Starting phenix.real_space_refine on Mon Sep 30 02:21:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra8_24347/09_2024/7ra8_24347.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra8_24347/09_2024/7ra8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra8_24347/09_2024/7ra8_24347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra8_24347/09_2024/7ra8_24347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra8_24347/09_2024/7ra8_24347.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ra8_24347/09_2024/7ra8_24347.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 16, 'ASP:plan': 21, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 8} 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, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} 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, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 16, 'ASP:plan': 21, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 8} 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, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} 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, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 16, 'ASP:plan': 21, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 8} 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, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} 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, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 4} 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: 17.43, per 1000 atoms: 0.73 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: 5.98 Conformation dependent library (CDL) restraints added in 2.9 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: 3.44 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: 10.60 Time building geometry restraints manager: 6.86 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 1145 or resid 1301 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 1145 or resid 1501 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: 16.050 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: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 55.470 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.280 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: 0.030 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.790 ------------------------------------------------------------------------------- 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 : 0.014 0.119 24489 Z= 0.971 Angle : 1.513 21.453 33491 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 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 TRP 0.031 0.006 TRP E 104 HIS 0.004 0.001 HIS B1083 PHE 0.026 0.004 PHE E 898 TYR 0.023 0.005 TYR B1067 ARG 0.003 0.001 ARG A1000 *********************** 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 fitting. rotamer outliers: 12 poor density : 338 time to evaluate : 2.679 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 347 average time/residue: 0.3587 time to fit residues: 197.8736 Evaluate side-chains 149 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 281 optimal weight: 0.9990 chunk 252 optimal weight: 30.0000 chunk 140 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 302 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 907 ASN E 992 GLN E1002 GLN E1048 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24489 Z= 0.270 Angle : 0.639 9.753 33491 Z= 0.338 Chirality : 0.048 0.362 4124 Planarity : 0.005 0.055 4347 Dihedral : 6.537 81.060 4644 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.64 % Favored : 98.18 % Rotamer: Outliers : 2.37 % Allowed : 6.80 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.14), residues: 3291 helix: 1.00 (0.21), residues: 603 sheet: 0.65 (0.16), residues: 948 loop : -0.10 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 104 HIS 0.003 0.001 HIS A1064 PHE 0.027 0.002 PHE E 86 TYR 0.024 0.002 TYR B1067 ARG 0.003 0.001 ARG B 237 *********************** 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 250 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 2.640 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.7365 (ttm) cc_final: 0.7074 (mtp) REVERT: B 48 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7453 (tp) REVERT: B 646 ARG cc_start: 0.6310 (tpp-160) cc_final: 0.6048 (tpm170) REVERT: E 48 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7564 (tp) REVERT: E 586 ASP cc_start: 0.7670 (m-30) cc_final: 0.7441 (m-30) REVERT: E 855 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: E 914 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8044 (p0) outliers start: 47 outliers final: 27 residues processed: 237 average time/residue: 0.3528 time to fit residues: 132.8383 Evaluate side-chains 175 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 2.598 ------------------------------------------------------------------------------- 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 B residue 959 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 271 GLN 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 Chi-restraints excluded: chain E residue 914 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 50.0000 chunk 251 optimal weight: 20.0000 chunk 205 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 chunk 327 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 103 optimal weight: 0.3980 chunk 243 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 764 ASN E 764 ASN E 907 ASN E 913 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24489 Z= 0.359 Angle : 0.632 9.738 33491 Z= 0.329 Chirality : 0.048 0.267 4124 Planarity : 0.005 0.058 4347 Dihedral : 6.022 81.458 4644 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.85 % Favored : 98.06 % Rotamer: Outliers : 2.22 % Allowed : 8.41 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3291 helix: 0.98 (0.21), residues: 612 sheet: 0.53 (0.16), residues: 909 loop : -0.41 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.002 PHE E 898 TYR 0.023 0.002 TYR B1067 ARG 0.005 0.001 ARG E1107 *********************** 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 213 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 2.498 Fit side-chains revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7628 (m-30) cc_final: 0.7387 (m-30) REVERT: B 646 ARG cc_start: 0.6627 (tpp-160) cc_final: 0.6320 (tpm170) REVERT: E 586 ASP cc_start: 0.7699 (m-30) cc_final: 0.7474 (m-30) REVERT: E 907 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7751 (m110) outliers start: 44 outliers final: 28 residues processed: 202 average time/residue: 0.3475 time to fit residues: 112.1306 Evaluate side-chains 167 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 2.684 ------------------------------------------------------------------------------- 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 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 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 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain E residue 271 GLN 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 750 SER Chi-restraints excluded: chain E residue 758 SER Chi-restraints excluded: chain E residue 761 THR Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 825 LYS Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 907 ASN Chi-restraints excluded: chain E residue 916 LEU 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 299 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 203 optimal weight: 50.0000 chunk 304 optimal weight: 0.5980 chunk 321 optimal weight: 40.0000 chunk 158 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24489 Z= 0.245 Angle : 0.553 9.261 33491 Z= 0.283 Chirality : 0.046 0.256 4124 Planarity : 0.004 0.058 4347 Dihedral : 5.557 75.472 4644 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.73 % Favored : 98.18 % Rotamer: Outliers : 1.96 % Allowed : 10.03 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.14), residues: 3291 helix: 1.32 (0.22), residues: 597 sheet: 0.57 (0.16), residues: 966 loop : -0.40 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.001 HIS B1064 PHE 0.020 0.002 PHE A 898 TYR 0.021 0.001 TYR B1067 ARG 0.002 0.000 ARG A1091 *********************** 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 190 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 2.534 Fit side-chains revert: symmetry clash REVERT: E 586 ASP cc_start: 0.7637 (m-30) cc_final: 0.7234 (m-30) outliers start: 39 outliers final: 15 residues processed: 183 average time/residue: 0.3485 time to fit residues: 101.9784 Evaluate side-chains 148 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 2.594 ------------------------------------------------------------------------------- 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 B residue 235 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 268 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 288 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24489 Z= 0.372 Angle : 0.608 9.364 33491 Z= 0.312 Chirality : 0.048 0.431 4124 Planarity : 0.005 0.058 4347 Dihedral : 5.191 63.616 4644 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.81 % Rotamer: Outliers : 2.12 % Allowed : 10.83 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3291 helix: 1.04 (0.21), residues: 621 sheet: 0.50 (0.17), residues: 960 loop : -0.50 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1102 HIS 0.005 0.001 HIS B1058 PHE 0.025 0.002 PHE A 86 TYR 0.023 0.002 TYR B1067 ARG 0.005 0.001 ARG B 237 *********************** 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 192 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 2.599 Fit side-chains revert: symmetry clash REVERT: A 731 MET cc_start: 0.8746 (ptt) cc_final: 0.8468 (ptt) REVERT: B 858 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8087 (mp) outliers start: 42 outliers final: 27 residues processed: 190 average time/residue: 0.3446 time to fit residues: 106.6512 Evaluate side-chains 159 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 2.508 ------------------------------------------------------------------------------- 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 768 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 732 THR 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 B residue 768 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 271 GLN Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 604 THR 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 768 THR Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 916 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 108 optimal weight: 50.0000 chunk 289 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 188 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 322 optimal weight: 30.0000 chunk 267 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24489 Z= 0.245 Angle : 0.543 8.129 33491 Z= 0.278 Chirality : 0.046 0.500 4124 Planarity : 0.004 0.056 4347 Dihedral : 4.880 52.460 4644 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.76 % Favored : 98.15 % Rotamer: Outliers : 1.56 % Allowed : 12.04 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3291 helix: 1.35 (0.22), residues: 606 sheet: 0.52 (0.17), residues: 957 loop : -0.43 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.002 0.001 HIS B1064 PHE 0.019 0.001 PHE E 898 TYR 0.021 0.001 TYR B1067 ARG 0.004 0.000 ARG E 319 *********************** 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 166 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.266 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7164 (mtp) REVERT: B 858 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8071 (mp) outliers start: 31 outliers final: 19 residues processed: 159 average time/residue: 0.3500 time to fit residues: 89.7546 Evaluate side-chains 150 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 2.504 ------------------------------------------------------------------------------- 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 900 MET Chi-restraints excluded: chain A residue 1104 VAL 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 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain E residue 271 GLN 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 858 LEU 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 310 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 0.4980 chunk 271 optimal weight: 2.9990 chunk 179 optimal weight: 0.2980 chunk 320 optimal weight: 30.0000 chunk 200 optimal weight: 0.6980 chunk 195 optimal weight: 0.0770 chunk 148 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24489 Z= 0.169 Angle : 0.508 7.493 33491 Z= 0.260 Chirality : 0.045 0.472 4124 Planarity : 0.004 0.053 4347 Dihedral : 4.545 43.968 4644 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.01 % Favored : 97.90 % Rotamer: Outliers : 1.36 % Allowed : 12.49 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3291 helix: 1.51 (0.21), residues: 633 sheet: 0.54 (0.17), residues: 957 loop : -0.37 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 104 HIS 0.001 0.000 HIS A1088 PHE 0.017 0.001 PHE B 238 TYR 0.020 0.001 TYR B1067 ARG 0.005 0.000 ARG E 319 *********************** 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 fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 778 THR cc_start: 0.8444 (m) cc_final: 0.8123 (m) REVERT: B 858 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8061 (mp) outliers start: 27 outliers final: 17 residues processed: 167 average time/residue: 0.3308 time to fit residues: 89.6725 Evaluate side-chains 148 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 2.490 ------------------------------------------------------------------------------- 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 763 LEU Chi-restraints excluded: chain A residue 894 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 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 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 198 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 218 optimal weight: 50.0000 chunk 158 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 252 optimal weight: 30.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN E 655 HIS ** E 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 24489 Z= 0.506 Angle : 0.653 9.978 33491 Z= 0.336 Chirality : 0.051 0.497 4124 Planarity : 0.005 0.060 4347 Dihedral : 4.915 45.421 4644 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.86 % Favored : 97.05 % Rotamer: Outliers : 1.51 % Allowed : 12.85 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3291 helix: 0.86 (0.21), residues: 645 sheet: 0.28 (0.16), residues: 993 loop : -0.57 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E1102 HIS 0.005 0.002 HIS A1058 PHE 0.027 0.002 PHE E 92 TYR 0.023 0.002 TYR B1067 ARG 0.006 0.001 ARG E 319 *********************** 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 156 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: B 858 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8111 (mp) outliers start: 30 outliers final: 23 residues processed: 151 average time/residue: 0.3586 time to fit residues: 87.0148 Evaluate side-chains 146 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 894 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 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain E residue 216 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 768 THR Chi-restraints excluded: chain E residue 796 ASP 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 291 optimal weight: 0.6980 chunk 307 optimal weight: 0.7980 chunk 280 optimal weight: 0.9990 chunk 299 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 234 optimal weight: 0.7980 chunk 91 optimal weight: 30.0000 chunk 270 optimal weight: 2.9990 chunk 282 optimal weight: 0.0570 chunk 298 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24489 Z= 0.199 Angle : 0.522 7.720 33491 Z= 0.267 Chirality : 0.046 0.558 4124 Planarity : 0.004 0.057 4347 Dihedral : 4.499 44.311 4644 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.79 % Favored : 98.12 % Rotamer: Outliers : 0.96 % Allowed : 13.45 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3291 helix: 1.35 (0.21), residues: 639 sheet: 0.38 (0.17), residues: 960 loop : -0.46 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.001 0.000 HIS B1064 PHE 0.019 0.001 PHE B 238 TYR 0.020 0.001 TYR B1067 ARG 0.006 0.000 ARG E 319 *********************** 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 152 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 2.662 Fit side-chains revert: symmetry clash REVERT: B 858 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (mp) outliers start: 19 outliers final: 18 residues processed: 150 average time/residue: 0.3458 time to fit residues: 84.9832 Evaluate side-chains 142 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 894 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 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 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 796 ASP 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 196 optimal weight: 0.6980 chunk 316 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 219 optimal weight: 50.0000 chunk 331 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 264 optimal weight: 0.4980 chunk 27 optimal weight: 30.0000 chunk 204 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24489 Z= 0.383 Angle : 0.582 8.646 33491 Z= 0.299 Chirality : 0.049 0.504 4124 Planarity : 0.005 0.060 4347 Dihedral : 4.573 36.849 4644 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 1.11 % Allowed : 13.50 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3291 helix: 0.90 (0.20), residues: 663 sheet: 0.37 (0.17), residues: 960 loop : -0.56 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1102 HIS 0.004 0.001 HIS B1064 PHE 0.023 0.002 PHE E 898 TYR 0.022 0.002 TYR B1067 ARG 0.007 0.001 ARG E 319 ********************** 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 146 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: B 858 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8100 (mp) outliers start: 22 outliers final: 20 residues processed: 142 average time/residue: 0.3472 time to fit residues: 80.5736 Evaluate side-chains 144 residues out of total 2943 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 758 SER Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 894 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 750 SER Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 858 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 786 LYS Chi-restraints excluded: chain E residue 796 ASP Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 931 ILE 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 209 optimal weight: 50.0000 chunk 281 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 264 optimal weight: 0.0060 chunk 110 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 33 optimal weight: 0.0010 chunk 48 optimal weight: 2.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.200688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130944 restraints weight = 28724.080| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.47 r_work: 0.3501 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24489 Z= 0.181 Angle : 0.513 8.582 33491 Z= 0.263 Chirality : 0.047 0.499 4124 Planarity : 0.004 0.056 4347 Dihedral : 4.321 36.007 4644 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.24 % Rotamer: Outliers : 1.11 % Allowed : 13.60 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3291 helix: 1.49 (0.21), residues: 642 sheet: 0.46 (0.17), residues: 948 loop : -0.50 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS B1064 PHE 0.019 0.001 PHE B 238 TYR 0.020 0.001 TYR B1067 ARG 0.007 0.000 ARG E 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4935.89 seconds wall clock time: 94 minutes 33.12 seconds (5673.12 seconds total)