pt0) REVERT: B 1001 LEU cc_start: 0.9490 (tp) cc_final: 0.9244 (tp) REVERT: C 104 TRP cc_start: 0.8505 (m-90) cc_final: 0.8050 (m-90) REVERT: C 153 MET cc_start: 0.6359 (pmm) cc_final: 0.5894 (ppp) REVERT: C 238 PHE cc_start: 0.9221 (p90) cc_final: 0.8816 (p90) REVERT: C 388 ASN cc_start: 0.9011 (p0) cc_final: 0.8430 (m-40) REVERT: C 869 MET cc_start: 0.8941 (mtt) cc_final: 0.8502 (mtp) REVERT: C 990 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8964 (pt0) REVERT: D 83 MET cc_start: -0.6200 (mmt) cc_final: -0.8127 (mtt) REVERT: D 110 MET cc_start: 0.5515 (mmp) cc_final: 0.4382 (mmp) REVERT: F 83 MET cc_start: -0.6384 (mmt) cc_final: -0.8199 (mtt) REVERT: F 110 MET cc_start: 0.5292 (mmp) cc_final: 0.4322 (mmp) REVERT: H 110 MET cc_start: 0.6075 (mmp) cc_final: 0.5065 (mmp) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4159 time to fit residues: 124.5905 Evaluate side-chains 138 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 2.9990 chunk 321 optimal weight: 50.0000 chunk 92 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 44 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 302 optimal weight: 0.6980 chunk 126 optimal weight: 0.2980 chunk 310 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.132557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082873 restraints weight = 109266.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080762 restraints weight = 73230.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081357 restraints weight = 56235.832| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 31332 Z= 0.157 Angle : 0.526 14.230 42606 Z= 0.272 Chirality : 0.043 0.280 4935 Planarity : 0.003 0.039 5451 Dihedral : 4.299 22.288 5289 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: 0.29 (0.14), residues: 3798 helix: 1.41 (0.20), residues: 681 sheet: 0.57 (0.17), residues: 957 loop : -0.33 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.012 0.001 HIS B1048 PHE 0.032 0.001 PHE C 377 TYR 0.017 0.001 TYR B 144 ARG 0.004 0.000 ARG A 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4831.61 seconds wall clock time: 93 minutes 23.70 seconds (5603.70 seconds total)