Starting phenix.real_space_refine on Fri Mar 6 12:12:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ndd_12284/03_2026/7ndd_12284.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ndd_12284/03_2026/7ndd_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ndd_12284/03_2026/7ndd_12284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ndd_12284/03_2026/7ndd_12284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ndd_12284/03_2026/7ndd_12284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ndd_12284/03_2026/7ndd_12284.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ASN:plan1': 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: {'ASP:plan': 1, 'ASN:plan1': 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: {'ASP:plan': 1, 'ASN:plan1': 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: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} 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: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} 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: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} 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: 7.70, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 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: 3.27 Conformation dependent library (CDL) restraints added in 1.4 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: 1.70 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: 9.30 Time building geometry restraints manager: 4.17 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: 0.00 - 5.44: 42576 5.44 - 10.88: 26 10.88 - 16.32: 2 16.32 - 21.76: 1 21.76 - 27.20: 1 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 3.040 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 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.241 3.040 ... (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 Time spend for trying shortcut: 0.03 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.300 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.490 ------------------------------------------------------------------------------- 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 31434 Z= 0.162 Angle : 0.624 27.202 42864 Z= 0.318 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG E 24 TYR 0.014 0.001 TYR C 200 PHE 0.012 0.001 PHE B1109 TRP 0.010 0.001 TRP A 258 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00337 (31332) covalent geometry : angle 0.61329 (42606) SS BOND : bond 0.00356 ( 48) SS BOND : angle 1.00826 ( 96) hydrogen bonds : bond 0.18912 ( 1221) hydrogen bonds : angle 7.73359 ( 3342) link_BETA1-4 : bond 0.00257 ( 15) link_BETA1-4 : angle 0.97567 ( 45) link_NAG-ASN : bond 0.00272 ( 39) link_NAG-ASN : angle 2.09650 ( 117) *********************** 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 to be fit. rotamer outliers: 14 poor density : 437 time to evaluate : 1.131 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: 0.9073 (tp) REVERT: A 191 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7641 (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: 0.8116 (p90) REVERT: A 299 THR cc_start: 0.9629 (m) cc_final: 0.9279 (p) REVERT: A 386 LYS cc_start: 0.9404 (mttt) cc_final: 0.8776 (ptmt) REVERT: A 518 LEU cc_start: 0.8083 (mt) cc_final: 0.7811 (mt) REVERT: A 759 PHE cc_start: 0.8342 (m-80) cc_final: 0.8016 (m-80) REVERT: A 819 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8069 (mt-10) REVERT: A 895 GLN cc_start: 0.8365 (pm20) cc_final: 0.7888 (pm20) REVERT: A 1119 ASN cc_start: 0.8390 (m-40) cc_final: 0.7578 (m110) REVERT: B 54 LEU cc_start: 0.9613 (mt) cc_final: 0.9220 (tp) REVERT: B 91 TYR cc_start: 0.8523 (t80) cc_final: 0.7590 (t80) REVERT: B 104 TRP cc_start: 0.8839 (m-90) cc_final: 0.8323 (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: 0.9060 (m-80) REVERT: B 238 PHE cc_start: 0.9432 (p90) cc_final: 0.9120 (p90) REVERT: B 270 LEU cc_start: 0.8973 (mt) cc_final: 0.8476 (mp) REVERT: B 611 LEU cc_start: 0.9046 (tp) cc_final: 0.8821 (tp) REVERT: B 727 LEU cc_start: 0.9565 (mt) cc_final: 0.9356 (mp) REVERT: B 731 MET cc_start: 0.8450 (ptm) cc_final: 0.7791 (ppp) REVERT: B 776 LYS cc_start: 0.9081 (tttt) cc_final: 0.8720 (tppt) REVERT: B 869 MET cc_start: 0.9319 (mtt) cc_final: 0.8970 (mtm) REVERT: B 901 GLN cc_start: 0.8458 (tt0) cc_final: 0.8258 (tm-30) REVERT: B 979 ASP cc_start: 0.8927 (m-30) cc_final: 0.8618 (m-30) REVERT: B 1010 GLN cc_start: 0.8529 (mm110) cc_final: 0.8042 (tp-100) REVERT: C 191 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8132 (pm20) REVERT: C 297 SER cc_start: 0.8462 (m) cc_final: 0.8148 (p) REVERT: C 398 ASP cc_start: 0.6894 (m-30) cc_final: 0.5476 (m-30) REVERT: C 552 LEU cc_start: 0.9225 (mt) cc_final: 0.8905 (pp) REVERT: C 707 TYR cc_start: 0.8937 (t80) cc_final: 0.8420 (t80) REVERT: C 805 ILE cc_start: 0.9175 (pt) cc_final: 0.8780 (mm) REVERT: C 869 MET cc_start: 0.8630 (mtt) cc_final: 0.7893 (mtm) REVERT: C 878 LEU cc_start: 0.8166 (tp) cc_final: 0.7840 (tp) REVERT: C 909 ILE cc_start: 0.9401 (pt) cc_final: 0.9026 (mt) REVERT: C 955 ASN cc_start: 0.8760 (m-40) cc_final: 0.8067 (p0) REVERT: C 978 ASN cc_start: 0.9101 (m-40) cc_final: 0.8698 (t0) REVERT: C 1029 MET cc_start: 0.8371 (tpp) cc_final: 0.8124 (tpp) REVERT: D 83 MET cc_start: -0.1351 (mtp) cc_final: -0.1797 (mmt) outliers start: 14 outliers final: 2 residues processed: 451 average time/residue: 0.2096 time to fit residues: 150.1000 Evaluate side-chains 224 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- 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 953 ASN A 978 ASN B 901 GLN C 321 GLN C 703 ASN C 774 GLN C 901 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.139441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.112527 restraints weight = 147160.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.109288 restraints weight = 175340.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.105313 restraints weight = 128374.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.105092 restraints weight = 135102.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.105400 restraints weight = 132263.773| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 31434 Z= 0.297 Angle : 0.739 10.835 42864 Z= 0.380 Chirality : 0.047 0.272 4935 Planarity : 0.005 0.103 5451 Dihedral : 6.955 58.696 5289 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.10 % Rotamer: Outliers : 0.12 % Allowed : 2.16 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 3798 helix: 1.30 (0.20), residues: 704 sheet: 0.22 (0.15), residues: 998 loop : -0.54 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 357 TYR 0.027 0.002 TYR A1067 PHE 0.023 0.002 PHE C1062 TRP 0.010 0.002 TRP C 104 HIS 0.019 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00656 (31332) covalent geometry : angle 0.72622 (42606) SS BOND : bond 0.00439 ( 48) SS BOND : angle 1.19811 ( 96) hydrogen bonds : bond 0.04956 ( 1221) hydrogen bonds : angle 6.28852 ( 3342) link_BETA1-4 : bond 0.00417 ( 15) link_BETA1-4 : angle 1.12619 ( 45) link_NAG-ASN : bond 0.00771 ( 39) link_NAG-ASN : angle 2.55487 ( 117) *********************** 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 241 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 237 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9455 (mt) cc_final: 0.9202 (tp) REVERT: A 223 LEU cc_start: 0.8424 (mp) cc_final: 0.8004 (mp) REVERT: A 224 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8670 (mp0) REVERT: A 287 ASP cc_start: 0.8646 (t0) cc_final: 0.8426 (t0) REVERT: A 299 THR cc_start: 0.9628 (m) cc_final: 0.9310 (p) REVERT: A 386 LYS cc_start: 0.9356 (mttt) cc_final: 0.8946 (ptpp) REVERT: A 388 ASN cc_start: 0.8652 (p0) cc_final: 0.8382 (p0) REVERT: A 518 LEU cc_start: 0.8994 (mt) cc_final: 0.8761 (mt) REVERT: A 869 MET cc_start: 0.8938 (mtt) cc_final: 0.8458 (mtt) REVERT: A 895 GLN cc_start: 0.8488 (pm20) cc_final: 0.8170 (pm20) REVERT: B 56 LEU cc_start: 0.9013 (tp) cc_final: 0.8516 (tp) REVERT: B 91 TYR cc_start: 0.8452 (t80) cc_final: 0.7947 (t80) REVERT: B 92 PHE cc_start: 0.8375 (t80) cc_final: 0.8119 (t80) REVERT: B 175 PHE cc_start: 0.9221 (m-80) cc_final: 0.8953 (m-80) REVERT: B 191 GLU cc_start: 0.9241 (mp0) cc_final: 0.8899 (pm20) REVERT: B 238 PHE cc_start: 0.9213 (p90) cc_final: 0.8848 (p90) REVERT: B 297 SER cc_start: 0.9237 (m) cc_final: 0.8940 (p) REVERT: B 731 MET cc_start: 0.8588 (ptm) cc_final: 0.7851 (ppp) REVERT: B 947 LYS cc_start: 0.8807 (mttt) cc_final: 0.8368 (mmmt) REVERT: B 1010 GLN cc_start: 0.8546 (mm110) cc_final: 0.8222 (tp-100) REVERT: C 95 THR cc_start: 0.8344 (p) cc_final: 0.8134 (p) REVERT: C 229 LEU cc_start: 0.9087 (tp) cc_final: 0.8655 (tp) REVERT: C 277 LEU cc_start: 0.9310 (mp) cc_final: 0.8923 (tp) REVERT: C 297 SER cc_start: 0.8766 (m) cc_final: 0.8376 (p) REVERT: C 365 TYR cc_start: 0.8848 (m-80) cc_final: 0.8620 (m-10) REVERT: C 414 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8303 (tp-100) REVERT: C 552 LEU cc_start: 0.9281 (mt) cc_final: 0.8892 (pp) REVERT: C 707 TYR cc_start: 0.9188 (t80) cc_final: 0.8570 (t80) REVERT: C 740 MET cc_start: 0.8887 (ttp) cc_final: 0.8278 (tmm) REVERT: C 869 MET cc_start: 0.8458 (mtt) cc_final: 0.7964 (mtp) REVERT: C 978 ASN cc_start: 0.9169 (m-40) cc_final: 0.8774 (t0) REVERT: C 984 LEU cc_start: 0.8467 (mt) cc_final: 0.8079 (tp) REVERT: C 1029 MET cc_start: 0.7859 (tpp) cc_final: 0.7235 (tpp) REVERT: C 1092 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7611 (tp30) REVERT: H 110 MET cc_start: 0.5472 (mmp) cc_final: 0.4962 (mmp) outliers start: 4 outliers final: 1 residues processed: 241 average time/residue: 0.1872 time to fit residues: 73.3559 Evaluate side-chains 161 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 213 optimal weight: 0.0050 chunk 190 optimal weight: 0.5980 chunk 238 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 278 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN A 901 GLN B 207 HIS B 901 GLN B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.134215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.083500 restraints weight = 110299.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085309 restraints weight = 66698.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085627 restraints weight = 42020.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085949 restraints weight = 34192.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.085996 restraints weight = 34776.961| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31434 Z= 0.122 Angle : 0.556 9.342 42864 Z= 0.288 Chirality : 0.044 0.236 4935 Planarity : 0.004 0.079 5451 Dihedral : 6.360 59.310 5289 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.13), residues: 3798 helix: 1.61 (0.20), residues: 718 sheet: 0.28 (0.15), residues: 1004 loop : -0.41 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 357 TYR 0.015 0.001 TYR A 449 PHE 0.019 0.001 PHE C 906 TRP 0.010 0.001 TRP A 64 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00274 (31332) covalent geometry : angle 0.54534 (42606) SS BOND : bond 0.00246 ( 48) SS BOND : angle 0.99892 ( 96) hydrogen bonds : bond 0.04093 ( 1221) hydrogen bonds : angle 5.72816 ( 3342) link_BETA1-4 : bond 0.00327 ( 15) link_BETA1-4 : angle 0.97912 ( 45) link_NAG-ASN : bond 0.00327 ( 39) link_NAG-ASN : angle 1.97036 ( 117) *********************** 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 231 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.108 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: A 54 LEU cc_start: 0.9410 (mt) cc_final: 0.9104 (tp) REVERT: A 223 LEU cc_start: 0.8554 (mp) cc_final: 0.7995 (mp) REVERT: A 224 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8913 (mp0) REVERT: A 238 PHE cc_start: 0.8980 (p90) cc_final: 0.8756 (p90) REVERT: A 287 ASP cc_start: 0.8952 (t0) cc_final: 0.8699 (t0) REVERT: A 299 THR cc_start: 0.9564 (m) cc_final: 0.9242 (p) REVERT: A 386 LYS cc_start: 0.9376 (mttt) cc_final: 0.9137 (ptpp) REVERT: A 388 ASN cc_start: 0.8857 (p0) cc_final: 0.7685 (m-40) REVERT: A 1002 GLN cc_start: 0.8931 (tt0) cc_final: 0.8563 (tm-30) REVERT: B 56 LEU cc_start: 0.9203 (tp) cc_final: 0.8828 (tp) REVERT: B 91 TYR cc_start: 0.8264 (t80) cc_final: 0.7855 (t80) REVERT: B 175 PHE cc_start: 0.9191 (m-80) cc_final: 0.8803 (m-10) REVERT: B 223 LEU cc_start: 0.8802 (mp) cc_final: 0.8544 (mp) REVERT: B 238 PHE cc_start: 0.9457 (p90) cc_final: 0.8947 (p90) REVERT: B 297 SER cc_start: 0.9131 (m) cc_final: 0.8806 (p) REVERT: B 611 LEU cc_start: 0.8976 (tp) cc_final: 0.8759 (tp) REVERT: B 697 MET cc_start: 0.8530 (ptm) cc_final: 0.7948 (ptp) REVERT: C 95 THR cc_start: 0.8372 (p) cc_final: 0.8164 (p) REVERT: C 229 LEU cc_start: 0.9129 (tp) cc_final: 0.8743 (tp) REVERT: C 277 LEU cc_start: 0.9218 (mp) cc_final: 0.8840 (tp) REVERT: C 297 SER cc_start: 0.8532 (m) cc_final: 0.8078 (p) REVERT: C 365 TYR cc_start: 0.8678 (m-80) cc_final: 0.8455 (m-10) REVERT: C 414 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8497 (tp-100) REVERT: C 552 LEU cc_start: 0.9282 (mt) cc_final: 0.8910 (pp) REVERT: C 707 TYR cc_start: 0.9192 (t80) cc_final: 0.8524 (t80) REVERT: C 740 MET cc_start: 0.9021 (ttp) cc_final: 0.8244 (tmm) REVERT: C 774 GLN cc_start: 0.9325 (mm-40) cc_final: 0.8430 (mm-40) REVERT: C 869 MET cc_start: 0.8345 (mtt) cc_final: 0.7846 (mtp) REVERT: C 878 LEU cc_start: 0.8775 (tp) cc_final: 0.8533 (tp) REVERT: C 978 ASN cc_start: 0.9286 (m-40) cc_final: 0.8779 (t0) REVERT: C 1029 MET cc_start: 0.8921 (tpp) cc_final: 0.8427 (tpp) REVERT: C 1108 ASN cc_start: 0.8730 (m-40) cc_final: 0.8441 (m-40) REVERT: F 29 PHE cc_start: 0.7878 (t80) cc_final: 0.7619 (t80) REVERT: H 110 MET cc_start: 0.5451 (mmp) cc_final: 0.4590 (mmp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1755 time to fit residues: 67.3575 Evaluate side-chains 162 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 370 optimal weight: 50.0000 chunk 252 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 316 optimal weight: 0.8980 chunk 106 optimal weight: 20.0000 chunk 101 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 300 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN B 913 GLN C 394 ASN C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.114150 restraints weight = 145445.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111057 restraints weight = 175265.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.108359 restraints weight = 150631.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.108519 restraints weight = 136806.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108720 restraints weight = 123480.781| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 31434 Z= 0.177 Angle : 0.573 11.590 42864 Z= 0.296 Chirality : 0.043 0.237 4935 Planarity : 0.004 0.050 5451 Dihedral : 5.888 59.989 5289 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.13), residues: 3798 helix: 1.64 (0.20), residues: 706 sheet: 0.32 (0.15), residues: 998 loop : -0.35 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1019 TYR 0.015 0.001 TYR A1067 PHE 0.020 0.001 PHE C1062 TRP 0.017 0.001 TRP C 104 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00394 (31332) covalent geometry : angle 0.56156 (42606) SS BOND : bond 0.00318 ( 48) SS BOND : angle 1.04064 ( 96) hydrogen bonds : bond 0.04042 ( 1221) hydrogen bonds : angle 5.58608 ( 3342) link_BETA1-4 : bond 0.00429 ( 15) link_BETA1-4 : angle 1.10880 ( 45) link_NAG-ASN : bond 0.00382 ( 39) link_NAG-ASN : angle 2.03727 ( 117) *********************** 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 202 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9352 (mt) cc_final: 0.9110 (tp) REVERT: A 223 LEU cc_start: 0.8442 (mp) cc_final: 0.8130 (mp) REVERT: A 224 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8925 (mp0) REVERT: A 229 LEU cc_start: 0.8821 (mm) cc_final: 0.8566 (tp) REVERT: A 287 ASP cc_start: 0.8716 (t0) cc_final: 0.8469 (t0) REVERT: A 299 THR cc_start: 0.9538 (m) cc_final: 0.9239 (p) REVERT: A 869 MET cc_start: 0.9197 (mtt) cc_final: 0.8997 (mtp) REVERT: A 985 ASP cc_start: 0.9098 (t0) cc_final: 0.8844 (t0) REVERT: A 990 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8692 (pt0) REVERT: B 56 LEU cc_start: 0.8871 (tp) cc_final: 0.8382 (tp) REVERT: B 91 TYR cc_start: 0.7846 (t80) cc_final: 0.7540 (t80) REVERT: B 175 PHE cc_start: 0.8936 (m-80) cc_final: 0.8721 (m-10) REVERT: B 238 PHE cc_start: 0.8895 (p90) cc_final: 0.8575 (p90) REVERT: B 297 SER cc_start: 0.9125 (m) cc_final: 0.8822 (p) REVERT: B 611 LEU cc_start: 0.9026 (tp) cc_final: 0.8801 (tp) REVERT: B 697 MET cc_start: 0.8121 (ptm) cc_final: 0.7921 (ptp) REVERT: B 731 MET cc_start: 0.8737 (ptm) cc_final: 0.7913 (ppp) REVERT: C 95 THR cc_start: 0.7851 (p) cc_final: 0.7622 (p) REVERT: C 229 LEU cc_start: 0.9003 (tp) cc_final: 0.8686 (tp) REVERT: C 277 LEU cc_start: 0.8966 (mp) cc_final: 0.8766 (tp) REVERT: C 297 SER cc_start: 0.8659 (m) cc_final: 0.8178 (p) REVERT: C 414 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8448 (tp-100) REVERT: C 552 LEU cc_start: 0.9133 (mt) cc_final: 0.8850 (pp) REVERT: C 740 MET cc_start: 0.8955 (ttp) cc_final: 0.8532 (tmm) REVERT: C 869 MET cc_start: 0.8382 (mtt) cc_final: 0.8026 (mtp) REVERT: C 878 LEU cc_start: 0.8467 (tp) cc_final: 0.8184 (tp) REVERT: C 978 ASN cc_start: 0.9194 (m-40) cc_final: 0.8892 (t0) REVERT: C 1029 MET cc_start: 0.8872 (tpp) cc_final: 0.8166 (tpp) REVERT: D 110 MET cc_start: 0.3743 (mmp) cc_final: 0.3325 (mmp) REVERT: F 29 PHE cc_start: 0.8163 (t80) cc_final: 0.7597 (t80) REVERT: H 110 MET cc_start: 0.4931 (mmp) cc_final: 0.4112 (mmp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1829 time to fit residues: 61.7721 Evaluate side-chains 147 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 326 optimal weight: 50.0000 chunk 155 optimal weight: 20.0000 chunk 248 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 367 optimal weight: 40.0000 chunk 317 optimal weight: 5.9990 chunk 362 optimal weight: 50.0000 chunk 244 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 394 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 954 GLN C 207 HIS C 321 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN D 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.138765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.113005 restraints weight = 146409.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108993 restraints weight = 185388.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.106749 restraints weight = 170327.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.107329 restraints weight = 146793.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.107331 restraints weight = 125349.268| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31434 Z= 0.193 Angle : 0.577 10.790 42864 Z= 0.297 Chirality : 0.043 0.269 4935 Planarity : 0.004 0.048 5451 Dihedral : 5.534 58.898 5289 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3798 helix: 1.53 (0.20), residues: 708 sheet: 0.35 (0.16), residues: 970 loop : -0.30 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1014 TYR 0.020 0.001 TYR C 365 PHE 0.029 0.002 PHE C 135 TRP 0.030 0.001 TRP C 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00431 (31332) covalent geometry : angle 0.56431 (42606) SS BOND : bond 0.00320 ( 48) SS BOND : angle 0.89807 ( 96) hydrogen bonds : bond 0.04021 ( 1221) hydrogen bonds : angle 5.55178 ( 3342) link_BETA1-4 : bond 0.00261 ( 15) link_BETA1-4 : angle 1.05803 ( 45) link_NAG-ASN : bond 0.00469 ( 39) link_NAG-ASN : angle 2.20518 ( 117) *********************** 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 200 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9293 (mt) cc_final: 0.9036 (tp) REVERT: A 223 LEU cc_start: 0.8552 (mp) cc_final: 0.8216 (mp) REVERT: A 224 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8924 (mp0) REVERT: A 287 ASP cc_start: 0.8813 (t0) cc_final: 0.8561 (t0) REVERT: A 299 THR cc_start: 0.9553 (m) cc_final: 0.9263 (p) REVERT: A 820 ASP cc_start: 0.8829 (m-30) cc_final: 0.8612 (p0) REVERT: A 869 MET cc_start: 0.9292 (mtt) cc_final: 0.8967 (mtp) REVERT: A 985 ASP cc_start: 0.9214 (t0) cc_final: 0.8971 (t0) REVERT: A 990 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8712 (pt0) REVERT: B 54 LEU cc_start: 0.9242 (tp) cc_final: 0.8894 (tp) REVERT: B 56 LEU cc_start: 0.8896 (tp) cc_final: 0.8490 (tp) REVERT: B 91 TYR cc_start: 0.7885 (t80) cc_final: 0.7599 (t80) REVERT: B 238 PHE cc_start: 0.9016 (p90) cc_final: 0.8674 (p90) REVERT: B 297 SER cc_start: 0.9162 (m) cc_final: 0.8850 (p) REVERT: B 697 MET cc_start: 0.8213 (ptm) cc_final: 0.8006 (ptp) REVERT: B 731 MET cc_start: 0.8820 (ptm) cc_final: 0.7905 (ppp) REVERT: C 95 THR cc_start: 0.7929 (p) cc_final: 0.7698 (p) REVERT: C 269 TYR cc_start: 0.7278 (m-80) cc_final: 0.7060 (m-80) REVERT: C 277 LEU cc_start: 0.9025 (mp) cc_final: 0.8740 (tp) REVERT: C 297 SER cc_start: 0.8745 (m) cc_final: 0.8243 (p) REVERT: C 414 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8483 (tp-100) REVERT: C 552 LEU cc_start: 0.9191 (mt) cc_final: 0.8853 (pp) REVERT: C 740 MET cc_start: 0.8881 (ttp) cc_final: 0.8470 (tmm) REVERT: C 869 MET cc_start: 0.8474 (mtt) cc_final: 0.8029 (mtp) REVERT: C 878 LEU cc_start: 0.7949 (tp) cc_final: 0.7708 (tp) REVERT: C 955 ASN cc_start: 0.8974 (m-40) cc_final: 0.8273 (p0) REVERT: C 978 ASN cc_start: 0.9223 (m-40) cc_final: 0.8853 (t0) REVERT: C 1029 MET cc_start: 0.8927 (tpp) cc_final: 0.8083 (tpp) REVERT: C 1031 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8235 (tt0) REVERT: D 110 MET cc_start: 0.3462 (mmp) cc_final: 0.2732 (mmp) REVERT: F 29 PHE cc_start: 0.8193 (t80) cc_final: 0.7620 (t80) REVERT: H 110 MET cc_start: 0.5350 (mmp) cc_final: 0.4397 (mmp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.1852 time to fit residues: 61.8730 Evaluate side-chains 149 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 290 optimal weight: 0.8980 chunk 152 optimal weight: 50.0000 chunk 69 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 350 optimal weight: 7.9990 chunk 304 optimal weight: 0.6980 chunk 250 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 299 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN B 703 ASN B 954 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.139466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.113353 restraints weight = 145630.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.109269 restraints weight = 168826.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.106205 restraints weight = 129476.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.105349 restraints weight = 126710.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.105402 restraints weight = 128827.400| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31434 Z= 0.140 Angle : 0.538 11.540 42864 Z= 0.276 Chirality : 0.043 0.280 4935 Planarity : 0.004 0.087 5451 Dihedral : 5.078 55.796 5289 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 0.03 % Allowed : 1.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3798 helix: 1.53 (0.20), residues: 708 sheet: 0.43 (0.16), residues: 959 loop : -0.27 (0.14), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1014 TYR 0.013 0.001 TYR A1067 PHE 0.031 0.001 PHE A 906 TRP 0.050 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00315 (31332) covalent geometry : angle 0.52684 (42606) SS BOND : bond 0.00278 ( 48) SS BOND : angle 0.85011 ( 96) hydrogen bonds : bond 0.03756 ( 1221) hydrogen bonds : angle 5.34656 ( 3342) link_BETA1-4 : bond 0.00290 ( 15) link_BETA1-4 : angle 1.00498 ( 45) link_NAG-ASN : bond 0.00408 ( 39) link_NAG-ASN : angle 1.97846 ( 117) *********************** 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 204 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 1.070 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: A 54 LEU cc_start: 0.9357 (mt) cc_final: 0.9110 (tp) REVERT: A 223 LEU cc_start: 0.8616 (mp) cc_final: 0.8179 (mp) REVERT: A 224 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8940 (mp0) REVERT: A 287 ASP cc_start: 0.8852 (t0) cc_final: 0.8569 (t0) REVERT: A 299 THR cc_start: 0.9499 (m) cc_final: 0.9190 (p) REVERT: A 740 MET cc_start: 0.8761 (ppp) cc_final: 0.8557 (ppp) REVERT: A 869 MET cc_start: 0.9101 (mtt) cc_final: 0.8890 (mtp) REVERT: A 985 ASP cc_start: 0.9159 (t0) cc_final: 0.8946 (t0) REVERT: A 990 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8704 (pt0) REVERT: B 56 LEU cc_start: 0.9059 (tp) cc_final: 0.8555 (tp) REVERT: B 91 TYR cc_start: 0.8038 (t80) cc_final: 0.7702 (t80) REVERT: B 238 PHE cc_start: 0.9322 (p90) cc_final: 0.8813 (p90) REVERT: B 297 SER cc_start: 0.9162 (m) cc_final: 0.8844 (p) REVERT: B 731 MET cc_start: 0.8642 (ptm) cc_final: 0.7947 (ppp) REVERT: C 269 TYR cc_start: 0.7419 (m-80) cc_final: 0.7086 (m-80) REVERT: C 277 LEU cc_start: 0.8998 (mp) cc_final: 0.8694 (tp) REVERT: C 297 SER cc_start: 0.8823 (m) cc_final: 0.8277 (p) REVERT: C 414 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8538 (tp-100) REVERT: C 552 LEU cc_start: 0.9387 (mt) cc_final: 0.8985 (pp) REVERT: C 740 MET cc_start: 0.8822 (ttp) cc_final: 0.8405 (tmm) REVERT: C 869 MET cc_start: 0.8318 (mtt) cc_final: 0.7915 (mtp) REVERT: C 950 ASP cc_start: 0.8784 (p0) cc_final: 0.8503 (p0) REVERT: C 978 ASN cc_start: 0.9255 (m-40) cc_final: 0.8514 (t0) REVERT: C 1029 MET cc_start: 0.8362 (tpp) cc_final: 0.7499 (tpp) REVERT: F 29 PHE cc_start: 0.8287 (t80) cc_final: 0.7669 (t80) REVERT: H 110 MET cc_start: 0.4921 (mmp) cc_final: 0.4047 (mmp) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1874 time to fit residues: 64.1300 Evaluate side-chains 147 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 18 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 292 optimal weight: 0.0770 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 336 optimal weight: 30.0000 chunk 131 optimal weight: 10.0000 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 337 optimal weight: 10.0000 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1010 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.138353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.111974 restraints weight = 145856.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.109304 restraints weight = 180111.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.105859 restraints weight = 131748.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.105246 restraints weight = 147983.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105528 restraints weight = 140397.282| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 31434 Z= 0.186 Angle : 0.565 11.466 42864 Z= 0.290 Chirality : 0.043 0.260 4935 Planarity : 0.004 0.046 5451 Dihedral : 4.887 56.769 5289 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3798 helix: 1.51 (0.20), residues: 698 sheet: 0.36 (0.16), residues: 984 loop : -0.27 (0.14), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1107 TYR 0.016 0.001 TYR C 365 PHE 0.022 0.001 PHE C1062 TRP 0.044 0.001 TRP C 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00416 (31332) covalent geometry : angle 0.55356 (42606) SS BOND : bond 0.00382 ( 48) SS BOND : angle 0.90339 ( 96) hydrogen bonds : bond 0.03919 ( 1221) hydrogen bonds : angle 5.39938 ( 3342) link_BETA1-4 : bond 0.00235 ( 15) link_BETA1-4 : angle 1.08436 ( 45) link_NAG-ASN : bond 0.00445 ( 39) link_NAG-ASN : angle 2.02266 ( 117) *********************** 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 189 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.9358 (mt) cc_final: 0.9155 (tp) REVERT: A 223 LEU cc_start: 0.8720 (mp) cc_final: 0.8298 (mp) REVERT: A 224 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8986 (mp0) REVERT: A 287 ASP cc_start: 0.8774 (t0) cc_final: 0.8491 (t0) REVERT: A 299 THR cc_start: 0.9476 (m) cc_final: 0.9172 (p) REVERT: B 54 LEU cc_start: 0.9226 (tp) cc_final: 0.8741 (tp) REVERT: B 56 LEU cc_start: 0.9002 (tp) cc_final: 0.8643 (tp) REVERT: B 91 TYR cc_start: 0.7899 (t80) cc_final: 0.7455 (t80) REVERT: B 175 PHE cc_start: 0.9554 (m-10) cc_final: 0.9345 (m-10) REVERT: B 238 PHE cc_start: 0.9254 (p90) cc_final: 0.8814 (p90) REVERT: B 270 LEU cc_start: 0.8466 (mp) cc_final: 0.7449 (mp) REVERT: B 297 SER cc_start: 0.9157 (m) cc_final: 0.8842 (p) REVERT: B 731 MET cc_start: 0.8707 (ptm) cc_final: 0.7973 (ppp) REVERT: C 229 LEU cc_start: 0.8860 (tp) cc_final: 0.8541 (tp) REVERT: C 269 TYR cc_start: 0.7372 (m-80) cc_final: 0.7122 (m-80) REVERT: C 297 SER cc_start: 0.8849 (m) cc_final: 0.8266 (p) REVERT: C 414 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8710 (tp-100) REVERT: C 552 LEU cc_start: 0.9294 (mt) cc_final: 0.8908 (pp) REVERT: C 740 MET cc_start: 0.8709 (ttp) cc_final: 0.8360 (tmm) REVERT: C 869 MET cc_start: 0.8441 (mtt) cc_final: 0.8051 (mtp) REVERT: C 955 ASN cc_start: 0.8934 (m-40) cc_final: 0.8556 (p0) REVERT: C 978 ASN cc_start: 0.9255 (m-40) cc_final: 0.8621 (t0) REVERT: C 1029 MET cc_start: 0.8338 (tpp) cc_final: 0.7621 (tpp) REVERT: C 1031 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8355 (mt-10) REVERT: D 110 MET cc_start: 0.3475 (mmp) cc_final: 0.2780 (mmp) REVERT: F 29 PHE cc_start: 0.8251 (t80) cc_final: 0.7641 (t80) REVERT: H 110 MET cc_start: 0.4935 (mmp) cc_final: 0.4216 (mmp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1932 time to fit residues: 61.3822 Evaluate side-chains 146 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 338 optimal weight: 30.0000 chunk 252 optimal weight: 0.7980 chunk 225 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 323 optimal weight: 30.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 GLN B 613 GLN B 703 ASN B1010 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.138738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.113155 restraints weight = 146572.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.109026 restraints weight = 185211.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.106103 restraints weight = 169485.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.106413 restraints weight = 156240.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.106578 restraints weight = 131544.269| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31434 Z= 0.151 Angle : 0.545 11.228 42864 Z= 0.281 Chirality : 0.043 0.211 4935 Planarity : 0.004 0.060 5451 Dihedral : 4.661 57.940 5289 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3798 helix: 1.54 (0.20), residues: 696 sheet: 0.35 (0.16), residues: 1040 loop : -0.26 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1019 TYR 0.014 0.001 TYR A1067 PHE 0.022 0.001 PHE C 906 TRP 0.043 0.001 TRP C 104 HIS 0.005 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00338 (31332) covalent geometry : angle 0.53218 (42606) SS BOND : bond 0.00358 ( 48) SS BOND : angle 1.32677 ( 96) hydrogen bonds : bond 0.03775 ( 1221) hydrogen bonds : angle 5.28301 ( 3342) link_BETA1-4 : bond 0.00279 ( 15) link_BETA1-4 : angle 1.01915 ( 45) link_NAG-ASN : bond 0.00373 ( 39) link_NAG-ASN : angle 1.94322 ( 117) *********************** 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 190 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8611 (mp) cc_final: 0.8279 (mp) REVERT: A 224 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8843 (mp0) REVERT: A 287 ASP cc_start: 0.8704 (t0) cc_final: 0.8439 (t0) REVERT: A 299 THR cc_start: 0.9510 (m) cc_final: 0.9193 (p) REVERT: A 773 GLU cc_start: 0.9097 (tt0) cc_final: 0.8546 (mm-30) REVERT: A 869 MET cc_start: 0.9613 (mtp) cc_final: 0.9149 (mtp) REVERT: B 54 LEU cc_start: 0.9200 (tp) cc_final: 0.8633 (tp) REVERT: B 56 LEU cc_start: 0.8938 (tp) cc_final: 0.8607 (tp) REVERT: B 91 TYR cc_start: 0.7914 (t80) cc_final: 0.7402 (t80) REVERT: B 238 PHE cc_start: 0.8961 (p90) cc_final: 0.8695 (p90) REVERT: B 270 LEU cc_start: 0.8516 (mp) cc_final: 0.7611 (mp) REVERT: B 297 SER cc_start: 0.9192 (m) cc_final: 0.8874 (p) REVERT: B 697 MET cc_start: 0.8473 (ptm) cc_final: 0.8159 (ptm) REVERT: B 731 MET cc_start: 0.8810 (ptm) cc_final: 0.8001 (ppp) REVERT: C 229 LEU cc_start: 0.8750 (tp) cc_final: 0.8536 (tp) REVERT: C 297 SER cc_start: 0.8856 (m) cc_final: 0.8269 (p) REVERT: C 414 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8698 (tp-100) REVERT: C 552 LEU cc_start: 0.9217 (mt) cc_final: 0.8876 (pp) REVERT: C 740 MET cc_start: 0.8726 (ttp) cc_final: 0.8502 (tmm) REVERT: C 869 MET cc_start: 0.8372 (mtt) cc_final: 0.8022 (mtp) REVERT: C 950 ASP cc_start: 0.8766 (p0) cc_final: 0.8539 (p0) REVERT: C 955 ASN cc_start: 0.8972 (m-40) cc_final: 0.8469 (p0) REVERT: C 978 ASN cc_start: 0.9229 (m-40) cc_final: 0.8634 (t0) REVERT: C 1029 MET cc_start: 0.9029 (tpp) cc_final: 0.8297 (tpp) REVERT: D 110 MET cc_start: 0.3225 (mmp) cc_final: 0.2551 (mmp) REVERT: F 29 PHE cc_start: 0.8224 (t80) cc_final: 0.7632 (t80) REVERT: H 110 MET cc_start: 0.4803 (mmp) cc_final: 0.4273 (mmp) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1874 time to fit residues: 59.8308 Evaluate side-chains 138 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 375 optimal weight: 0.5980 chunk 244 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 212 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B1010 GLN C 901 GLN C1108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.138184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.112880 restraints weight = 146484.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.109107 restraints weight = 177567.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107846 restraints weight = 156294.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107969 restraints weight = 140053.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.107801 restraints weight = 123447.483| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31434 Z= 0.171 Angle : 0.555 11.449 42864 Z= 0.286 Chirality : 0.043 0.259 4935 Planarity : 0.004 0.055 5451 Dihedral : 4.578 59.355 5289 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3798 helix: 1.48 (0.20), residues: 698 sheet: 0.41 (0.16), residues: 1031 loop : -0.26 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.028 0.001 TYR C 365 PHE 0.024 0.001 PHE A 275 TRP 0.041 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00384 (31332) covalent geometry : angle 0.54304 (42606) SS BOND : bond 0.00414 ( 48) SS BOND : angle 1.28346 ( 96) hydrogen bonds : bond 0.03890 ( 1221) hydrogen bonds : angle 5.28491 ( 3342) link_BETA1-4 : bond 0.00234 ( 15) link_BETA1-4 : angle 1.05582 ( 45) link_NAG-ASN : bond 0.00400 ( 39) link_NAG-ASN : angle 1.97030 ( 117) *********************** 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 185 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8539 (mp) cc_final: 0.8258 (mp) REVERT: A 224 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8803 (mp0) REVERT: A 287 ASP cc_start: 0.8725 (t0) cc_final: 0.8455 (t0) REVERT: A 299 THR cc_start: 0.9502 (m) cc_final: 0.9202 (p) REVERT: A 571 ASP cc_start: 0.8433 (m-30) cc_final: 0.8145 (m-30) REVERT: A 773 GLU cc_start: 0.8820 (tt0) cc_final: 0.8449 (tp30) REVERT: A 869 MET cc_start: 0.9610 (mtp) cc_final: 0.9145 (mtp) REVERT: A 895 GLN cc_start: 0.8167 (pm20) cc_final: 0.7902 (pm20) REVERT: A 1118 ASP cc_start: 0.8869 (p0) cc_final: 0.8661 (p0) REVERT: B 54 LEU cc_start: 0.9181 (tp) cc_final: 0.8627 (tp) REVERT: B 56 LEU cc_start: 0.8965 (tp) cc_final: 0.8636 (tp) REVERT: B 91 TYR cc_start: 0.7840 (t80) cc_final: 0.7342 (t80) REVERT: B 270 LEU cc_start: 0.8335 (mp) cc_final: 0.7322 (mp) REVERT: B 297 SER cc_start: 0.9223 (m) cc_final: 0.8924 (p) REVERT: B 697 MET cc_start: 0.8453 (ptm) cc_final: 0.7604 (ttm) REVERT: B 731 MET cc_start: 0.8782 (ptm) cc_final: 0.7878 (ppp) REVERT: C 229 LEU cc_start: 0.8658 (tp) cc_final: 0.8445 (tp) REVERT: C 297 SER cc_start: 0.8875 (m) cc_final: 0.8301 (p) REVERT: C 414 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8612 (tp-100) REVERT: C 552 LEU cc_start: 0.9001 (mt) cc_final: 0.8720 (pp) REVERT: C 740 MET cc_start: 0.8749 (ttp) cc_final: 0.8520 (tmm) REVERT: C 869 MET cc_start: 0.8391 (mtt) cc_final: 0.8003 (mtp) REVERT: C 955 ASN cc_start: 0.8992 (m-40) cc_final: 0.8441 (p0) REVERT: C 978 ASN cc_start: 0.9206 (m-40) cc_final: 0.8534 (t0) REVERT: C 1029 MET cc_start: 0.8995 (tpp) cc_final: 0.8134 (tpp) REVERT: D 110 MET cc_start: 0.2996 (mmp) cc_final: 0.2374 (mmp) REVERT: F 29 PHE cc_start: 0.8128 (t80) cc_final: 0.7573 (t80) REVERT: H 110 MET cc_start: 0.4988 (mmp) cc_final: 0.4510 (mmp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1783 time to fit residues: 56.1716 Evaluate side-chains 132 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 141 optimal weight: 6.9990 chunk 96 optimal weight: 0.2980 chunk 95 optimal weight: 0.5980 chunk 363 optimal weight: 40.0000 chunk 298 optimal weight: 0.0470 chunk 314 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 266 optimal weight: 0.3980 chunk 216 optimal weight: 0.7980 chunk 320 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN B 613 GLN B 703 ASN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 519 HIS C 901 GLN C1108 ASN C1135 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.140114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.113443 restraints weight = 145971.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.109056 restraints weight = 151254.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.106187 restraints weight = 145320.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.105934 restraints weight = 140526.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.106449 restraints weight = 116993.100| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31434 Z= 0.098 Angle : 0.516 11.742 42864 Z= 0.266 Chirality : 0.043 0.258 4935 Planarity : 0.004 0.055 5451 Dihedral : 4.310 58.944 5289 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 0.03 % Allowed : 0.12 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3798 helix: 1.51 (0.20), residues: 710 sheet: 0.63 (0.17), residues: 942 loop : -0.30 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.019 0.001 TYR C 365 PHE 0.025 0.001 PHE C 275 TRP 0.032 0.001 TRP C 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00214 (31332) covalent geometry : angle 0.50490 (42606) SS BOND : bond 0.00279 ( 48) SS BOND : angle 1.16542 ( 96) hydrogen bonds : bond 0.03552 ( 1221) hydrogen bonds : angle 5.03487 ( 3342) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 0.97407 ( 45) link_NAG-ASN : bond 0.00366 ( 39) link_NAG-ASN : angle 1.84981 ( 117) ********************** 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 201 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8513 (mp) cc_final: 0.8093 (mp) REVERT: A 224 GLU cc_start: 0.9305 (mt-10) cc_final: 0.8828 (mp0) REVERT: A 287 ASP cc_start: 0.8826 (t0) cc_final: 0.8537 (t0) REVERT: A 299 THR cc_start: 0.9472 (m) cc_final: 0.9131 (p) REVERT: A 354 ASN cc_start: 0.9436 (t0) cc_final: 0.9146 (t0) REVERT: A 571 ASP cc_start: 0.8731 (m-30) cc_final: 0.8458 (m-30) REVERT: A 773 GLU cc_start: 0.8832 (tt0) cc_final: 0.8569 (tp30) REVERT: A 869 MET cc_start: 0.9650 (mtp) cc_final: 0.9267 (mtp) REVERT: A 979 ASP cc_start: 0.8994 (m-30) cc_final: 0.8692 (t0) REVERT: A 1118 ASP cc_start: 0.8677 (p0) cc_final: 0.8463 (p0) REVERT: B 54 LEU cc_start: 0.9249 (tp) cc_final: 0.8814 (tp) REVERT: B 56 LEU cc_start: 0.9048 (tp) cc_final: 0.8779 (tp) REVERT: B 91 TYR cc_start: 0.8026 (t80) cc_final: 0.7419 (t80) REVERT: B 104 TRP cc_start: 0.8556 (m-90) cc_final: 0.8293 (m-90) REVERT: B 270 LEU cc_start: 0.8547 (mp) cc_final: 0.7578 (mp) REVERT: B 297 SER cc_start: 0.9201 (m) cc_final: 0.8850 (p) REVERT: B 697 MET cc_start: 0.8382 (ptm) cc_final: 0.7318 (ttm) REVERT: C 229 LEU cc_start: 0.8833 (tp) cc_final: 0.8614 (tp) REVERT: C 276 LEU cc_start: 0.7746 (mm) cc_final: 0.6749 (mm) REVERT: C 297 SER cc_start: 0.8882 (m) cc_final: 0.8355 (p) REVERT: C 414 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8776 (tp-100) REVERT: C 552 LEU cc_start: 0.9231 (mt) cc_final: 0.8913 (pp) REVERT: C 774 GLN cc_start: 0.9262 (mm-40) cc_final: 0.8407 (mm-40) REVERT: C 869 MET cc_start: 0.8194 (mtt) cc_final: 0.7698 (mtp) REVERT: C 950 ASP cc_start: 0.8759 (p0) cc_final: 0.8389 (p0) REVERT: C 1029 MET cc_start: 0.9088 (tpp) cc_final: 0.8398 (tpp) REVERT: D 110 MET cc_start: 0.3698 (mmp) cc_final: 0.2796 (mmp) REVERT: F 29 PHE cc_start: 0.8260 (t80) cc_final: 0.7693 (t80) REVERT: H 110 MET cc_start: 0.5139 (mmp) cc_final: 0.4652 (mmp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1791 time to fit residues: 60.7733 Evaluate side-chains 151 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 304 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 350 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 221 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 348 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN B 613 GLN B 703 ASN B 953 ASN B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.138645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.112395 restraints weight = 146381.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.107081 restraints weight = 172355.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.105800 restraints weight = 161579.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.104710 restraints weight = 142075.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.104768 restraints weight = 142421.814| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31434 Z= 0.139 Angle : 0.525 11.621 42864 Z= 0.270 Chirality : 0.043 0.252 4935 Planarity : 0.004 0.053 5451 Dihedral : 4.255 56.066 5289 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3798 helix: 1.50 (0.20), residues: 710 sheet: 0.63 (0.16), residues: 977 loop : -0.26 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.016 0.001 TYR C 873 PHE 0.018 0.001 PHE C 906 TRP 0.025 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00313 (31332) covalent geometry : angle 0.51296 (42606) SS BOND : bond 0.00316 ( 48) SS BOND : angle 1.08302 ( 96) hydrogen bonds : bond 0.03656 ( 1221) hydrogen bonds : angle 5.06248 ( 3342) link_BETA1-4 : bond 0.00262 ( 15) link_BETA1-4 : angle 1.04780 ( 45) link_NAG-ASN : bond 0.00365 ( 39) link_NAG-ASN : angle 1.89648 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.02 seconds wall clock time: 88 minutes 47.19 seconds (5327.19 seconds total)