Starting phenix.real_space_refine on Thu Nov 20 05:26:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ndd_12284/11_2025/7ndd_12284.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ndd_12284/11_2025/7ndd_12284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ndd_12284/11_2025/7ndd_12284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ndd_12284/11_2025/7ndd_12284.map" model { file = "/net/cci-nas-00/data/ceres_data/7ndd_12284/11_2025/7ndd_12284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ndd_12284/11_2025/7ndd_12284.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/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: 7.46, per 1000 atoms: 0.24 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: 2.66 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: 1.42 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: 8.56 Time building geometry restraints manager: 3.60 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: 0.010 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.460 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- 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 : 1.112 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: 0.8084 (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: 0.8388 (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: 0.8459 (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: 0.8843 (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: -0.1798 (mmt) outliers start: 14 outliers final: 2 residues processed: 451 average time/residue: 0.2093 time to fit residues: 149.6694 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 : 1.163 ------------------------------------------------------------------------------- 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 : 1.181 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: 0.8653 (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: 0.8587 (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: 0.8135 (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: 0.2016 time to fit residues: 78.8609 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 : 1.140 ------------------------------------------------------------------------------- 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 : 1.077 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: 0.1954 time to fit residues: 74.7041 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 : 1.081 ------------------------------------------------------------------------------- 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 : 1.208 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: 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: 0.8131 (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: 0.7847 (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: 0.9124 (m) cc_final: 0.8822 (p) REVERT: B 611 LEU cc_start: 0.9026 (tp) cc_final: 0.8801 (tp) 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: 0.8533 (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: 0.1879 time to fit residues: 63.6122 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 : 0.852 ------------------------------------------------------------------------------- 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 = 0.138776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.113072 restraints weight = 146401.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.109726 restraints weight = 184813.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106955 restraints weight = 169346.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.107368 restraints weight = 154999.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.107508 restraints weight = 131335.587| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 31434 Z= 0.195 Angle : 0.577 10.631 42864 Z= 0.297 Chirality : 0.043 0.272 4935 Planarity : 0.004 0.048 5451 Dihedral : 5.534 58.827 5289 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 0.29 (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 0.028 0.002 PHE C 135 TRP 0.031 0.001 TRP C 104 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00432 (31332) covalent geometry : angle 0.56379 (42606) SS BOND : bond 0.00330 ( 48) SS BOND : angle 0.89526 ( 96) hydrogen bonds : bond 0.04015 ( 1221) hydrogen bonds : angle 5.55280 ( 3342) link_BETA1-4 : bond 0.00208 ( 15) link_BETA1-4 : angle 1.04182 ( 45) link_NAG-ASN : bond 0.00468 ( 39) link_NAG-ASN : angle 2.23607 ( 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 199 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.167 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: 0.9312 (mt) cc_final: 0.9071 (tp) REVERT: A 223 LEU cc_start: 0.8545 (mp) cc_final: 0.8226 (mp) REVERT: A 224 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8921 (mp0) REVERT: A 287 ASP cc_start: 0.8789 (t0) cc_final: 0.8547 (t0) REVERT: A 299 THR cc_start: 0.9550 (m) cc_final: 0.9261 (p) REVERT: A 869 MET cc_start: 0.9266 (mtt) cc_final: 0.8967 (mtp) REVERT: A 985 ASP cc_start: 0.9210 (t0) cc_final: 0.8966 (t0) REVERT: A 990 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8713 (pt0) REVERT: B 54 LEU cc_start: 0.9225 (tp) cc_final: 0.8877 (tp) REVERT: B 56 LEU cc_start: 0.8886 (tp) cc_final: 0.8479 (tp) REVERT: B 91 TYR cc_start: 0.7867 (t80) cc_final: 0.7584 (t80) REVERT: B 238 PHE cc_start: 0.8970 (p90) cc_final: 0.8644 (p90) REVERT: B 297 SER cc_start: 0.9163 (m) cc_final: 0.8857 (p) REVERT: B 731 MET cc_start: 0.8893 (ptm) cc_final: 0.7909 (ppp) REVERT: C 95 THR cc_start: 0.7911 (p) cc_final: 0.7680 (p) REVERT: C 277 LEU cc_start: 0.8998 (mp) cc_final: 0.8724 (tp) REVERT: C 297 SER cc_start: 0.8747 (m) cc_final: 0.8247 (p) REVERT: C 414 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8475 (tp-100) REVERT: C 552 LEU cc_start: 0.9163 (mt) cc_final: 0.8836 (pp) REVERT: C 740 MET cc_start: 0.8882 (ttp) cc_final: 0.8465 (tmm) REVERT: C 869 MET cc_start: 0.8466 (mtt) cc_final: 0.8046 (mtp) REVERT: C 878 LEU cc_start: 0.8295 (tp) cc_final: 0.8018 (tp) REVERT: C 950 ASP cc_start: 0.8843 (p0) cc_final: 0.8610 (p0) REVERT: C 978 ASN cc_start: 0.9223 (m-40) cc_final: 0.8852 (t0) REVERT: C 1029 MET cc_start: 0.8299 (tpp) cc_final: 0.7696 (tpp) REVERT: C 1031 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8468 (tt0) REVERT: D 110 MET cc_start: 0.3376 (mmp) cc_final: 0.2683 (mmp) REVERT: F 29 PHE cc_start: 0.8176 (t80) cc_final: 0.7615 (t80) REVERT: H 110 MET cc_start: 0.5339 (mmp) cc_final: 0.4390 (mmp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1909 time to fit residues: 63.5384 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 : 1.185 ------------------------------------------------------------------------------- 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: 0.2980 chunk 152 optimal weight: 50.0000 chunk 69 optimal weight: 0.8980 chunk 245 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 304 optimal weight: 0.5980 chunk 250 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 299 optimal weight: 0.6980 chunk 121 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.132955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.089339 restraints weight = 133709.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088473 restraints weight = 114656.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088227 restraints weight = 93059.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088311 restraints weight = 93792.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088387 restraints weight = 86685.170| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31434 Z= 0.113 Angle : 0.522 11.513 42864 Z= 0.269 Chirality : 0.043 0.270 4935 Planarity : 0.004 0.076 5451 Dihedral : 5.055 55.323 5289 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 0.03 % Allowed : 1.19 % Favored : 98.78 % 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: 0.37 (0.14), residues: 3798 helix: 1.59 (0.20), residues: 708 sheet: 0.45 (0.16), residues: 972 loop : -0.26 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B1014 TYR 0.013 0.001 TYR B 873 PHE 0.027 0.001 PHE C 194 TRP 0.050 0.001 TRP C 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00251 (31332) covalent geometry : angle 0.51068 (42606) SS BOND : bond 0.00264 ( 48) SS BOND : angle 0.84486 ( 96) hydrogen bonds : bond 0.03663 ( 1221) hydrogen bonds : angle 5.29253 ( 3342) link_BETA1-4 : bond 0.00338 ( 15) link_BETA1-4 : angle 0.97897 ( 45) link_NAG-ASN : bond 0.00404 ( 39) link_NAG-ASN : angle 1.95820 ( 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 208 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.271 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: 0.9403 (mt) cc_final: 0.9029 (tp) REVERT: A 223 LEU cc_start: 0.8645 (mp) cc_final: 0.7982 (mp) REVERT: A 224 GLU cc_start: 0.9380 (mt-10) cc_final: 0.8931 (mp0) REVERT: A 238 PHE cc_start: 0.9309 (p90) cc_final: 0.8990 (p90) REVERT: A 287 ASP cc_start: 0.9234 (t0) cc_final: 0.8925 (t0) REVERT: A 299 THR cc_start: 0.9534 (m) cc_final: 0.9216 (p) REVERT: A 740 MET cc_start: 0.8808 (ppp) cc_final: 0.8602 (ppp) REVERT: A 773 GLU cc_start: 0.9053 (tt0) cc_final: 0.8540 (mm-30) REVERT: A 869 MET cc_start: 0.9148 (mtt) cc_final: 0.8946 (mtp) REVERT: A 985 ASP cc_start: 0.9331 (t0) cc_final: 0.9091 (t0) REVERT: A 990 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8782 (pt0) REVERT: B 56 LEU cc_start: 0.9272 (tp) cc_final: 0.8914 (tp) REVERT: B 91 TYR cc_start: 0.8235 (t80) cc_final: 0.7921 (t80) REVERT: B 104 TRP cc_start: 0.9341 (m-90) cc_final: 0.8863 (m-90) REVERT: B 153 MET cc_start: 0.8520 (mtm) cc_final: 0.8125 (mpp) REVERT: B 175 PHE cc_start: 0.9722 (m-10) cc_final: 0.9462 (m-80) REVERT: B 238 PHE cc_start: 0.9710 (p90) cc_final: 0.9126 (p90) REVERT: B 297 SER cc_start: 0.9081 (m) cc_final: 0.8752 (p) REVERT: B 984 LEU cc_start: 0.9154 (tp) cc_final: 0.8922 (tp) REVERT: C 104 TRP cc_start: 0.8438 (m-10) cc_final: 0.8119 (m-10) REVERT: C 238 PHE cc_start: 0.9168 (p90) cc_final: 0.8786 (p90) REVERT: C 277 LEU cc_start: 0.9321 (mp) cc_final: 0.8944 (tp) REVERT: C 297 SER cc_start: 0.8866 (m) cc_final: 0.8286 (p) REVERT: C 414 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8403 (tp-100) REVERT: C 552 LEU cc_start: 0.9683 (mt) cc_final: 0.9229 (pp) REVERT: C 740 MET cc_start: 0.8921 (ttp) cc_final: 0.8471 (tmm) REVERT: C 774 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8609 (mm-40) REVERT: C 869 MET cc_start: 0.8229 (mtt) cc_final: 0.7836 (mtp) REVERT: C 978 ASN cc_start: 0.9367 (m-40) cc_final: 0.8591 (t0) REVERT: C 1029 MET cc_start: 0.9016 (tpp) cc_final: 0.8189 (tpp) REVERT: H 110 MET cc_start: 0.4622 (mmp) cc_final: 0.3985 (mmp) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.1897 time to fit residues: 65.9526 Evaluate side-chains 155 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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: 2.9990 chunk 162 optimal weight: 7.9990 chunk 292 optimal weight: 0.3980 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 336 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 179 optimal weight: 0.8980 chunk 337 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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** B1010 GLN C 52 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 = 0.4350 r_free = 0.4350 target = 0.137749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.111734 restraints weight = 146118.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107243 restraints weight = 185890.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104773 restraints weight = 156618.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103954 restraints weight = 147902.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104016 restraints weight = 143914.331| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 31434 Z= 0.223 Angle : 0.599 11.462 42864 Z= 0.308 Chirality : 0.044 0.260 4935 Planarity : 0.004 0.061 5451 Dihedral : 4.950 55.719 5289 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 0.26 (0.14), residues: 3798 helix: 1.43 (0.20), residues: 696 sheet: 0.30 (0.16), residues: 1001 loop : -0.26 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1107 TYR 0.022 0.001 TYR A 873 PHE 0.029 0.002 PHE C1062 TRP 0.033 0.001 TRP C 104 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00495 (31332) covalent geometry : angle 0.58823 (42606) SS BOND : bond 0.00725 ( 48) SS BOND : angle 0.94964 ( 96) hydrogen bonds : bond 0.04094 ( 1221) hydrogen bonds : angle 5.51182 ( 3342) link_BETA1-4 : bond 0.00253 ( 15) link_BETA1-4 : angle 1.15077 ( 45) link_NAG-ASN : bond 0.00504 ( 39) link_NAG-ASN : angle 2.09616 ( 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 186 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.185 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: 0.9386 (mt) cc_final: 0.9184 (tp) REVERT: A 223 LEU cc_start: 0.8727 (mp) cc_final: 0.8306 (mp) REVERT: A 224 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8922 (mp0) REVERT: A 287 ASP cc_start: 0.8848 (t0) cc_final: 0.8567 (t0) REVERT: A 299 THR cc_start: 0.9532 (m) cc_final: 0.9245 (p) REVERT: A 780 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8431 (mm-30) REVERT: A 895 GLN cc_start: 0.8052 (pm20) cc_final: 0.7829 (pm20) REVERT: B 54 LEU cc_start: 0.9293 (tp) cc_final: 0.8985 (tp) REVERT: B 56 LEU cc_start: 0.9039 (tp) cc_final: 0.8631 (tp) REVERT: B 91 TYR cc_start: 0.7901 (t80) cc_final: 0.7491 (t80) REVERT: B 238 PHE cc_start: 0.9241 (p90) cc_final: 0.8817 (p90) REVERT: B 297 SER cc_start: 0.9162 (m) cc_final: 0.8832 (p) REVERT: B 697 MET cc_start: 0.8479 (ptm) cc_final: 0.8177 (ptm) REVERT: B 731 MET cc_start: 0.8783 (ptm) cc_final: 0.7939 (ppp) REVERT: B 979 ASP cc_start: 0.8650 (m-30) cc_final: 0.8421 (t0) REVERT: C 229 LEU cc_start: 0.8860 (tp) cc_final: 0.8566 (tp) REVERT: C 297 SER cc_start: 0.8877 (m) cc_final: 0.8296 (p) REVERT: C 414 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8721 (tp-100) REVERT: C 552 LEU cc_start: 0.9306 (mt) cc_final: 0.8919 (pp) REVERT: C 740 MET cc_start: 0.8767 (ttp) cc_final: 0.8404 (tmm) REVERT: C 858 LEU cc_start: 0.8929 (mt) cc_final: 0.8726 (mp) REVERT: C 869 MET cc_start: 0.8438 (mtt) cc_final: 0.8094 (mtp) REVERT: C 950 ASP cc_start: 0.8815 (p0) cc_final: 0.8604 (p0) REVERT: C 955 ASN cc_start: 0.9052 (m-40) cc_final: 0.8452 (p0) REVERT: C 978 ASN cc_start: 0.9297 (m-40) cc_final: 0.8525 (t0) REVERT: C 1029 MET cc_start: 0.8043 (tpp) cc_final: 0.7361 (tpp) REVERT: D 110 MET cc_start: 0.3782 (mmp) cc_final: 0.3263 (mmp) REVERT: F 29 PHE cc_start: 0.8427 (t80) cc_final: 0.8189 (t80) REVERT: H 110 MET cc_start: 0.4910 (mmp) cc_final: 0.4192 (mmp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1914 time to fit residues: 59.9674 Evaluate side-chains 143 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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: 2.9990 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 277 optimal weight: 0.1980 chunk 251 optimal weight: 0.9980 chunk 323 optimal weight: 30.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.138765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.112519 restraints weight = 146722.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.108200 restraints weight = 171718.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104694 restraints weight = 126703.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.104681 restraints weight = 125849.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.104890 restraints weight = 126043.790| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31434 Z= 0.150 Angle : 0.545 11.235 42864 Z= 0.281 Chirality : 0.043 0.209 4935 Planarity : 0.004 0.059 5451 Dihedral : 4.683 56.882 5289 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.29 (0.14), residues: 3798 helix: 1.48 (0.20), residues: 698 sheet: 0.32 (0.16), residues: 1027 loop : -0.25 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.013 0.001 TYR A1067 PHE 0.021 0.001 PHE C 906 TRP 0.045 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00336 (31332) covalent geometry : angle 0.53296 (42606) SS BOND : bond 0.00337 ( 48) SS BOND : angle 1.12361 ( 96) hydrogen bonds : bond 0.03816 ( 1221) hydrogen bonds : angle 5.31766 ( 3342) link_BETA1-4 : bond 0.00277 ( 15) link_BETA1-4 : angle 1.02160 ( 45) link_NAG-ASN : bond 0.00387 ( 39) link_NAG-ASN : angle 1.94374 ( 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 187 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.607 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: A 54 LEU cc_start: 0.9396 (mt) cc_final: 0.9175 (tp) REVERT: A 223 LEU cc_start: 0.8674 (mp) cc_final: 0.8244 (mp) REVERT: A 224 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8858 (mp0) REVERT: A 287 ASP cc_start: 0.8842 (t0) cc_final: 0.8568 (t0) REVERT: A 299 THR cc_start: 0.9513 (m) cc_final: 0.9202 (p) REVERT: A 780 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 869 MET cc_start: 0.9624 (mtp) cc_final: 0.9155 (mtp) REVERT: A 895 GLN cc_start: 0.8178 (pm20) cc_final: 0.7780 (pm20) REVERT: A 1019 ARG cc_start: 0.8100 (tmm-80) cc_final: 0.7222 (ttp80) REVERT: B 54 LEU cc_start: 0.9277 (tp) cc_final: 0.8956 (tp) REVERT: B 56 LEU cc_start: 0.9078 (tp) cc_final: 0.8659 (tp) REVERT: B 91 TYR cc_start: 0.7993 (t80) cc_final: 0.7563 (t80) REVERT: B 175 PHE cc_start: 0.9042 (m-80) cc_final: 0.8832 (m-80) REVERT: B 238 PHE cc_start: 0.9145 (p90) cc_final: 0.8801 (p90) REVERT: B 297 SER cc_start: 0.9198 (m) cc_final: 0.8882 (p) REVERT: B 611 LEU cc_start: 0.8759 (tp) cc_final: 0.8299 (tp) REVERT: B 731 MET cc_start: 0.8786 (ptm) cc_final: 0.7992 (ppp) REVERT: B 979 ASP cc_start: 0.8536 (m-30) cc_final: 0.8329 (t0) REVERT: C 229 LEU cc_start: 0.8825 (tp) cc_final: 0.8608 (tp) REVERT: C 297 SER cc_start: 0.8884 (m) cc_final: 0.8291 (p) REVERT: C 414 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8733 (tp-100) REVERT: C 552 LEU cc_start: 0.9321 (mt) cc_final: 0.8941 (pp) REVERT: C 740 MET cc_start: 0.8718 (ttp) cc_final: 0.8508 (tmm) REVERT: C 869 MET cc_start: 0.8364 (mtt) cc_final: 0.8020 (mtp) REVERT: C 950 ASP cc_start: 0.8740 (p0) cc_final: 0.8527 (p0) REVERT: C 955 ASN cc_start: 0.9020 (m-40) cc_final: 0.8477 (p0) REVERT: C 978 ASN cc_start: 0.9210 (m-40) cc_final: 0.8526 (t0) REVERT: C 1029 MET cc_start: 0.8966 (tpp) cc_final: 0.8226 (tpp) REVERT: D 110 MET cc_start: 0.3487 (mmp) cc_final: 0.2728 (mmp) REVERT: F 29 PHE cc_start: 0.8422 (t80) cc_final: 0.8200 (t80) REVERT: H 110 MET cc_start: 0.4905 (mmp) cc_final: 0.4341 (mmp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1926 time to fit residues: 60.2888 Evaluate side-chains 143 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 0.0770 chunk 244 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 212 optimal weight: 30.0000 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1010 GLN B1011 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.136866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.111277 restraints weight = 146845.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.109055 restraints weight = 176555.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.106963 restraints weight = 149701.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.107284 restraints weight = 131342.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106316 restraints weight = 111273.013| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 31434 Z= 0.249 Angle : 0.626 11.156 42864 Z= 0.323 Chirality : 0.044 0.258 4935 Planarity : 0.004 0.056 5451 Dihedral : 4.801 58.527 5289 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.11 % Favored : 95.87 % 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: 0.13 (0.14), residues: 3798 helix: 1.17 (0.20), residues: 696 sheet: 0.33 (0.16), residues: 1008 loop : -0.35 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1014 TYR 0.016 0.001 TYR A1067 PHE 0.031 0.002 PHE C1062 TRP 0.033 0.001 TRP C 104 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00554 (31332) covalent geometry : angle 0.61402 (42606) SS BOND : bond 0.00362 ( 48) SS BOND : angle 1.36691 ( 96) hydrogen bonds : bond 0.04256 ( 1221) hydrogen bonds : angle 5.55839 ( 3342) link_BETA1-4 : bond 0.00226 ( 15) link_BETA1-4 : angle 1.14896 ( 45) link_NAG-ASN : bond 0.00511 ( 39) link_NAG-ASN : angle 2.10420 ( 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 177 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8628 (m) cc_final: 0.8036 (t) REVERT: A 223 LEU cc_start: 0.8598 (mp) cc_final: 0.8313 (mp) REVERT: A 224 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8792 (mp0) REVERT: A 287 ASP cc_start: 0.8610 (t0) cc_final: 0.8308 (t0) REVERT: A 299 THR cc_start: 0.9521 (m) cc_final: 0.9248 (p) REVERT: A 388 ASN cc_start: 0.8404 (p0) cc_final: 0.7720 (t0) REVERT: A 571 ASP cc_start: 0.8513 (m-30) cc_final: 0.8234 (m-30) REVERT: A 780 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 869 MET cc_start: 0.9613 (mtp) cc_final: 0.9169 (mtp) REVERT: A 1118 ASP cc_start: 0.8951 (p0) cc_final: 0.8748 (p0) REVERT: B 54 LEU cc_start: 0.9227 (tp) cc_final: 0.8916 (tp) REVERT: B 91 TYR cc_start: 0.7650 (t80) cc_final: 0.7249 (t80) REVERT: B 238 PHE cc_start: 0.8696 (p90) cc_final: 0.8461 (p90) REVERT: B 297 SER cc_start: 0.9248 (m) cc_final: 0.8937 (p) REVERT: B 697 MET cc_start: 0.8464 (ptm) cc_final: 0.7411 (ttm) REVERT: B 731 MET cc_start: 0.8871 (ptm) cc_final: 0.7946 (ppp) REVERT: C 229 LEU cc_start: 0.8705 (tp) cc_final: 0.8504 (tp) REVERT: C 297 SER cc_start: 0.8905 (m) cc_final: 0.8347 (p) REVERT: C 740 MET cc_start: 0.8828 (ttp) cc_final: 0.8576 (tmm) REVERT: C 869 MET cc_start: 0.8354 (mtt) cc_final: 0.8009 (mtp) REVERT: C 955 ASN cc_start: 0.9125 (m-40) cc_final: 0.8490 (p0) REVERT: C 1029 MET cc_start: 0.8876 (tpp) cc_final: 0.8034 (tpp) REVERT: D 110 MET cc_start: 0.2954 (mmp) cc_final: 0.2347 (mmp) REVERT: F 29 PHE cc_start: 0.8134 (t80) cc_final: 0.7808 (t80) REVERT: H 110 MET cc_start: 0.4965 (mmp) cc_final: 0.4499 (mmp) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2012 time to fit residues: 58.7080 Evaluate side-chains 135 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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: 9.9990 chunk 96 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 363 optimal weight: 20.0000 chunk 298 optimal weight: 0.7980 chunk 314 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 320 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B1010 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.138936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113683 restraints weight = 145491.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.110669 restraints weight = 181557.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108428 restraints weight = 154711.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108678 restraints weight = 136275.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108684 restraints weight = 129126.364| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4067 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 : 0.536 11.616 42864 Z= 0.276 Chirality : 0.043 0.261 4935 Planarity : 0.004 0.057 5451 Dihedral : 4.534 59.266 5289 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % 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: 0.30 (0.14), residues: 3798 helix: 1.38 (0.20), residues: 710 sheet: 0.48 (0.16), residues: 987 loop : -0.30 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.029 0.001 TYR C 365 PHE 0.021 0.001 PHE C 906 TRP 0.041 0.001 TRP C 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00272 (31332) covalent geometry : angle 0.52421 (42606) SS BOND : bond 0.00344 ( 48) SS BOND : angle 1.25990 ( 96) hydrogen bonds : bond 0.03772 ( 1221) hydrogen bonds : angle 5.22233 ( 3342) link_BETA1-4 : bond 0.00278 ( 15) link_BETA1-4 : angle 0.99812 ( 45) link_NAG-ASN : bond 0.00363 ( 39) link_NAG-ASN : angle 1.90906 ( 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 193 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.8502 (mp) cc_final: 0.8243 (mp) REVERT: A 224 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8805 (mp0) REVERT: A 287 ASP cc_start: 0.8687 (t0) cc_final: 0.8401 (t0) REVERT: A 299 THR cc_start: 0.9495 (m) cc_final: 0.9166 (p) REVERT: A 354 ASN cc_start: 0.9230 (t0) cc_final: 0.8934 (t0) REVERT: A 388 ASN cc_start: 0.8391 (p0) cc_final: 0.7675 (t0) REVERT: A 571 ASP cc_start: 0.8523 (m-30) cc_final: 0.8257 (m-30) REVERT: A 773 GLU cc_start: 0.8869 (tt0) cc_final: 0.8626 (tp30) REVERT: A 780 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 869 MET cc_start: 0.9596 (mtp) cc_final: 0.9208 (mtp) REVERT: A 1019 ARG cc_start: 0.8126 (tmm-80) cc_final: 0.7319 (ttp80) REVERT: A 1118 ASP cc_start: 0.8761 (p0) cc_final: 0.8475 (p0) REVERT: B 54 LEU cc_start: 0.9233 (tp) cc_final: 0.8897 (tp) REVERT: B 55 PHE cc_start: 0.8531 (m-80) cc_final: 0.8008 (m-80) REVERT: B 91 TYR cc_start: 0.7732 (t80) cc_final: 0.7304 (t80) REVERT: B 297 SER cc_start: 0.9228 (m) cc_final: 0.8911 (p) REVERT: B 697 MET cc_start: 0.8408 (ptm) cc_final: 0.7357 (ttm) REVERT: B 993 ILE cc_start: 0.9055 (mt) cc_final: 0.8773 (tt) REVERT: C 229 LEU cc_start: 0.8703 (tp) cc_final: 0.8494 (tp) REVERT: C 276 LEU cc_start: 0.7643 (mm) cc_final: 0.6687 (mm) REVERT: C 297 SER cc_start: 0.8988 (m) cc_final: 0.8488 (p) REVERT: C 869 MET cc_start: 0.8203 (mtt) cc_final: 0.7817 (mtp) REVERT: C 950 ASP cc_start: 0.8791 (p0) cc_final: 0.8482 (p0) REVERT: C 955 ASN cc_start: 0.8935 (m-40) cc_final: 0.8541 (p0) REVERT: D 110 MET cc_start: 0.3320 (mmp) cc_final: 0.2602 (mmp) REVERT: F 29 PHE cc_start: 0.8155 (t80) cc_final: 0.7559 (t80) REVERT: H 110 MET cc_start: 0.5000 (mmp) cc_final: 0.4582 (mmp) outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1915 time to fit residues: 61.7934 Evaluate side-chains 141 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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: 0.6980 chunk 237 optimal weight: 0.8980 chunk 350 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 0.0470 chunk 85 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 221 optimal weight: 8.9990 chunk 174 optimal weight: 0.4980 chunk 348 optimal weight: 20.0000 chunk 345 optimal weight: 9.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN B 580 GLN B 613 GLN B 703 ASN B1010 GLN C 519 HIS C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.139341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.113748 restraints weight = 146178.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.108449 restraints weight = 167687.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.105735 restraints weight = 157780.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.105901 restraints weight = 147313.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106201 restraints weight = 124802.925| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 31434 Z= 0.109 Angle : 0.519 11.691 42864 Z= 0.267 Chirality : 0.043 0.259 4935 Planarity : 0.004 0.055 5451 Dihedral : 4.278 55.770 5289 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % 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: 1.45 (0.20), residues: 710 sheet: 0.55 (0.16), residues: 1003 loop : -0.32 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.017 0.001 TYR C 365 PHE 0.016 0.001 PHE C 906 TRP 0.033 0.001 TRP C 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00242 (31332) covalent geometry : angle 0.50758 (42606) SS BOND : bond 0.00286 ( 48) SS BOND : angle 1.17397 ( 96) hydrogen bonds : bond 0.03610 ( 1221) hydrogen bonds : angle 5.05210 ( 3342) link_BETA1-4 : bond 0.00304 ( 15) link_BETA1-4 : angle 1.00988 ( 45) link_NAG-ASN : bond 0.00351 ( 39) link_NAG-ASN : angle 1.86818 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5214.88 seconds wall clock time: 91 minutes 10.67 seconds (5470.67 seconds total)