Starting phenix.real_space_refine on Thu Mar 5 17:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ra8_24347/03_2026/7ra8_24347.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ra8_24347/03_2026/7ra8_24347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ra8_24347/03_2026/7ra8_24347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ra8_24347/03_2026/7ra8_24347.map" model { file = "/net/cci-nas-00/data/ceres_data/7ra8_24347/03_2026/7ra8_24347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ra8_24347/03_2026/7ra8_24347.cif" } resolution = 3.1 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= -0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 15222 2.51 5 N 4101 2.21 5 O 4611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24036 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 917, 6676 Classifications: {'peptide': 917} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 52, 'TRANS': 864} Chain breaks: 13 Unresolved non-hydrogen bonds: 517 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASN:plan1': 16, 'PHE:plan': 4, 'GLU:plan': 11, 'TYR:plan': 9, 'ASP:plan': 21, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 315 Chain: "H" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 586 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 7, 'TRP:plan': 4, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 193 Chain: "L" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 496 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain breaks: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1, 'TRP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 6679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 917, 6679 Classifications: {'peptide': 917} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 52, 'TRANS': 864} Chain breaks: 13 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ASN:plan1': 16, 'PHE:plan': 4, 'GLU:plan': 11, 'TYR:plan': 9, 'ASP:plan': 21, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 315 Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 586 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 7, 'TRP:plan': 4, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 193 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 496 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain breaks: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1, 'TRP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "E" Number of atoms: 6679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 917, 6679 Classifications: {'peptide': 917} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 52, 'TRANS': 864} Chain breaks: 13 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 403 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ASN:plan1': 16, 'PHE:plan': 4, 'GLU:plan': 11, 'TYR:plan': 9, 'ASP:plan': 21, 'ARG:plan': 8, 'GLN:plan1': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 315 Chain: "F" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 586 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 7, 'TRP:plan': 4, 'ARG:plan': 4, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 193 Chain: "G" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 496 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain breaks: 2 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1, 'TRP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 135 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.90, per 1000 atoms: 0.25 Number of scatterers: 24036 At special positions: 0 Unit cell: (135.45, 140.7, 181.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4611 8.00 N 4101 7.00 C 15222 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.13 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.07 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.12 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.13 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.07 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.05 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.02 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.04 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.12 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.13 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.07 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 343 " " NAG B1310 " - " ASN B 331 " " NAG E1501 " - " ASN E 61 " " NAG E1502 " - " ASN E 234 " " NAG E1503 " - " ASN E 282 " " NAG E1504 " - " ASN E 603 " " NAG E1505 " - " ASN E 616 " " NAG E1506 " - " ASN E 657 " " NAG E1507 " - " ASN E 709 " " NAG E1508 " - " ASN E1074 " " NAG E1509 " - " ASN E 343 " " NAG E1510 " - " ASN E 331 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN E 717 " " NAG S 1 " - " ASN E 801 " " NAG T 1 " - " ASN E1098 " " NAG U 1 " - " ASN E1134 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 63 sheets defined 24.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.840A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.956A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 5.033A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A 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 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.774A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.057A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) 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 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.891A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) 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: 3.965A 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 984 removed outlier: 3.577A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.754A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 77 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.840A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.955A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.033A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.356A 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 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 754 through 757 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.774A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 4.057A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) 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 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.891A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) 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: 3.965A 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 984 removed outlier: 3.577A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.754A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.840A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 370 removed outlier: 3.956A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 5.032A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.356A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 616 through 620 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 753 Processing helix chain 'E' and resid 754 through 757 Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.774A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 removed outlier: 4.057A pdb=" N LEU E 821 " --> pdb=" O PRO E 817 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 913 through 918 Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.891A pdb=" N ILE E 934 " --> pdb=" O ALA E 930 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN E 935 " --> pdb=" O ILE E 931 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER E 939 " --> pdb=" O GLN E 935 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 940 " --> pdb=" O ASP E 936 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.965A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.578A pdb=" N SER E 982 " --> pdb=" O ASN E 978 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.754A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 74 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.290A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.690A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.306A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.396A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.231A 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: 6.596A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.701A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.645A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.088A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.675A 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: 6.461A pdb=" N ALA A 701 " --> pdb=" O ILE E 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: 6.531A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.747A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.735A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.735A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS H 96 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP H 116 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG H 98 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 15 through 20 removed outlier: 4.481A pdb=" N SER H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AC4, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN L 101 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.290A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.690A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 324 " --> pdb=" O CYS E 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.306A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.395A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.645A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.088A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.747A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.735A pdb=" N GLU C 10 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.735A pdb=" N GLU C 10 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N CYS C 96 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP C 116 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG C 98 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP C 114 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 15 through 20 removed outlier: 4.480A pdb=" N SER C 16 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AE7, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP D 37 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 101 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP D 37 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.289A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 224 " --> pdb=" O SER E 205 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.306A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 83 through 85 Processing sheet with id=AF3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.396A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AF5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.645A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AF7, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.089A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.531A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.747A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.735A pdb=" N GLU F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N THR F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.735A pdb=" N GLU F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP F 114 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 15 through 20 removed outlier: 4.481A pdb=" N SER F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AG8, first strand: chain 'G' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN G 101 " --> pdb=" O ASP G 94 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 47 through 50 removed outlier: 6.564A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) 1218 hydrogen bonds defined for protein. 3222 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: 6.15 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7054 1.33 - 1.47: 6788 1.47 - 1.60: 10509 1.60 - 1.73: 12 1.73 - 1.87: 126 Bond restraints: 24489 Sorted by residual: bond pdb=" C CYS B 738 " pdb=" O CYS B 738 " ideal model delta sigma weight residual 1.236 1.340 -0.104 1.15e-02 7.56e+03 8.16e+01 bond pdb=" C CYS A 738 " pdb=" O CYS A 738 " ideal model delta sigma weight residual 1.236 1.340 -0.103 1.15e-02 7.56e+03 8.07e+01 bond pdb=" C CYS E 738 " pdb=" O CYS E 738 " ideal model delta sigma weight residual 1.236 1.340 -0.103 1.15e-02 7.56e+03 8.05e+01 bond pdb=" C CYS A 538 " pdb=" O CYS A 538 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.17e-02 7.31e+03 2.73e+01 bond pdb=" C CYS E 538 " pdb=" O CYS E 538 " ideal model delta sigma weight residual 1.236 1.297 -0.061 1.17e-02 7.31e+03 2.71e+01 ... (remaining 24484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 32819 4.29 - 8.58: 657 8.58 - 12.87: 6 12.87 - 17.16: 3 17.16 - 21.45: 6 Bond angle restraints: 33491 Sorted by residual: angle pdb=" CD1 LEU A 84 " pdb=" CG LEU A 84 " pdb=" CD2 LEU A 84 " ideal model delta sigma weight residual 110.80 132.25 -21.45 2.20e+00 2.07e-01 9.51e+01 angle pdb=" CD1 LEU B 84 " pdb=" CG LEU B 84 " pdb=" CD2 LEU B 84 " ideal model delta sigma weight residual 110.80 132.25 -21.45 2.20e+00 2.07e-01 9.50e+01 angle pdb=" CD1 LEU E 84 " pdb=" CG LEU E 84 " pdb=" CD2 LEU E 84 " ideal model delta sigma weight residual 110.80 132.25 -21.45 2.20e+00 2.07e-01 9.50e+01 angle pdb=" CD1 LEU E 582 " pdb=" CG LEU E 582 " pdb=" CD2 LEU E 582 " ideal model delta sigma weight residual 110.80 131.20 -20.40 2.20e+00 2.07e-01 8.60e+01 angle pdb=" CD1 LEU A 582 " pdb=" CG LEU A 582 " pdb=" CD2 LEU A 582 " ideal model delta sigma weight residual 110.80 131.20 -20.40 2.20e+00 2.07e-01 8.60e+01 ... (remaining 33486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14522 17.95 - 35.91: 479 35.91 - 53.86: 114 53.86 - 71.82: 21 71.82 - 89.77: 24 Dihedral angle restraints: 15160 sinusoidal: 5410 harmonic: 9750 Sorted by residual: dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.90 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.89 61.89 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -147.86 61.86 1 1.00e+01 1.00e-02 5.07e+01 ... (remaining 15157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3274 0.103 - 0.206: 596 0.206 - 0.310: 168 0.310 - 0.413: 77 0.413 - 0.516: 9 Chirality restraints: 4124 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.06e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.94e+01 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.80e+01 ... (remaining 4121 not shown) Planarity restraints: 4389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.061 2.00e-02 2.50e+03 6.38e-02 5.10e+01 pdb=" CG ASN B 331 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.099 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 331 " -0.061 2.00e-02 2.50e+03 6.38e-02 5.09e+01 pdb=" CG ASN E 331 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN E 331 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 331 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG E1510 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.061 2.00e-02 2.50e+03 6.37e-02 5.08e+01 pdb=" CG ASN A 331 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.077 2.00e-02 2.50e+03 ... (remaining 4386 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 8644 2.87 - 3.38: 20885 3.38 - 3.89: 38252 3.89 - 4.39: 42590 4.39 - 4.90: 72341 Nonbonded interactions: 182712 Sorted by model distance: nonbonded pdb=" NZ LYS B 790 " pdb=" OE2 GLU E 702 " model vdw 2.367 3.120 nonbonded pdb=" NZ LYS A 790 " pdb=" OE2 GLU B 702 " model vdw 2.368 3.120 nonbonded pdb=" OE2 GLU A 702 " pdb=" NZ LYS E 790 " model vdw 2.368 3.120 nonbonded pdb=" OD1 ASP A1084 " pdb=" NZ LYS A1086 " model vdw 2.461 3.120 nonbonded pdb=" OD1 ASP E1084 " pdb=" NZ LYS E1086 " model vdw 2.461 3.120 ... (remaining 182707 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 311 or (resid 312 and (name N or name CA or nam \ e C or name O or name CB )) or resid 313 through 1310)) selection = (chain 'E' and (resid 27 through 311 or (resid 312 and (name N or name CA or nam \ e C or name O or name CB )) or resid 313 through 1510)) } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.720 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 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 : 0.015 0.119 24582 Z= 0.804 Angle : 1.525 21.453 33731 Z= 1.011 Chirality : 0.100 0.516 4124 Planarity : 0.006 0.035 4347 Dihedral : 10.535 89.774 8737 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.82 % Favored : 97.90 % Rotamer: Outliers : 0.60 % Allowed : 2.72 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.13), residues: 3291 helix: -0.46 (0.19), residues: 636 sheet: 0.80 (0.17), residues: 876 loop : -0.20 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1000 TYR 0.023 0.005 TYR B1067 PHE 0.026 0.004 PHE E 898 TRP 0.031 0.006 TRP E 104 HIS 0.004 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.01425 (24489) covalent geometry : angle 1.51262 (33491) SS BOND : bond 0.03898 ( 39) SS BOND : angle 2.48749 ( 78) hydrogen bonds : bond 0.17397 ( 1149) hydrogen bonds : angle 8.89192 ( 3222) link_BETA1-4 : bond 0.05387 ( 12) link_BETA1-4 : angle 3.98623 ( 36) link_NAG-ASN : bond 0.06974 ( 42) link_NAG-ASN : angle 2.40398 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 338 time to evaluate : 0.826 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 347 average time/residue: 0.1525 time to fit residues: 84.6039 Evaluate side-chains 148 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 50.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 907 ASN A 992 GLN A1002 GLN A1005 GLN A1048 HIS B 954 GLN B 992 GLN B1002 GLN B1048 HIS E 196 ASN E 907 ASN E 992 GLN E1002 GLN E1048 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.208804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141380 restraints weight = 28983.150| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.52 r_work: 0.3586 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24582 Z= 0.172 Angle : 0.678 15.889 33731 Z= 0.346 Chirality : 0.048 0.287 4124 Planarity : 0.005 0.053 4347 Dihedral : 6.570 81.751 4644 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.58 % Favored : 98.24 % Rotamer: Outliers : 2.27 % Allowed : 6.85 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3291 helix: 0.89 (0.21), residues: 621 sheet: 0.67 (0.16), residues: 954 loop : -0.13 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 237 TYR 0.024 0.002 TYR B1067 PHE 0.025 0.002 PHE E 86 TRP 0.014 0.001 TRP E 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00391 (24489) covalent geometry : angle 0.63457 (33491) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.57078 ( 78) hydrogen bonds : bond 0.04819 ( 1149) hydrogen bonds : angle 6.15003 ( 3222) link_BETA1-4 : bond 0.00530 ( 12) link_BETA1-4 : angle 2.26187 ( 36) link_NAG-ASN : bond 0.00613 ( 42) link_NAG-ASN : angle 3.58966 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 544 ASN cc_start: 0.8673 (t0) cc_final: 0.8364 (t0) REVERT: A 755 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7291 (mm-40) REVERT: A 900 MET cc_start: 0.8371 (ttm) cc_final: 0.8106 (mtp) REVERT: B 48 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8205 (tp) REVERT: B 532 ASN cc_start: 0.8290 (t0) cc_final: 0.7576 (m110) REVERT: B 556 ASN cc_start: 0.8307 (m-40) cc_final: 0.7910 (p0) REVERT: B 748 GLU cc_start: 0.8716 (pm20) cc_final: 0.8424 (pm20) REVERT: B 855 PHE cc_start: 0.6403 (m-80) cc_final: 0.6006 (m-80) REVERT: E 48 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8279 (tp) REVERT: E 544 ASN cc_start: 0.8624 (t0) cc_final: 0.8358 (t0) REVERT: E 764 ASN cc_start: 0.7943 (t0) cc_final: 0.7211 (m110) REVERT: E 918 GLU cc_start: 0.8200 (mp0) cc_final: 0.7998 (mp0) outliers start: 45 outliers final: 26 residues processed: 236 average time/residue: 0.1573 time to fit residues: 58.5895 Evaluate side-chains 182 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 736 VAL Chi-restraints excluded: chain E residue 750 SER Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 894 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 5 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 221 optimal weight: 0.0670 chunk 331 optimal weight: 10.0000 chunk 28 optimal weight: 50.0000 chunk 60 optimal weight: 0.5980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 196 ASN E 907 ASN E 913 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.205164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136438 restraints weight = 28913.389| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.51 r_work: 0.3528 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24582 Z= 0.187 Angle : 0.641 13.518 33731 Z= 0.323 Chirality : 0.047 0.399 4124 Planarity : 0.004 0.055 4347 Dihedral : 5.979 82.267 4644 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 97.99 % Rotamer: Outliers : 1.81 % Allowed : 8.72 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.14), residues: 3291 helix: 1.10 (0.21), residues: 612 sheet: 0.62 (0.16), residues: 909 loop : -0.38 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E1107 TYR 0.022 0.001 TYR B1067 PHE 0.021 0.002 PHE E 898 TRP 0.009 0.001 TRP A1102 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00436 (24489) covalent geometry : angle 0.59980 (33491) SS BOND : bond 0.00264 ( 39) SS BOND : angle 1.94030 ( 78) hydrogen bonds : bond 0.04210 ( 1149) hydrogen bonds : angle 5.80921 ( 3222) link_BETA1-4 : bond 0.00714 ( 12) link_BETA1-4 : angle 1.82978 ( 36) link_NAG-ASN : bond 0.00771 ( 42) link_NAG-ASN : angle 3.34945 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 544 ASN cc_start: 0.8684 (t0) cc_final: 0.8406 (t0) REVERT: A 586 ASP cc_start: 0.7762 (m-30) cc_final: 0.7195 (m-30) REVERT: A 755 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7383 (mm-40) REVERT: A 900 MET cc_start: 0.8482 (ttm) cc_final: 0.8249 (mtp) REVERT: A 984 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7668 (tt) REVERT: B 532 ASN cc_start: 0.8181 (t0) cc_final: 0.7547 (m110) REVERT: B 556 ASN cc_start: 0.8122 (m-40) cc_final: 0.7741 (p0) REVERT: B 764 ASN cc_start: 0.8191 (t0) cc_final: 0.7418 (m110) REVERT: B 855 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6254 (m-80) REVERT: B 859 THR cc_start: 0.8337 (t) cc_final: 0.8120 (p) REVERT: E 206 LYS cc_start: 0.7933 (tttt) cc_final: 0.7645 (ttmm) REVERT: E 564 GLN cc_start: 0.8003 (mt0) cc_final: 0.7493 (mm-40) REVERT: E 592 PHE cc_start: 0.8772 (p90) cc_final: 0.8516 (p90) REVERT: E 764 ASN cc_start: 0.7821 (t0) cc_final: 0.7189 (m110) REVERT: E 855 PHE cc_start: 0.6769 (m-80) cc_final: 0.6258 (m-80) REVERT: E 907 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8364 (m110) outliers start: 36 outliers final: 20 residues processed: 203 average time/residue: 0.1516 time to fit residues: 49.9629 Evaluate side-chains 176 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 555 SER Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 294 optimal weight: 3.9990 chunk 206 optimal weight: 40.0000 chunk 258 optimal weight: 0.0870 chunk 211 optimal weight: 50.0000 chunk 87 optimal weight: 0.4980 chunk 305 optimal weight: 0.9980 chunk 313 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 907 ASN A 913 GLN B 804 GLN E 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.204881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136117 restraints weight = 28821.121| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.51 r_work: 0.3523 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24582 Z= 0.153 Angle : 0.585 12.993 33731 Z= 0.290 Chirality : 0.046 0.259 4124 Planarity : 0.004 0.055 4347 Dihedral : 5.491 74.799 4644 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.70 % Favored : 98.21 % Rotamer: Outliers : 2.02 % Allowed : 9.32 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.14), residues: 3291 helix: 1.43 (0.22), residues: 597 sheet: 0.64 (0.17), residues: 930 loop : -0.33 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1107 TYR 0.021 0.001 TYR B1067 PHE 0.022 0.002 PHE E 906 TRP 0.007 0.001 TRP A1102 HIS 0.002 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00355 (24489) covalent geometry : angle 0.54342 (33491) SS BOND : bond 0.00310 ( 39) SS BOND : angle 1.50463 ( 78) hydrogen bonds : bond 0.03689 ( 1149) hydrogen bonds : angle 5.55039 ( 3222) link_BETA1-4 : bond 0.00563 ( 12) link_BETA1-4 : angle 1.61523 ( 36) link_NAG-ASN : bond 0.00630 ( 42) link_NAG-ASN : angle 3.32260 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.853 Fit side-chains REVERT: A 544 ASN cc_start: 0.8774 (t0) cc_final: 0.8508 (t0) REVERT: A 586 ASP cc_start: 0.7757 (m-30) cc_final: 0.7205 (m-30) REVERT: A 900 MET cc_start: 0.8452 (ttm) cc_final: 0.8167 (mtp) REVERT: A 984 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (tt) REVERT: A 995 ARG cc_start: 0.7644 (tpt-90) cc_final: 0.7424 (mtp180) REVERT: B 532 ASN cc_start: 0.8230 (t0) cc_final: 0.7586 (m110) REVERT: B 556 ASN cc_start: 0.8041 (m-40) cc_final: 0.7711 (p0) REVERT: B 586 ASP cc_start: 0.7851 (m-30) cc_final: 0.7431 (m-30) REVERT: B 764 ASN cc_start: 0.8106 (t0) cc_final: 0.7395 (m110) REVERT: B 855 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: B 995 ARG cc_start: 0.7749 (tpt-90) cc_final: 0.7494 (ttt90) REVERT: B 1050 MET cc_start: 0.8959 (ptm) cc_final: 0.8732 (ptm) REVERT: E 206 LYS cc_start: 0.7929 (tttt) cc_final: 0.7670 (ttmm) REVERT: E 564 GLN cc_start: 0.7970 (mt0) cc_final: 0.7505 (mm110) REVERT: E 764 ASN cc_start: 0.7867 (t0) cc_final: 0.7355 (m110) REVERT: E 855 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6603 (m-80) outliers start: 40 outliers final: 15 residues processed: 188 average time/residue: 0.1609 time to fit residues: 48.2842 Evaluate side-chains 159 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 894 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 264 optimal weight: 4.9990 chunk 324 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 198 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 218 optimal weight: 50.0000 chunk 286 optimal weight: 1.9990 chunk 102 optimal weight: 0.0030 chunk 271 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN E 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.205460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137044 restraints weight = 28694.329| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.49 r_work: 0.3542 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24582 Z= 0.127 Angle : 0.578 17.793 33731 Z= 0.282 Chirality : 0.046 0.429 4124 Planarity : 0.004 0.055 4347 Dihedral : 4.888 64.174 4644 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.96 % Rotamer: Outliers : 1.56 % Allowed : 10.68 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.14), residues: 3291 helix: 1.60 (0.22), residues: 597 sheet: 0.67 (0.17), residues: 927 loop : -0.29 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.021 0.001 TYR B1067 PHE 0.017 0.001 PHE A 898 TRP 0.007 0.001 TRP E 104 HIS 0.002 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00290 (24489) covalent geometry : angle 0.52389 (33491) SS BOND : bond 0.00246 ( 39) SS BOND : angle 1.87896 ( 78) hydrogen bonds : bond 0.03450 ( 1149) hydrogen bonds : angle 5.48194 ( 3222) link_BETA1-4 : bond 0.00565 ( 12) link_BETA1-4 : angle 1.50393 ( 36) link_NAG-ASN : bond 0.00916 ( 42) link_NAG-ASN : angle 3.69519 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 SER cc_start: 0.9349 (t) cc_final: 0.9056 (p) REVERT: A 544 ASN cc_start: 0.8769 (t0) cc_final: 0.8512 (t0) REVERT: A 984 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 995 ARG cc_start: 0.7610 (tpt-90) cc_final: 0.7399 (mtp180) REVERT: B 532 ASN cc_start: 0.8202 (t0) cc_final: 0.7557 (m110) REVERT: B 556 ASN cc_start: 0.8029 (m-40) cc_final: 0.7706 (p0) REVERT: B 764 ASN cc_start: 0.8038 (t0) cc_final: 0.7357 (m110) REVERT: B 787 GLN cc_start: 0.8361 (mp10) cc_final: 0.7950 (mt0) REVERT: B 855 PHE cc_start: 0.6854 (m-80) cc_final: 0.6441 (m-80) REVERT: B 1050 MET cc_start: 0.8910 (ptm) cc_final: 0.8675 (ptm) REVERT: E 564 GLN cc_start: 0.7935 (mt0) cc_final: 0.7453 (mm-40) REVERT: E 586 ASP cc_start: 0.7747 (m-30) cc_final: 0.7487 (m-30) REVERT: E 764 ASN cc_start: 0.7683 (t0) cc_final: 0.7189 (m110) REVERT: E 855 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6531 (m-80) outliers start: 31 outliers final: 19 residues processed: 179 average time/residue: 0.1597 time to fit residues: 45.5290 Evaluate side-chains 167 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 984 LEU Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 53 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 260 optimal weight: 4.9990 chunk 101 optimal weight: 50.0000 chunk 249 optimal weight: 30.0000 chunk 327 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.194395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119566 restraints weight = 29720.717| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.99 r_work: 0.3361 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24582 Z= 0.202 Angle : 0.618 15.615 33731 Z= 0.304 Chirality : 0.047 0.464 4124 Planarity : 0.004 0.057 4347 Dihedral : 4.823 49.574 4644 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.13 % Favored : 97.78 % Rotamer: Outliers : 1.61 % Allowed : 11.54 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.14), residues: 3291 helix: 1.44 (0.21), residues: 609 sheet: 0.60 (0.16), residues: 969 loop : -0.39 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 905 TYR 0.023 0.002 TYR B1067 PHE 0.023 0.002 PHE E 898 TRP 0.009 0.001 TRP E1102 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00486 (24489) covalent geometry : angle 0.56740 (33491) SS BOND : bond 0.00319 ( 39) SS BOND : angle 1.73905 ( 78) hydrogen bonds : bond 0.03729 ( 1149) hydrogen bonds : angle 5.48111 ( 3222) link_BETA1-4 : bond 0.00506 ( 12) link_BETA1-4 : angle 1.40465 ( 36) link_NAG-ASN : bond 0.00806 ( 42) link_NAG-ASN : angle 3.78364 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 ASP cc_start: 0.6934 (m-30) cc_final: 0.6522 (m-30) REVERT: A 984 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7505 (tt) REVERT: B 532 ASN cc_start: 0.8086 (t0) cc_final: 0.7417 (m110) REVERT: B 556 ASN cc_start: 0.8001 (m-40) cc_final: 0.7728 (p0) REVERT: B 564 GLN cc_start: 0.7657 (mt0) cc_final: 0.7206 (mm-40) REVERT: B 764 ASN cc_start: 0.7780 (t0) cc_final: 0.7135 (m110) REVERT: B 787 GLN cc_start: 0.7964 (mp10) cc_final: 0.7549 (mt0) REVERT: B 823 PHE cc_start: 0.7741 (m-80) cc_final: 0.7541 (m-80) REVERT: B 855 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: B 858 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7636 (mp) REVERT: B 995 ARG cc_start: 0.7496 (tpt-90) cc_final: 0.7195 (mtp180) REVERT: B 1050 MET cc_start: 0.8462 (ptm) cc_final: 0.8233 (ptm) REVERT: E 564 GLN cc_start: 0.7750 (mt0) cc_final: 0.7146 (mm-40) REVERT: E 764 ASN cc_start: 0.7295 (t0) cc_final: 0.6824 (m110) REVERT: E 786 LYS cc_start: 0.7408 (mtmt) cc_final: 0.7176 (mtmt) REVERT: E 855 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6394 (m-80) outliers start: 32 outliers final: 17 residues processed: 182 average time/residue: 0.1581 time to fit residues: 46.0613 Evaluate side-chains 162 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 26 optimal weight: 10.0000 chunk 141 optimal weight: 40.0000 chunk 12 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 115 optimal weight: 0.0060 chunk 217 optimal weight: 50.0000 chunk 176 optimal weight: 0.7980 chunk 254 optimal weight: 0.0070 chunk 330 optimal weight: 50.0000 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 914 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.205284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.138286 restraints weight = 28715.636| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.08 r_work: 0.3504 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24582 Z= 0.112 Angle : 0.566 16.200 33731 Z= 0.275 Chirality : 0.045 0.477 4124 Planarity : 0.004 0.055 4347 Dihedral : 4.550 44.070 4644 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 1.16 % Allowed : 11.89 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.14), residues: 3291 helix: 1.66 (0.22), residues: 597 sheet: 0.64 (0.17), residues: 957 loop : -0.33 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 319 TYR 0.019 0.001 TYR B1067 PHE 0.017 0.001 PHE B 238 TRP 0.008 0.001 TRP B 104 HIS 0.001 0.000 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00255 (24489) covalent geometry : angle 0.51112 (33491) SS BOND : bond 0.00336 ( 39) SS BOND : angle 2.05241 ( 78) hydrogen bonds : bond 0.03272 ( 1149) hydrogen bonds : angle 5.39577 ( 3222) link_BETA1-4 : bond 0.00490 ( 12) link_BETA1-4 : angle 1.34903 ( 36) link_NAG-ASN : bond 0.00763 ( 42) link_NAG-ASN : angle 3.63136 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 323 THR cc_start: 0.8089 (p) cc_final: 0.7879 (t) REVERT: A 586 ASP cc_start: 0.7503 (m-30) cc_final: 0.7031 (m-30) REVERT: A 984 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7789 (tt) REVERT: B 532 ASN cc_start: 0.8166 (t0) cc_final: 0.7550 (m110) REVERT: B 556 ASN cc_start: 0.7991 (m-40) cc_final: 0.7771 (p0) REVERT: B 764 ASN cc_start: 0.7973 (t0) cc_final: 0.7381 (m110) REVERT: B 787 GLN cc_start: 0.8369 (mp10) cc_final: 0.7979 (mt0) REVERT: B 855 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: B 858 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7812 (mp) REVERT: B 995 ARG cc_start: 0.7729 (tpt-90) cc_final: 0.7515 (mtp180) REVERT: B 1050 MET cc_start: 0.8837 (ptm) cc_final: 0.8599 (ptm) REVERT: E 564 GLN cc_start: 0.7977 (mt0) cc_final: 0.7493 (mm-40) REVERT: E 586 ASP cc_start: 0.7769 (m-30) cc_final: 0.7511 (m-30) REVERT: E 764 ASN cc_start: 0.7618 (t0) cc_final: 0.7168 (m110) REVERT: E 855 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6544 (m-80) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.1525 time to fit residues: 40.4285 Evaluate side-chains 159 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 176 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 108 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 248 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 225 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.200305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.130080 restraints weight = 28653.602| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.49 r_work: 0.3460 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 24582 Z= 0.244 Angle : 0.648 15.968 33731 Z= 0.318 Chirality : 0.049 0.557 4124 Planarity : 0.004 0.058 4347 Dihedral : 4.623 42.549 4644 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 1.56 % Allowed : 11.99 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.15 (0.14), residues: 3291 helix: 1.06 (0.21), residues: 648 sheet: 0.43 (0.16), residues: 993 loop : -0.43 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1107 TYR 0.022 0.002 TYR B1067 PHE 0.024 0.002 PHE A 898 TRP 0.010 0.002 TRP B1102 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00586 (24489) covalent geometry : angle 0.59248 (33491) SS BOND : bond 0.00540 ( 39) SS BOND : angle 2.06811 ( 78) hydrogen bonds : bond 0.03834 ( 1149) hydrogen bonds : angle 5.48483 ( 3222) link_BETA1-4 : bond 0.00464 ( 12) link_BETA1-4 : angle 1.30058 ( 36) link_NAG-ASN : bond 0.00936 ( 42) link_NAG-ASN : angle 3.99935 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7629 (m-30) cc_final: 0.7199 (m-30) REVERT: A 984 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7752 (tt) REVERT: B 532 ASN cc_start: 0.8186 (t0) cc_final: 0.7586 (m110) REVERT: B 564 GLN cc_start: 0.7916 (mt0) cc_final: 0.7569 (mm-40) REVERT: B 764 ASN cc_start: 0.8148 (t0) cc_final: 0.7517 (m110) REVERT: B 787 GLN cc_start: 0.8432 (mp10) cc_final: 0.8021 (mt0) REVERT: B 823 PHE cc_start: 0.7961 (m-80) cc_final: 0.7694 (m-10) REVERT: B 855 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: B 858 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 995 ARG cc_start: 0.7852 (tpt-90) cc_final: 0.7615 (mtp180) REVERT: E 564 GLN cc_start: 0.8036 (mt0) cc_final: 0.7573 (mm-40) REVERT: E 764 ASN cc_start: 0.7769 (t0) cc_final: 0.7257 (m110) REVERT: E 855 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6538 (m-80) outliers start: 31 outliers final: 18 residues processed: 171 average time/residue: 0.1614 time to fit residues: 43.7246 Evaluate side-chains 154 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 228 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 96 optimal weight: 50.0000 chunk 258 optimal weight: 3.9990 chunk 329 optimal weight: 50.0000 chunk 116 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 273 optimal weight: 0.6980 chunk 230 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS B 655 HIS E 655 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.201579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133538 restraints weight = 28670.598| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.99 r_work: 0.3451 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24582 Z= 0.192 Angle : 0.620 17.182 33731 Z= 0.302 Chirality : 0.048 0.517 4124 Planarity : 0.004 0.059 4347 Dihedral : 4.484 36.333 4644 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.96 % Rotamer: Outliers : 1.36 % Allowed : 12.29 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.14), residues: 3291 helix: 1.23 (0.21), residues: 627 sheet: 0.39 (0.16), residues: 990 loop : -0.44 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 319 TYR 0.021 0.001 TYR B1067 PHE 0.021 0.002 PHE A 898 TRP 0.009 0.001 TRP B 104 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00459 (24489) covalent geometry : angle 0.55379 (33491) SS BOND : bond 0.00284 ( 39) SS BOND : angle 2.21715 ( 78) hydrogen bonds : bond 0.03605 ( 1149) hydrogen bonds : angle 5.48910 ( 3222) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 1.28089 ( 36) link_NAG-ASN : bond 0.01087 ( 42) link_NAG-ASN : angle 4.23813 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7604 (m-30) cc_final: 0.7170 (m-30) REVERT: A 984 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7749 (tt) REVERT: A 1138 TYR cc_start: 0.7330 (t80) cc_final: 0.6339 (m-80) REVERT: B 231 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6437 (tt) REVERT: B 532 ASN cc_start: 0.8182 (t0) cc_final: 0.7515 (m110) REVERT: B 564 GLN cc_start: 0.7947 (mt0) cc_final: 0.7574 (mm-40) REVERT: B 764 ASN cc_start: 0.8115 (t0) cc_final: 0.7498 (m110) REVERT: B 787 GLN cc_start: 0.8475 (mp10) cc_final: 0.8054 (mp10) REVERT: B 823 PHE cc_start: 0.7994 (m-80) cc_final: 0.7748 (m-10) REVERT: B 855 PHE cc_start: 0.6847 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: B 858 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 995 ARG cc_start: 0.7854 (tpt-90) cc_final: 0.7623 (mtp180) REVERT: E 564 GLN cc_start: 0.8072 (mt0) cc_final: 0.7572 (mm-40) REVERT: E 758 SER cc_start: 0.7842 (OUTLIER) cc_final: 0.7576 (p) REVERT: E 764 ASN cc_start: 0.7691 (t0) cc_final: 0.7193 (m110) outliers start: 27 outliers final: 21 residues processed: 160 average time/residue: 0.1538 time to fit residues: 39.8654 Evaluate side-chains 162 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 901 GLN Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 232 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 106 optimal weight: 40.0000 chunk 169 optimal weight: 0.9990 chunk 158 optimal weight: 0.0570 chunk 32 optimal weight: 5.9990 chunk 304 optimal weight: 0.0970 chunk 284 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.204678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136187 restraints weight = 28847.640| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.49 r_work: 0.3527 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24582 Z= 0.112 Angle : 0.570 16.483 33731 Z= 0.274 Chirality : 0.046 0.487 4124 Planarity : 0.004 0.055 4347 Dihedral : 4.169 35.545 4644 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.91 % Favored : 97.99 % Rotamer: Outliers : 1.26 % Allowed : 12.54 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3291 helix: 1.51 (0.21), residues: 660 sheet: 0.45 (0.16), residues: 996 loop : -0.35 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 319 TYR 0.020 0.001 TYR B1067 PHE 0.016 0.001 PHE B 238 TRP 0.008 0.001 TRP A 104 HIS 0.001 0.000 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00253 (24489) covalent geometry : angle 0.50227 (33491) SS BOND : bond 0.00416 ( 39) SS BOND : angle 1.96515 ( 78) hydrogen bonds : bond 0.03168 ( 1149) hydrogen bonds : angle 5.32745 ( 3222) link_BETA1-4 : bond 0.00460 ( 12) link_BETA1-4 : angle 1.23812 ( 36) link_NAG-ASN : bond 0.01011 ( 42) link_NAG-ASN : angle 4.12398 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6582 Ramachandran restraints generated. 3291 Oldfield, 0 Emsley, 3291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7610 (m-30) cc_final: 0.7179 (m-30) REVERT: A 984 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7836 (tt) REVERT: A 1045 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8298 (tttt) REVERT: A 1138 TYR cc_start: 0.7363 (t80) cc_final: 0.6539 (m-80) REVERT: B 532 ASN cc_start: 0.8147 (t0) cc_final: 0.7483 (m110) REVERT: B 564 GLN cc_start: 0.7861 (mt0) cc_final: 0.7530 (mm-40) REVERT: B 764 ASN cc_start: 0.8004 (t0) cc_final: 0.7442 (m110) REVERT: B 787 GLN cc_start: 0.8480 (mp10) cc_final: 0.8098 (mp10) REVERT: B 823 PHE cc_start: 0.7968 (m-80) cc_final: 0.7736 (m-10) REVERT: B 855 PHE cc_start: 0.6884 (m-80) cc_final: 0.6412 (m-80) REVERT: E 564 GLN cc_start: 0.8038 (mt0) cc_final: 0.7598 (mm-40) REVERT: E 758 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7566 (p) REVERT: E 764 ASN cc_start: 0.7700 (t0) cc_final: 0.7336 (m110) REVERT: E 855 PHE cc_start: 0.7107 (OUTLIER) cc_final: 0.6592 (m-80) outliers start: 25 outliers final: 17 residues processed: 171 average time/residue: 0.1550 time to fit residues: 42.6801 Evaluate side-chains 163 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 747 THR Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 855 PHE Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 120 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 220 optimal weight: 40.0000 chunk 287 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 322 optimal weight: 8.9990 chunk 292 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 330 optimal weight: 50.0000 chunk 1 optimal weight: 0.0980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.201236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132937 restraints weight = 28633.591| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.98 r_work: 0.3455 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24582 Z= 0.183 Angle : 0.606 16.608 33731 Z= 0.295 Chirality : 0.048 0.481 4124 Planarity : 0.004 0.055 4347 Dihedral : 4.286 35.713 4644 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.81 % Rotamer: Outliers : 1.11 % Allowed : 12.95 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.14), residues: 3291 helix: 1.23 (0.21), residues: 669 sheet: 0.43 (0.16), residues: 996 loop : -0.40 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 995 TYR 0.022 0.001 TYR B1067 PHE 0.022 0.002 PHE E 898 TRP 0.008 0.001 TRP A1102 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00439 (24489) covalent geometry : angle 0.54161 (33491) SS BOND : bond 0.00294 ( 39) SS BOND : angle 2.04743 ( 78) hydrogen bonds : bond 0.03483 ( 1149) hydrogen bonds : angle 5.37883 ( 3222) link_BETA1-4 : bond 0.00425 ( 12) link_BETA1-4 : angle 1.20825 ( 36) link_NAG-ASN : bond 0.00933 ( 42) link_NAG-ASN : angle 4.14864 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8390.30 seconds wall clock time: 143 minutes 1.61 seconds (8581.61 seconds total)