Starting phenix.real_space_refine on Wed Feb 21 12:34:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndd_12284/02_2024/7ndd_12284.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndd_12284/02_2024/7ndd_12284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndd_12284/02_2024/7ndd_12284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndd_12284/02_2024/7ndd_12284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndd_12284/02_2024/7ndd_12284.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ndd_12284/02_2024/7ndd_12284.pdb" } resolution = 4.2 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= 0.022 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 Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 15.47, per 1000 atoms: 0.50 Number of scatterers: 30645 At special positions: 0 Unit cell: (168.92, 182.04, 193.52, 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=2.05 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=2.02 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=2.03 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=2.03 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: 12.00 Conformation dependent library (CDL) restraints added in 5.5 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 59 sheets defined 22.6% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 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: 3.798A 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: 4.381A 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: 3.612A 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: 3.646A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.577A 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: 4.138A 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: 3.905A 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: 4.633A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.979A 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: 3.805A 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: 4.405A 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: 3.632A 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: 3.632A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.080A 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: 3.850A 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: 4.622A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.949A 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: 3.843A 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: 4.385A 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: 3.620A 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: 3.664A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.596A 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: 4.096A 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: 3.880A 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: 4.611A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.955A 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: 3.607A 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: 3.994A 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: 3.605A 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: 3.992A 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: 3.607A 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: 3.988A 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: 7.708A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.508A 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: 6.183A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.591A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.331A 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: 5.181A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.284A 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: 6.912A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.240A 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: 5.741A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.266A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (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: 5.817A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.678A 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: 6.447A 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: 3.655A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.655A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.452A 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 1120 through 1125 removed outlier: 4.466A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.560A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.533A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.181A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.367A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.127A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.468A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.880A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.880A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.400A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.621A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.700A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.802A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.181A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.981A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.802A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.802A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.424A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.429A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.505A pdb=" N THR E 97 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.227A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.445A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.393A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 1257 hydrogen bonds defined for protein. 3342 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: 14.28 Time building geometry restraints manager: 12.96 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: 9806 1.35 - 1.47: 8061 1.47 - 1.59: 13291 1.59 - 1.72: 0 1.72 - 1.84: 174 Bond restraints: 31332 Sorted by residual: bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.80e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.40e+00 ... (remaining 31327 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.04: 587 105.04 - 112.28: 15898 112.28 - 119.52: 9718 119.52 - 126.75: 16048 126.75 - 133.99: 355 Bond angle restraints: 42606 Sorted by residual: angle pdb=" C ASN B 334 " pdb=" N LEU B 335 " pdb=" CA LEU B 335 " ideal model delta sigma weight residual 121.98 110.72 11.26 1.35e+00 5.49e-01 6.95e+01 angle pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 125.00 97.80 27.20 4.10e+00 5.95e-02 4.40e+01 angle pdb=" N THR B 333 " pdb=" CA THR B 333 " pdb=" C THR B 333 " ideal model delta sigma weight residual 108.65 98.55 10.10 1.85e+00 2.92e-01 2.98e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 104.73 7.27 1.40e+00 5.10e-01 2.70e+01 angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 105.46 6.54 1.40e+00 5.10e-01 2.18e+01 ... (remaining 42601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 18101 17.43 - 34.87: 895 34.87 - 52.30: 228 52.30 - 69.73: 72 69.73 - 87.17: 27 Dihedral angle restraints: 19323 sinusoidal: 8157 harmonic: 11166 Sorted by residual: dihedral pdb=" CA PRO B 527 " pdb=" C PRO B 527 " pdb=" N LYS B 528 " pdb=" CA LYS B 528 " ideal model delta harmonic sigma weight residual -180.00 -118.08 -61.92 0 5.00e+00 4.00e-02 1.53e+02 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 -166.41 80.41 1 1.00e+01 1.00e-02 8.00e+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 -165.51 79.51 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 19320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4879 0.123 - 0.246: 51 0.246 - 0.369: 3 0.369 - 0.492: 1 0.492 - 0.615: 1 Chirality restraints: 4935 Sorted by residual: chirality pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" C PRO B 527 " pdb=" CB PRO B 527 " both_signs ideal model delta sigma weight residual False 2.72 2.10 0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.85e+00 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 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4932 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.144 5.00e-02 4.00e+02 2.18e-01 7.57e+01 pdb=" N PRO B 527 " -0.375 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.137 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.117 5.00e-02 4.00e+02 1.74e-01 4.85e+01 pdb=" N PRO C 527 " -0.301 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.102 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 321 " -0.094 5.00e-02 4.00e+02 1.48e-01 3.51e+01 pdb=" N PRO B 322 " 0.256 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " -0.088 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " -0.075 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2076 2.74 - 3.28: 29458 3.28 - 3.82: 49997 3.82 - 4.36: 59901 4.36 - 4.90: 104914 Nonbonded interactions: 246346 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 2.194 2.440 nonbonded pdb=" O THR B 333 " pdb=" O ASN B 334 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.229 2.440 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.239 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.241 2.440 ... (remaining 246341 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.260 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 81.190 Find NCS groups from input model: 1.860 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 0.072 31332 Z= 0.223 Angle : 0.613 27.202 42606 Z= 0.316 Chirality : 0.046 0.615 4935 Planarity : 0.006 0.218 5451 Dihedral : 11.909 87.167 12021 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.11 % Favored : 95.66 % Rotamer: Outliers : 0.43 % Allowed : 4.02 % Favored : 95.55 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.14 % 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: -0.40 (0.13), residues: 3798 helix: 0.65 (0.19), residues: 725 sheet: 0.29 (0.15), residues: 979 loop : -0.86 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.008 0.001 HIS C1048 PHE 0.012 0.001 PHE B1109 TYR 0.014 0.001 TYR C 200 ARG 0.004 0.000 ARG E 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 451 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 437 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 54 LEU cc_start: 0.9453 (mt) cc_final: 0.9072 (tp) REVERT: A 191 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7608 (mp0) REVERT: A 229 LEU cc_start: 0.8856 (mt) cc_final: 0.8500 (tt) REVERT: A 238 PHE cc_start: 0.8724 (p90) cc_final: 0.8115 (p90) REVERT: A 299 THR cc_start: 0.9629 (m) cc_final: 0.9280 (p) REVERT: A 386 LYS cc_start: 0.9404 (mttt) cc_final: 0.8778 (ptmt) REVERT: A 759 PHE cc_start: 0.8342 (m-80) cc_final: 0.8008 (m-80) REVERT: A 819 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8068 (mt-10) REVERT: A 895 GLN cc_start: 0.8365 (pm20) cc_final: 0.7885 (pm20) REVERT: A 1119 ASN cc_start: 0.8390 (m-40) cc_final: 0.7577 (m110) REVERT: B 54 LEU cc_start: 0.9613 (mt) cc_final: 0.9222 (tp) REVERT: B 91 TYR cc_start: 0.8523 (t80) cc_final: 0.7588 (t80) REVERT: B 92 PHE cc_start: 0.9051 (t80) cc_final: 0.8843 (t80) REVERT: B 104 TRP cc_start: 0.8839 (m-90) cc_final: 0.8223 (m-90) REVERT: B 137 ASN cc_start: 0.9447 (m-40) cc_final: 0.9087 (p0) REVERT: B 192 PHE cc_start: 0.9293 (m-80) cc_final: 0.8822 (m-80) REVERT: B 238 PHE cc_start: 0.9432 (p90) cc_final: 0.9117 (p90) REVERT: B 270 LEU cc_start: 0.8973 (mt) cc_final: 0.8474 (mp) REVERT: B 611 LEU cc_start: 0.9046 (tp) cc_final: 0.8790 (tp) REVERT: B 727 LEU cc_start: 0.9565 (mt) cc_final: 0.9358 (mp) REVERT: B 731 MET cc_start: 0.8450 (ptm) cc_final: 0.7792 (ppp) REVERT: B 776 LYS cc_start: 0.9081 (tttt) cc_final: 0.8717 (tppt) REVERT: B 869 MET cc_start: 0.9319 (mtt) cc_final: 0.8969 (mtm) REVERT: B 979 ASP cc_start: 0.8927 (m-30) cc_final: 0.8626 (m-30) REVERT: B 1010 GLN cc_start: 0.8529 (mm110) cc_final: 0.8042 (tp-100) REVERT: C 191 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8134 (pm20) REVERT: C 297 SER cc_start: 0.8462 (m) cc_final: 0.8152 (p) REVERT: C 398 ASP cc_start: 0.6894 (m-30) cc_final: 0.5497 (m-30) REVERT: C 552 LEU cc_start: 0.9225 (mt) cc_final: 0.9014 (tt) REVERT: C 707 TYR cc_start: 0.8937 (t80) cc_final: 0.8419 (t80) REVERT: C 805 ILE cc_start: 0.9175 (pt) cc_final: 0.8779 (mm) REVERT: C 869 MET cc_start: 0.8630 (mtt) cc_final: 0.7891 (mtm) REVERT: C 878 LEU cc_start: 0.8166 (tp) cc_final: 0.7843 (tp) REVERT: C 909 ILE cc_start: 0.9401 (pt) cc_final: 0.9025 (mt) REVERT: C 955 ASN cc_start: 0.8760 (m-40) cc_final: 0.8064 (p0) REVERT: C 978 ASN cc_start: 0.9101 (m-40) cc_final: 0.8689 (t0) REVERT: C 1029 MET cc_start: 0.8371 (tpp) cc_final: 0.8126 (tpp) REVERT: D 83 MET cc_start: -0.1351 (mtp) cc_final: -0.1796 (mmt) outliers start: 14 outliers final: 2 residues processed: 451 average time/residue: 0.4441 time to fit residues: 316.1650 Evaluate side-chains 225 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 3.155 ------------------------------------------------------------------------------- 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: 30.0000 chunk 288 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 345 optimal weight: 50.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 613 GLN A 914 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 321 GLN C 703 ASN C 901 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 31332 Z= 0.395 Angle : 0.695 13.583 42606 Z= 0.359 Chirality : 0.046 0.266 4935 Planarity : 0.005 0.103 5451 Dihedral : 6.939 59.235 5289 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.76 % Rotamer: Outliers : 0.15 % Allowed : 2.01 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.07 (0.13), residues: 3798 helix: 1.40 (0.20), residues: 704 sheet: 0.28 (0.15), residues: 996 loop : -0.51 (0.13), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 353 HIS 0.017 0.002 HIS A1064 PHE 0.021 0.002 PHE C1089 TYR 0.026 0.002 TYR A1067 ARG 0.012 0.001 ARG C 357 *********************** 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 245 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 3.441 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 54 LEU cc_start: 0.9530 (mt) cc_final: 0.9221 (tp) REVERT: A 223 LEU cc_start: 0.8453 (mp) cc_final: 0.7939 (mp) REVERT: A 224 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8616 (mp0) REVERT: A 238 PHE cc_start: 0.8938 (p90) cc_final: 0.8737 (p90) REVERT: A 299 THR cc_start: 0.9679 (m) cc_final: 0.9366 (p) REVERT: A 386 LYS cc_start: 0.9312 (mttt) cc_final: 0.8995 (mtpt) REVERT: A 390 LEU cc_start: 0.8913 (mt) cc_final: 0.8619 (mt) REVERT: A 869 MET cc_start: 0.9032 (mtt) cc_final: 0.8414 (mtt) REVERT: A 895 GLN cc_start: 0.8586 (pm20) cc_final: 0.8097 (pm20) REVERT: A 979 ASP cc_start: 0.9407 (m-30) cc_final: 0.9153 (m-30) REVERT: B 54 LEU cc_start: 0.9641 (mt) cc_final: 0.9341 (tp) REVERT: B 56 LEU cc_start: 0.9206 (tp) cc_final: 0.8707 (tp) REVERT: B 91 TYR cc_start: 0.8617 (t80) cc_final: 0.8038 (t80) REVERT: B 92 PHE cc_start: 0.8809 (t80) cc_final: 0.8571 (t80) REVERT: B 104 TRP cc_start: 0.8956 (m-90) cc_final: 0.8544 (m-90) REVERT: B 137 ASN cc_start: 0.9454 (m-40) cc_final: 0.9098 (p0) REVERT: B 175 PHE cc_start: 0.9289 (m-80) cc_final: 0.8951 (m-80) REVERT: B 191 GLU cc_start: 0.9320 (mp0) cc_final: 0.8877 (pm20) REVERT: B 223 LEU cc_start: 0.8879 (mp) cc_final: 0.8620 (mp) REVERT: B 238 PHE cc_start: 0.9503 (p90) cc_final: 0.9041 (p90) REVERT: B 297 SER cc_start: 0.9178 (m) cc_final: 0.8895 (p) REVERT: B 697 MET cc_start: 0.8306 (ptm) cc_final: 0.7961 (ptp) REVERT: B 731 MET cc_start: 0.8792 (ptm) cc_final: 0.7777 (ppp) REVERT: B 776 LYS cc_start: 0.9173 (tttt) cc_final: 0.8889 (tppt) REVERT: B 947 LYS cc_start: 0.8860 (mttt) cc_final: 0.8430 (mmmt) REVERT: B 1002 GLN cc_start: 0.9189 (tp40) cc_final: 0.8937 (tm-30) REVERT: C 229 LEU cc_start: 0.8984 (mm) cc_final: 0.8735 (tp) REVERT: C 238 PHE cc_start: 0.9296 (p90) cc_final: 0.9060 (p90) REVERT: C 277 LEU cc_start: 0.9360 (mp) cc_final: 0.9000 (tp) REVERT: C 297 SER cc_start: 0.8633 (m) cc_final: 0.8225 (p) REVERT: C 365 TYR cc_start: 0.8899 (m-80) cc_final: 0.8624 (m-10) REVERT: C 552 LEU cc_start: 0.9242 (mt) cc_final: 0.8911 (pp) REVERT: C 693 ILE cc_start: 0.9363 (pt) cc_final: 0.8972 (pt) REVERT: C 707 TYR cc_start: 0.9235 (t80) cc_final: 0.8605 (t80) REVERT: C 740 MET cc_start: 0.9114 (ttp) cc_final: 0.8514 (tmm) REVERT: C 869 MET cc_start: 0.8573 (mtt) cc_final: 0.7895 (mpp) REVERT: C 955 ASN cc_start: 0.9049 (m-40) cc_final: 0.8318 (p0) REVERT: C 978 ASN cc_start: 0.9181 (m-40) cc_final: 0.8751 (t0) REVERT: C 984 LEU cc_start: 0.8399 (mt) cc_final: 0.7999 (tp) REVERT: C 1029 MET cc_start: 0.8708 (tpp) cc_final: 0.7960 (tpp) REVERT: D 83 MET cc_start: -0.1716 (mtp) cc_final: -0.2098 (mmt) outliers start: 5 outliers final: 2 residues processed: 245 average time/residue: 0.4284 time to fit residues: 171.2620 Evaluate side-chains 171 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 3.584 ------------------------------------------------------------------------------- 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: 0.9990 chunk 107 optimal weight: 0.0570 chunk 287 optimal weight: 0.3980 chunk 235 optimal weight: 20.0000 chunk 95 optimal weight: 0.6980 chunk 346 optimal weight: 5.9990 chunk 374 optimal weight: 50.0000 chunk 308 optimal weight: 0.7980 chunk 343 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 278 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 901 GLN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN D 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31332 Z= 0.164 Angle : 0.523 10.249 42606 Z= 0.273 Chirality : 0.043 0.231 4935 Planarity : 0.004 0.064 5451 Dihedral : 6.278 59.639 5289 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 0.03 % Allowed : 1.49 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.32 (0.13), residues: 3798 helix: 1.68 (0.20), residues: 719 sheet: 0.38 (0.15), residues: 1006 loop : -0.36 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.006 0.001 HIS C1048 PHE 0.020 0.001 PHE C 906 TYR 0.013 0.001 TYR A 904 ARG 0.007 0.000 ARG A 357 *********************** 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 237 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9426 (mt) cc_final: 0.9082 (tp) REVERT: A 223 LEU cc_start: 0.8635 (mp) cc_final: 0.8092 (mp) REVERT: A 224 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8795 (mp0) REVERT: A 238 PHE cc_start: 0.8857 (p90) cc_final: 0.8501 (p90) REVERT: A 275 PHE cc_start: 0.8972 (m-80) cc_final: 0.8764 (m-80) REVERT: A 299 THR cc_start: 0.9590 (m) cc_final: 0.9302 (p) REVERT: A 386 LYS cc_start: 0.9345 (mttt) cc_final: 0.9033 (mtpt) REVERT: A 388 ASN cc_start: 0.8708 (p0) cc_final: 0.7674 (m-40) REVERT: A 869 MET cc_start: 0.9099 (mtt) cc_final: 0.8659 (mtp) REVERT: A 1017 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8861 (tm-30) REVERT: A 1118 ASP cc_start: 0.8654 (p0) cc_final: 0.8331 (p0) REVERT: A 1119 ASN cc_start: 0.7602 (m-40) cc_final: 0.7304 (m110) REVERT: B 54 LEU cc_start: 0.9634 (mt) cc_final: 0.9333 (tp) REVERT: B 56 LEU cc_start: 0.9199 (tp) cc_final: 0.8891 (tp) REVERT: B 91 TYR cc_start: 0.8421 (t80) cc_final: 0.7998 (t80) REVERT: B 104 TRP cc_start: 0.8895 (m-90) cc_final: 0.8528 (m-90) REVERT: B 137 ASN cc_start: 0.9505 (m-40) cc_final: 0.9131 (p0) REVERT: B 175 PHE cc_start: 0.9206 (m-80) cc_final: 0.8820 (m-10) REVERT: B 238 PHE cc_start: 0.9505 (p90) cc_final: 0.9026 (p90) REVERT: B 297 SER cc_start: 0.9153 (m) cc_final: 0.8857 (p) REVERT: B 611 LEU cc_start: 0.9092 (tp) cc_final: 0.8889 (tp) REVERT: B 697 MET cc_start: 0.8274 (ptm) cc_final: 0.8000 (ptp) REVERT: B 731 MET cc_start: 0.8610 (ptm) cc_final: 0.7807 (ppp) REVERT: B 887 THR cc_start: 0.8187 (p) cc_final: 0.7606 (t) REVERT: B 995 ARG cc_start: 0.9027 (ttm-80) cc_final: 0.8755 (ttm-80) REVERT: B 1002 GLN cc_start: 0.8988 (tp40) cc_final: 0.8601 (tm-30) REVERT: C 86 PHE cc_start: 0.8459 (t80) cc_final: 0.7977 (t80) REVERT: C 229 LEU cc_start: 0.8986 (mm) cc_final: 0.8752 (tp) REVERT: C 277 LEU cc_start: 0.9237 (mp) cc_final: 0.8971 (tp) REVERT: C 297 SER cc_start: 0.8568 (m) cc_final: 0.8143 (p) REVERT: C 414 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8476 (tp-100) REVERT: C 552 LEU cc_start: 0.9259 (mt) cc_final: 0.8916 (pp) REVERT: C 707 TYR cc_start: 0.9122 (t80) cc_final: 0.8488 (t80) REVERT: C 740 MET cc_start: 0.9047 (ttp) cc_final: 0.8538 (tmm) REVERT: C 869 MET cc_start: 0.8466 (mtt) cc_final: 0.7874 (mtp) REVERT: C 878 LEU cc_start: 0.8625 (tp) cc_final: 0.8343 (tp) REVERT: C 978 ASN cc_start: 0.9242 (m-40) cc_final: 0.8755 (t0) REVERT: C 1029 MET cc_start: 0.8798 (tpp) cc_final: 0.8382 (tpp) REVERT: D 83 MET cc_start: -0.1974 (mtp) cc_final: -0.2282 (mmt) REVERT: F 83 MET cc_start: -0.2607 (mmt) cc_final: -0.2911 (mmt) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.4053 time to fit residues: 159.3025 Evaluate side-chains 169 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 3.078 ------------------------------------------------------------------------------- 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: 8.9990 chunk 260 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 38 optimal weight: 0.0010 chunk 165 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 347 optimal weight: 40.0000 chunk 368 optimal weight: 40.0000 chunk 181 optimal weight: 8.9990 chunk 329 optimal weight: 50.0000 chunk 99 optimal weight: 0.7980 overall best weight: 3.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 703 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN C 321 GLN C 703 ASN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 31332 Z= 0.531 Angle : 0.785 15.833 42606 Z= 0.401 Chirality : 0.047 0.233 4935 Planarity : 0.005 0.081 5451 Dihedral : 6.382 55.427 5289 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.13), residues: 3798 helix: 0.90 (0.20), residues: 690 sheet: 0.10 (0.16), residues: 969 loop : -0.50 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 104 HIS 0.013 0.002 HIS A1064 PHE 0.053 0.003 PHE C1062 TYR 0.028 0.002 TYR C 873 ARG 0.020 0.001 ARG C1107 *********************** 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 191 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 3.448 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 223 LEU cc_start: 0.8924 (mp) cc_final: 0.8333 (mp) REVERT: A 224 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8718 (mp0) REVERT: A 238 PHE cc_start: 0.9003 (p90) cc_final: 0.8705 (p90) REVERT: A 299 THR cc_start: 0.9662 (m) cc_final: 0.9445 (p) REVERT: A 388 ASN cc_start: 0.8983 (p0) cc_final: 0.7887 (m-40) REVERT: A 390 LEU cc_start: 0.9182 (mt) cc_final: 0.8834 (mt) REVERT: A 869 MET cc_start: 0.9412 (mtt) cc_final: 0.8751 (mtp) REVERT: A 979 ASP cc_start: 0.9497 (m-30) cc_final: 0.9290 (m-30) REVERT: A 1017 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8901 (tm-30) REVERT: A 1119 ASN cc_start: 0.7898 (m-40) cc_final: 0.7536 (m110) REVERT: B 56 LEU cc_start: 0.9197 (tp) cc_final: 0.8706 (tp) REVERT: B 91 TYR cc_start: 0.8526 (t80) cc_final: 0.8218 (t80) REVERT: B 104 TRP cc_start: 0.9165 (m-90) cc_final: 0.8962 (m-90) REVERT: B 137 ASN cc_start: 0.9405 (m-40) cc_final: 0.9034 (p0) REVERT: B 175 PHE cc_start: 0.9276 (m-80) cc_final: 0.8814 (m-80) REVERT: B 238 PHE cc_start: 0.9658 (p90) cc_final: 0.9069 (p90) REVERT: B 297 SER cc_start: 0.9181 (m) cc_final: 0.8912 (p) REVERT: B 611 LEU cc_start: 0.9196 (tp) cc_final: 0.8988 (tp) REVERT: B 697 MET cc_start: 0.8537 (ptm) cc_final: 0.7924 (ptp) REVERT: B 731 MET cc_start: 0.8901 (ptm) cc_final: 0.7696 (ppp) REVERT: B 979 ASP cc_start: 0.9050 (m-30) cc_final: 0.8817 (t0) REVERT: B 1010 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7685 (tm-30) REVERT: B 1014 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7491 (ttm170) REVERT: C 118 LEU cc_start: 0.9583 (tt) cc_final: 0.9369 (mt) REVERT: C 297 SER cc_start: 0.8783 (m) cc_final: 0.8381 (p) REVERT: C 552 LEU cc_start: 0.9323 (mt) cc_final: 0.9090 (tt) REVERT: C 740 MET cc_start: 0.9107 (ttp) cc_final: 0.8540 (tmm) REVERT: C 780 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 869 MET cc_start: 0.8584 (mtt) cc_final: 0.8090 (mtp) REVERT: C 968 SER cc_start: 0.9627 (m) cc_final: 0.9223 (t) REVERT: C 978 ASN cc_start: 0.9229 (m-40) cc_final: 0.8844 (t0) REVERT: C 1029 MET cc_start: 0.8664 (tpp) cc_final: 0.7916 (tpp) REVERT: D 83 MET cc_start: -0.1882 (mtp) cc_final: -0.2305 (mmt) outliers start: 3 outliers final: 2 residues processed: 191 average time/residue: 0.4264 time to fit residues: 136.1820 Evaluate side-chains 141 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 3.141 ------------------------------------------------------------------------------- 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: 0.5980 chunk 5 optimal weight: 2.9990 chunk 274 optimal weight: 5.9990 chunk 151 optimal weight: 0.3980 chunk 314 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 188 optimal weight: 0.5980 chunk 330 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 953 ASN A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 613 GLN B 703 ASN B 901 GLN B1119 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31332 Z= 0.165 Angle : 0.528 10.358 42606 Z= 0.273 Chirality : 0.043 0.237 4935 Planarity : 0.004 0.052 5451 Dihedral : 5.578 59.259 5289 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 0.03 % Allowed : 1.34 % Favored : 98.63 % 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: 0.28 (0.14), residues: 3798 helix: 1.62 (0.20), residues: 706 sheet: 0.35 (0.16), residues: 977 loop : -0.34 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 104 HIS 0.011 0.001 HIS A1048 PHE 0.025 0.001 PHE A 464 TYR 0.018 0.001 TYR C 365 ARG 0.007 0.000 ARG C1107 *********************** 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 214 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 3.753 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 54 LEU cc_start: 0.9414 (mm) cc_final: 0.8840 (tp) REVERT: A 223 LEU cc_start: 0.8871 (mp) cc_final: 0.8320 (mp) REVERT: A 224 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8782 (mp0) REVERT: A 238 PHE cc_start: 0.8978 (p90) cc_final: 0.8625 (p90) REVERT: A 299 THR cc_start: 0.9585 (m) cc_final: 0.9293 (p) REVERT: A 388 ASN cc_start: 0.8801 (p0) cc_final: 0.7574 (m-40) REVERT: A 869 MET cc_start: 0.9187 (mtt) cc_final: 0.8585 (mtp) REVERT: A 985 ASP cc_start: 0.9202 (t0) cc_final: 0.8996 (t0) REVERT: A 1017 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 1019 ARG cc_start: 0.8112 (tmm-80) cc_final: 0.7654 (ttp80) REVERT: A 1119 ASN cc_start: 0.7754 (m-40) cc_final: 0.7361 (m110) REVERT: B 54 LEU cc_start: 0.9629 (mm) cc_final: 0.9270 (tp) REVERT: B 56 LEU cc_start: 0.9046 (tp) cc_final: 0.8465 (tp) REVERT: B 104 TRP cc_start: 0.9035 (m-90) cc_final: 0.8702 (m-90) REVERT: B 137 ASN cc_start: 0.9407 (m-40) cc_final: 0.9047 (p0) REVERT: B 175 PHE cc_start: 0.9138 (m-80) cc_final: 0.8793 (m-80) REVERT: B 238 PHE cc_start: 0.9620 (p90) cc_final: 0.9122 (p90) REVERT: B 270 LEU cc_start: 0.8884 (mt) cc_final: 0.8048 (mp) REVERT: B 297 SER cc_start: 0.9123 (m) cc_final: 0.8819 (p) REVERT: B 697 MET cc_start: 0.8227 (ptm) cc_final: 0.7900 (ptp) REVERT: B 985 ASP cc_start: 0.8805 (p0) cc_final: 0.8585 (p0) REVERT: B 1010 GLN cc_start: 0.8004 (tp-100) cc_final: 0.7769 (tp-100) REVERT: B 1107 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7060 (mtp85) REVERT: C 229 LEU cc_start: 0.9251 (tp) cc_final: 0.8966 (tp) REVERT: C 238 PHE cc_start: 0.9102 (p90) cc_final: 0.8764 (p90) REVERT: C 277 LEU cc_start: 0.9230 (mp) cc_final: 0.8777 (tp) REVERT: C 297 SER cc_start: 0.8702 (m) cc_final: 0.8255 (p) REVERT: C 414 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8552 (tp-100) REVERT: C 552 LEU cc_start: 0.9245 (mt) cc_final: 0.8924 (pp) REVERT: C 692 ILE cc_start: 0.8779 (mm) cc_final: 0.8451 (mt) REVERT: C 740 MET cc_start: 0.8952 (ttp) cc_final: 0.8401 (tmm) REVERT: C 780 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6942 (mt-10) REVERT: C 869 MET cc_start: 0.8315 (mtt) cc_final: 0.7625 (mtp) REVERT: C 978 ASN cc_start: 0.9224 (m-40) cc_final: 0.8845 (t0) REVERT: C 1029 MET cc_start: 0.8948 (tpp) cc_final: 0.8425 (tpp) REVERT: D 83 MET cc_start: -0.2028 (mtp) cc_final: -0.2426 (mmt) REVERT: D 110 MET cc_start: 0.2288 (mmp) cc_final: 0.2062 (mmp) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.3918 time to fit residues: 140.1887 Evaluate side-chains 149 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 3.111 ------------------------------------------------------------------------------- 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: 2.9990 chunk 331 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 368 optimal weight: 50.0000 chunk 306 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31332 Z= 0.255 Angle : 0.549 9.803 42606 Z= 0.284 Chirality : 0.043 0.216 4935 Planarity : 0.004 0.050 5451 Dihedral : 5.163 59.254 5289 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.32 (0.14), residues: 3798 helix: 1.75 (0.21), residues: 686 sheet: 0.26 (0.16), residues: 1017 loop : -0.28 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 104 HIS 0.012 0.001 HIS A1048 PHE 0.024 0.001 PHE A 464 TYR 0.030 0.001 TYR C 365 ARG 0.006 0.000 ARG C1014 *********************** 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 195 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9479 (mm) cc_final: 0.8953 (tp) REVERT: A 223 LEU cc_start: 0.8830 (mp) cc_final: 0.8243 (mp) REVERT: A 224 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8775 (mp0) REVERT: A 238 PHE cc_start: 0.9028 (p90) cc_final: 0.8666 (p90) REVERT: A 299 THR cc_start: 0.9590 (m) cc_final: 0.9328 (p) REVERT: A 388 ASN cc_start: 0.9087 (p0) cc_final: 0.7678 (m-40) REVERT: A 869 MET cc_start: 0.9213 (mtt) cc_final: 0.8616 (mtp) REVERT: A 985 ASP cc_start: 0.9215 (t0) cc_final: 0.8914 (t0) REVERT: A 1017 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8906 (tm-30) REVERT: A 1019 ARG cc_start: 0.8174 (tmm-80) cc_final: 0.7734 (ttp80) REVERT: A 1119 ASN cc_start: 0.7825 (m-40) cc_final: 0.7445 (m110) REVERT: B 54 LEU cc_start: 0.9638 (mm) cc_final: 0.9354 (tp) REVERT: B 56 LEU cc_start: 0.9182 (tp) cc_final: 0.8567 (tp) REVERT: B 104 TRP cc_start: 0.9089 (m-90) cc_final: 0.8797 (m-90) REVERT: B 137 ASN cc_start: 0.9416 (m-40) cc_final: 0.8931 (p0) REVERT: B 153 MET cc_start: 0.8484 (mtm) cc_final: 0.7974 (mpp) REVERT: B 175 PHE cc_start: 0.9171 (m-80) cc_final: 0.8879 (m-80) REVERT: B 238 PHE cc_start: 0.9635 (p90) cc_final: 0.9147 (p90) REVERT: B 270 LEU cc_start: 0.8808 (mt) cc_final: 0.7895 (mp) REVERT: B 297 SER cc_start: 0.9181 (m) cc_final: 0.8910 (p) REVERT: B 611 LEU cc_start: 0.9070 (tp) cc_final: 0.8793 (tp) REVERT: B 697 MET cc_start: 0.8264 (ptm) cc_final: 0.7963 (ptp) REVERT: B 731 MET cc_start: 0.8895 (ptm) cc_final: 0.7830 (ppp) REVERT: B 1010 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7263 (tp-100) REVERT: B 1014 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7654 (ttm170) REVERT: C 229 LEU cc_start: 0.9236 (tp) cc_final: 0.8920 (tp) REVERT: C 238 PHE cc_start: 0.9098 (p90) cc_final: 0.8645 (p90) REVERT: C 269 TYR cc_start: 0.7534 (m-80) cc_final: 0.7043 (m-80) REVERT: C 277 LEU cc_start: 0.9041 (mp) cc_final: 0.8643 (tp) REVERT: C 297 SER cc_start: 0.8757 (m) cc_final: 0.8323 (p) REVERT: C 414 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8492 (tp-100) REVERT: C 552 LEU cc_start: 0.9259 (mt) cc_final: 0.8943 (pp) REVERT: C 740 MET cc_start: 0.8758 (ttp) cc_final: 0.8430 (tmm) REVERT: C 869 MET cc_start: 0.8406 (mtt) cc_final: 0.7879 (mtp) REVERT: C 955 ASN cc_start: 0.8841 (m-40) cc_final: 0.8164 (p0) REVERT: C 978 ASN cc_start: 0.9245 (m-40) cc_final: 0.8863 (t0) REVERT: C 1029 MET cc_start: 0.8789 (tpp) cc_final: 0.8047 (tpp) REVERT: C 1050 MET cc_start: 0.8923 (ptp) cc_final: 0.8684 (ptp) REVERT: D 83 MET cc_start: -0.2091 (mtp) cc_final: -0.2452 (mmt) REVERT: D 110 MET cc_start: 0.2139 (mmp) cc_final: 0.1846 (mmp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3981 time to fit residues: 129.7593 Evaluate side-chains 145 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 3.409 ------------------------------------------------------------------------------- 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: 10.0000 chunk 41 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 208 optimal weight: 0.5980 chunk 310 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 367 optimal weight: 0.9980 chunk 229 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 703 ASN B 901 GLN ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31332 Z= 0.179 Angle : 0.504 8.484 42606 Z= 0.263 Chirality : 0.042 0.214 4935 Planarity : 0.003 0.051 5451 Dihedral : 4.720 54.670 5289 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 0.03 % Allowed : 0.88 % Favored : 99.09 % 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: 0.45 (0.14), residues: 3798 helix: 1.92 (0.21), residues: 688 sheet: 0.36 (0.16), residues: 1057 loop : -0.24 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP C 104 HIS 0.008 0.001 HIS A1048 PHE 0.024 0.001 PHE A 464 TYR 0.022 0.001 TYR C 365 ARG 0.006 0.000 ARG A1107 *********************** 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 193 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 3.293 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 54 LEU cc_start: 0.9439 (mm) cc_final: 0.8869 (tp) REVERT: A 223 LEU cc_start: 0.8895 (mp) cc_final: 0.8331 (mp) REVERT: A 224 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8895 (mp0) REVERT: A 238 PHE cc_start: 0.8935 (p90) cc_final: 0.8678 (p90) REVERT: A 299 THR cc_start: 0.9579 (m) cc_final: 0.9296 (p) REVERT: A 388 ASN cc_start: 0.9083 (p0) cc_final: 0.7772 (m-40) REVERT: A 571 ASP cc_start: 0.8144 (t0) cc_final: 0.7938 (m-30) REVERT: A 740 MET cc_start: 0.8988 (ppp) cc_final: 0.8615 (ppp) REVERT: A 869 MET cc_start: 0.9193 (mtt) cc_final: 0.8621 (mtp) REVERT: A 985 ASP cc_start: 0.9221 (t0) cc_final: 0.8945 (t0) REVERT: A 1017 GLU cc_start: 0.9223 (tm-30) cc_final: 0.9018 (tm-30) REVERT: A 1019 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7720 (ttp80) REVERT: A 1119 ASN cc_start: 0.7711 (m-40) cc_final: 0.7332 (m110) REVERT: B 54 LEU cc_start: 0.9659 (mm) cc_final: 0.9318 (tp) REVERT: B 56 LEU cc_start: 0.9225 (tp) cc_final: 0.8579 (tp) REVERT: B 104 TRP cc_start: 0.9032 (m-90) cc_final: 0.8547 (m-90) REVERT: B 137 ASN cc_start: 0.9360 (m-40) cc_final: 0.8881 (p0) REVERT: B 238 PHE cc_start: 0.9594 (p90) cc_final: 0.9065 (p90) REVERT: B 270 LEU cc_start: 0.9132 (mt) cc_final: 0.8104 (mp) REVERT: B 297 SER cc_start: 0.9198 (m) cc_final: 0.8927 (p) REVERT: B 611 LEU cc_start: 0.9086 (tp) cc_final: 0.8829 (tp) REVERT: B 697 MET cc_start: 0.8237 (ptm) cc_final: 0.7889 (ptp) REVERT: B 731 MET cc_start: 0.8854 (ptm) cc_final: 0.7833 (ppp) REVERT: B 887 THR cc_start: 0.8664 (p) cc_final: 0.8109 (t) REVERT: B 1010 GLN cc_start: 0.8058 (tp-100) cc_final: 0.7785 (tp-100) REVERT: C 229 LEU cc_start: 0.9326 (tp) cc_final: 0.8989 (tp) REVERT: C 238 PHE cc_start: 0.9098 (p90) cc_final: 0.8809 (p90) REVERT: C 269 TYR cc_start: 0.7434 (m-80) cc_final: 0.7121 (m-80) REVERT: C 297 SER cc_start: 0.8761 (m) cc_final: 0.8304 (p) REVERT: C 414 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8680 (tp40) REVERT: C 552 LEU cc_start: 0.9261 (mt) cc_final: 0.8952 (pp) REVERT: C 740 MET cc_start: 0.8686 (ttp) cc_final: 0.8444 (tmm) REVERT: C 869 MET cc_start: 0.8471 (mtt) cc_final: 0.7790 (mtp) REVERT: C 978 ASN cc_start: 0.9223 (m-40) cc_final: 0.8851 (t0) REVERT: C 1029 MET cc_start: 0.8822 (tpp) cc_final: 0.8075 (tpp) REVERT: D 83 MET cc_start: -0.2155 (mtp) cc_final: -0.2492 (mmt) REVERT: F 83 MET cc_start: -0.2394 (mmt) cc_final: -0.2658 (mmt) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.3970 time to fit residues: 130.2283 Evaluate side-chains 147 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 3.150 ------------------------------------------------------------------------------- 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: 3.9990 chunk 146 optimal weight: 10.0000 chunk 219 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 181 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 901 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31332 Z= 0.156 Angle : 0.489 7.764 42606 Z= 0.255 Chirality : 0.042 0.253 4935 Planarity : 0.003 0.051 5451 Dihedral : 4.369 48.216 5289 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.68 % 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: 0.47 (0.14), residues: 3798 helix: 1.97 (0.21), residues: 688 sheet: 0.42 (0.16), residues: 991 loop : -0.25 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 104 HIS 0.007 0.001 HIS A1048 PHE 0.024 0.001 PHE A 464 TYR 0.018 0.001 TYR A 873 ARG 0.010 0.000 ARG B1014 *********************** 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 193 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 3.577 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 54 LEU cc_start: 0.9411 (mm) cc_final: 0.8817 (tp) REVERT: A 223 LEU cc_start: 0.8901 (mp) cc_final: 0.8417 (mp) REVERT: A 224 GLU cc_start: 0.9326 (mt-10) cc_final: 0.8881 (mp0) REVERT: A 238 PHE cc_start: 0.8899 (p90) cc_final: 0.8647 (p90) REVERT: A 299 THR cc_start: 0.9565 (m) cc_final: 0.9276 (p) REVERT: A 388 ASN cc_start: 0.8993 (p0) cc_final: 0.7656 (m-40) REVERT: A 773 GLU cc_start: 0.8937 (tt0) cc_final: 0.8369 (tp30) REVERT: A 775 ASP cc_start: 0.7987 (p0) cc_final: 0.7552 (p0) REVERT: A 780 GLU cc_start: 0.8438 (tp30) cc_final: 0.8153 (mm-30) REVERT: A 869 MET cc_start: 0.9133 (mtt) cc_final: 0.8741 (mtp) REVERT: A 904 TYR cc_start: 0.7704 (m-10) cc_final: 0.7434 (m-10) REVERT: A 985 ASP cc_start: 0.9211 (t0) cc_final: 0.8953 (t0) REVERT: A 1017 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8860 (tm-30) REVERT: A 1019 ARG cc_start: 0.8087 (tmm-80) cc_final: 0.7371 (ttp80) REVERT: A 1119 ASN cc_start: 0.7617 (m-40) cc_final: 0.7252 (m110) REVERT: B 54 LEU cc_start: 0.9666 (mm) cc_final: 0.9345 (tp) REVERT: B 56 LEU cc_start: 0.9232 (tp) cc_final: 0.8588 (tp) REVERT: B 104 TRP cc_start: 0.8992 (m-90) cc_final: 0.8623 (m-90) REVERT: B 135 PHE cc_start: 0.8410 (m-10) cc_final: 0.8105 (m-10) REVERT: B 137 ASN cc_start: 0.9405 (m-40) cc_final: 0.8985 (p0) REVERT: B 153 MET cc_start: 0.8704 (mtm) cc_final: 0.8410 (mpp) REVERT: B 238 PHE cc_start: 0.9577 (p90) cc_final: 0.9034 (p90) REVERT: B 270 LEU cc_start: 0.9106 (mt) cc_final: 0.8065 (mp) REVERT: B 297 SER cc_start: 0.9212 (m) cc_final: 0.8912 (p) REVERT: B 611 LEU cc_start: 0.9061 (tp) cc_final: 0.8811 (tp) REVERT: B 697 MET cc_start: 0.8035 (ptm) cc_final: 0.7781 (ptp) REVERT: B 887 THR cc_start: 0.8640 (p) cc_final: 0.8075 (t) REVERT: B 901 GLN cc_start: 0.8064 (tm130) cc_final: 0.7604 (tm-30) REVERT: B 979 ASP cc_start: 0.8834 (m-30) cc_final: 0.8586 (t0) REVERT: C 104 TRP cc_start: 0.8592 (m-10) cc_final: 0.8324 (m-10) REVERT: C 229 LEU cc_start: 0.9299 (tp) cc_final: 0.8961 (tp) REVERT: C 238 PHE cc_start: 0.9097 (p90) cc_final: 0.8848 (p90) REVERT: C 269 TYR cc_start: 0.7615 (m-80) cc_final: 0.6970 (m-80) REVERT: C 297 SER cc_start: 0.8761 (m) cc_final: 0.8289 (p) REVERT: C 552 LEU cc_start: 0.9187 (mt) cc_final: 0.8939 (pp) REVERT: C 869 MET cc_start: 0.8129 (mtt) cc_final: 0.7593 (mtp) REVERT: C 978 ASN cc_start: 0.9232 (m-40) cc_final: 0.8654 (t0) REVERT: C 1029 MET cc_start: 0.8906 (tpp) cc_final: 0.8023 (tpp) REVERT: D 83 MET cc_start: -0.2238 (mtp) cc_final: -0.2565 (mmt) REVERT: F 83 MET cc_start: -0.2403 (mmt) cc_final: -0.2692 (mmt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.3923 time to fit residues: 129.1331 Evaluate side-chains 148 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 3.353 ------------------------------------------------------------------------------- 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: 30.0000 chunk 351 optimal weight: 0.0970 chunk 320 optimal weight: 30.0000 chunk 342 optimal weight: 20.0000 chunk 205 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 323 optimal weight: 0.0870 chunk 341 optimal weight: 7.9990 overall best weight: 1.2360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 978 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31332 Z= 0.211 Angle : 0.517 11.221 42606 Z= 0.268 Chirality : 0.042 0.239 4935 Planarity : 0.003 0.051 5451 Dihedral : 4.296 43.488 5289 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % 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: 0.47 (0.14), residues: 3798 helix: 1.90 (0.21), residues: 686 sheet: 0.43 (0.16), residues: 1007 loop : -0.24 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.008 0.001 HIS A1048 PHE 0.022 0.001 PHE A 464 TYR 0.020 0.001 TYR B 873 ARG 0.018 0.000 ARG B1014 *********************** 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 180 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 3.332 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 54 LEU cc_start: 0.9439 (mm) cc_final: 0.8847 (tp) REVERT: A 62 VAL cc_start: 0.9118 (m) cc_final: 0.8627 (t) REVERT: A 223 LEU cc_start: 0.8918 (mp) cc_final: 0.8400 (mp) REVERT: A 224 GLU cc_start: 0.9318 (mt-10) cc_final: 0.8879 (mp0) REVERT: A 238 PHE cc_start: 0.8930 (p90) cc_final: 0.8670 (p90) REVERT: A 299 THR cc_start: 0.9578 (m) cc_final: 0.9294 (p) REVERT: A 388 ASN cc_start: 0.9041 (p0) cc_final: 0.7693 (m-40) REVERT: A 773 GLU cc_start: 0.8984 (tt0) cc_final: 0.8612 (tp30) REVERT: A 780 GLU cc_start: 0.8525 (tp30) cc_final: 0.8178 (mm-30) REVERT: A 869 MET cc_start: 0.9196 (mtt) cc_final: 0.8766 (mtp) REVERT: A 985 ASP cc_start: 0.9198 (t0) cc_final: 0.8960 (t0) REVERT: A 1017 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8894 (tm-30) REVERT: A 1019 ARG cc_start: 0.8211 (tmm-80) cc_final: 0.7467 (ttp80) REVERT: A 1119 ASN cc_start: 0.7123 (m-40) cc_final: 0.6836 (m110) REVERT: B 56 LEU cc_start: 0.9268 (tp) cc_final: 0.8600 (tp) REVERT: B 104 TRP cc_start: 0.9037 (m-90) cc_final: 0.8697 (m-90) REVERT: B 135 PHE cc_start: 0.8425 (m-10) cc_final: 0.8182 (m-10) REVERT: B 137 ASN cc_start: 0.9385 (m-40) cc_final: 0.8976 (p0) REVERT: B 153 MET cc_start: 0.8322 (mtm) cc_final: 0.7850 (mpp) REVERT: B 238 PHE cc_start: 0.9595 (p90) cc_final: 0.9061 (p90) REVERT: B 270 LEU cc_start: 0.9185 (mt) cc_final: 0.8962 (mp) REVERT: B 297 SER cc_start: 0.9195 (m) cc_final: 0.8907 (p) REVERT: B 611 LEU cc_start: 0.9055 (tp) cc_final: 0.8798 (tp) REVERT: B 697 MET cc_start: 0.8086 (ptm) cc_final: 0.7834 (ptp) REVERT: B 731 MET cc_start: 0.8887 (ptm) cc_final: 0.7764 (ppp) REVERT: B 887 THR cc_start: 0.8714 (p) cc_final: 0.8189 (t) REVERT: B 979 ASP cc_start: 0.8823 (m-30) cc_final: 0.8585 (t0) REVERT: C 229 LEU cc_start: 0.9320 (tp) cc_final: 0.8988 (tp) REVERT: C 269 TYR cc_start: 0.7681 (m-80) cc_final: 0.7227 (m-80) REVERT: C 297 SER cc_start: 0.8799 (m) cc_final: 0.8340 (p) REVERT: C 552 LEU cc_start: 0.9210 (mt) cc_final: 0.8955 (pp) REVERT: C 869 MET cc_start: 0.8248 (mtt) cc_final: 0.7639 (mtp) REVERT: C 978 ASN cc_start: 0.9217 (m-40) cc_final: 0.8654 (t0) REVERT: C 1029 MET cc_start: 0.8828 (tpp) cc_final: 0.7986 (tpp) REVERT: D 83 MET cc_start: -0.2247 (mtp) cc_final: -0.2567 (mmt) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.4081 time to fit residues: 126.2493 Evaluate side-chains 139 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 4.097 ------------------------------------------------------------------------------- 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: 20.0000 chunk 361 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 171 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 379 optimal weight: 9.9990 chunk 349 optimal weight: 0.0980 chunk 302 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 233 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 965 GLN A 978 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31332 Z= 0.225 Angle : 0.521 10.796 42606 Z= 0.271 Chirality : 0.042 0.238 4935 Planarity : 0.004 0.050 5451 Dihedral : 4.256 40.505 5289 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.44 (0.14), residues: 3798 helix: 1.84 (0.21), residues: 686 sheet: 0.56 (0.17), residues: 971 loop : -0.32 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 104 HIS 0.006 0.001 HIS A1048 PHE 0.036 0.001 PHE C 906 TYR 0.018 0.001 TYR C 904 ARG 0.035 0.000 ARG B1107 ********************** 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 : 3.906 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: A 54 LEU cc_start: 0.9466 (mm) cc_final: 0.8894 (tp) REVERT: A 62 VAL cc_start: 0.9136 (m) cc_final: 0.8655 (t) REVERT: A 223 LEU cc_start: 0.8895 (mp) cc_final: 0.8350 (mp) REVERT: A 224 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8874 (mp0) REVERT: A 238 PHE cc_start: 0.8949 (p90) cc_final: 0.8684 (p90) REVERT: A 299 THR cc_start: 0.9574 (m) cc_final: 0.9302 (p) REVERT: A 388 ASN cc_start: 0.9062 (p0) cc_final: 0.7732 (t0) REVERT: A 773 GLU cc_start: 0.8990 (tt0) cc_final: 0.8518 (tp30) REVERT: A 869 MET cc_start: 0.9231 (mtt) cc_final: 0.8724 (mtp) REVERT: A 985 ASP cc_start: 0.9209 (t0) cc_final: 0.8968 (t0) REVERT: A 1017 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8887 (tm-30) REVERT: A 1019 ARG cc_start: 0.8224 (tmm-80) cc_final: 0.7402 (ttp80) REVERT: A 1119 ASN cc_start: 0.7190 (m-40) cc_final: 0.6884 (m110) REVERT: B 56 LEU cc_start: 0.9240 (tp) cc_final: 0.8568 (tp) REVERT: B 104 TRP cc_start: 0.9100 (m-90) cc_final: 0.8749 (m-90) REVERT: B 153 MET cc_start: 0.8531 (mtm) cc_final: 0.8121 (mpp) REVERT: B 175 PHE cc_start: 0.9576 (m-10) cc_final: 0.9364 (m-80) REVERT: B 238 PHE cc_start: 0.9607 (p90) cc_final: 0.9078 (p90) REVERT: B 270 LEU cc_start: 0.9137 (mt) cc_final: 0.8917 (mp) REVERT: B 297 SER cc_start: 0.9181 (m) cc_final: 0.8895 (p) REVERT: B 731 MET cc_start: 0.8829 (ptm) cc_final: 0.7650 (ppp) REVERT: B 887 THR cc_start: 0.8731 (p) cc_final: 0.8213 (t) REVERT: B 979 ASP cc_start: 0.8838 (m-30) cc_final: 0.8595 (t0) REVERT: C 229 LEU cc_start: 0.9349 (tp) cc_final: 0.9025 (tp) REVERT: C 238 PHE cc_start: 0.9093 (p90) cc_final: 0.8749 (p90) REVERT: C 269 TYR cc_start: 0.7704 (m-80) cc_final: 0.7281 (m-80) REVERT: C 276 LEU cc_start: 0.8036 (mm) cc_final: 0.7056 (mm) REVERT: C 297 SER cc_start: 0.8821 (m) cc_final: 0.8359 (p) REVERT: C 955 ASN cc_start: 0.9024 (m-40) cc_final: 0.8311 (p0) REVERT: C 978 ASN cc_start: 0.9246 (m-40) cc_final: 0.8658 (t0) REVERT: C 1029 MET cc_start: 0.8822 (tpp) cc_final: 0.7974 (tpp) REVERT: D 83 MET cc_start: -0.2270 (mtp) cc_final: -0.2606 (mmt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.4017 time to fit residues: 122.0123 Evaluate side-chains 140 residues out of total 3336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 3.295 ------------------------------------------------------------------------------- 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: 0.8980 chunk 278 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 302 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 978 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1011 GLN B1119 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.137066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.111636 restraints weight = 146071.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.109753 restraints weight = 170547.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.107082 restraints weight = 145317.812| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31332 Z= 0.306 Angle : 0.569 10.447 42606 Z= 0.295 Chirality : 0.043 0.235 4935 Planarity : 0.004 0.049 5451 Dihedral : 4.407 38.758 5289 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.32 (0.14), residues: 3798 helix: 1.65 (0.21), residues: 686 sheet: 0.53 (0.17), residues: 973 loop : -0.38 (0.14), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 104 HIS 0.008 0.001 HIS A1048 PHE 0.027 0.002 PHE C1062 TYR 0.053 0.001 TYR C 904 ARG 0.010 0.001 ARG B1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4828.26 seconds wall clock time: 92 minutes 19.92 seconds (5539.92 seconds total)