Starting phenix.real_space_refine on Tue Jun 24 16:12:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9t_25767/06_2025/7t9t_25767_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9t_25767/06_2025/7t9t_25767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t9t_25767/06_2025/7t9t_25767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9t_25767/06_2025/7t9t_25767.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9t_25767/06_2025/7t9t_25767_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9t_25767/06_2025/7t9t_25767_neut.cif" } resolution = 3.7 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= 0.003 sd= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5430 atoms to isotropic. 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 140 5.16 5 C 15078 2.51 5 N 4074 2.21 5 O 4773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.84s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24065 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 3453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3453 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3454 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "K" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "a" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" 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: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" 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: 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: "E" 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: "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 Time building chain proxies: 15.66, per 1000 atoms: 0.65 Number of scatterers: 24065 At special positions: 0 Unit cell: (168.48, 184.68, 123.12, 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 140 16.00 O 4773 8.00 N 4074 7.00 C 15078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 499 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS I 499 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA R 3 " - " MAN R 6 " " BMA X 3 " - " MAN X 6 " " BMA d 3 " - " MAN d 6 " ALPHA1-6 " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " " BMA d 3 " - " MAN d 4 " " MAN d 4 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " BMA O 3 " - " NAG O 4 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " BMA U 3 " - " NAG U 4 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " BMA a 3 " - " NAG a 4 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 230 " " NAG A 602 " - " ASN A 241 " " NAG E 601 " - " ASN E 230 " " NAG E 602 " - " ASN E 241 " " NAG I 601 " - " ASN I 230 " " NAG I 602 " - " ASN I 241 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 339 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 392 " " NAG R 1 " - " ASN A 197 " " NAG S 1 " - " ASN E 386 " " NAG T 1 " - " ASN E 339 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 160 " " NAG W 1 " - " ASN E 392 " " NAG X 1 " - " ASN E 197 " " NAG Y 1 " - " ASN I 386 " " NAG Z 1 " - " ASN I 339 " " NAG a 1 " - " ASN I 262 " " NAG b 1 " - " ASN I 160 " " NAG c 1 " - " ASN I 392 " " NAG d 1 " - " ASN I 197 " Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.0 seconds 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5550 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 46 sheets defined 16.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.982A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.965A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.859A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 596 removed outlier: 3.617A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 removed outlier: 3.807A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.881A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.007A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.945A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 127 removed outlier: 3.996A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.570A pdb=" N PHE E 391 " --> pdb=" O THR E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 478 removed outlier: 3.929A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 526 removed outlier: 3.933A pdb=" N ALA F 525 " --> pdb=" O PHE F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 576 through 596 removed outlier: 3.627A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.630A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.754A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.834A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 4.077A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.856A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR G 87 " --> pdb=" O TYR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 127 removed outlier: 3.895A pdb=" N VAL I 127 " --> pdb=" O PRO I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 3.611A pdb=" N PHE I 391 " --> pdb=" O THR I 387 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN I 392 " --> pdb=" O SER I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 392' Processing helix chain 'I' and resid 473 through 479 removed outlier: 4.023A pdb=" N TRP I 477 " --> pdb=" O MET I 473 " (cutoff:3.500A) Processing helix chain 'J' and resid 531 through 535 Processing helix chain 'J' and resid 536 through 542 removed outlier: 3.598A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 575 through 596 removed outlier: 3.593A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 582 " --> pdb=" O ALA J 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL J 583 " --> pdb=" O ARG J 579 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.577A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 4.518A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU J 645 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.046A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.802A pdb=" N ARG K 64 " --> pdb=" O GLY K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'K' and resid 156 through 158 No H-bonds generated for 'chain 'K' and resid 156 through 158' Processing helix chain 'K' and resid 187 through 191 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 493 through 497 removed outlier: 5.456A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.972A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 244 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.675A pdb=" N ALA A 433 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.269A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 464 through 468 Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.024A pdb=" N THR A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 320 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.508A pdb=" N SER C 25 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA C 5 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 21 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET C 80 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100B through 100D Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.948A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 135 through 145 current: chain 'C' and resid 176 through 185 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.537A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 13 current: chain 'D' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 53 through 54 current: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.539A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.264A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 493 through 497 removed outlier: 5.466A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.721A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR E 244 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AC5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.556A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 308 removed outlier: 6.040A pdb=" N THR E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR E 320 " --> pdb=" O THR E 305 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 316 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 464 through 468 Processing sheet with id=AC7, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.565A pdb=" N TYR G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G 21 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100E through 103 Processing sheet with id=AC9, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.947A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 135 through 145 current: chain 'G' and resid 176 through 185 Processing sheet with id=AD1, first strand: chain 'G' and resid 150 through 154 Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.555A pdb=" N ARG H 24 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 13 current: chain 'H' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 53 through 54 current: chain 'H' and resid 97 through 98 Processing sheet with id=AD4, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.622A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.277A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 493 through 497 removed outlier: 5.560A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.812A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL I 242 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR I 244 " --> pdb=" O MET I 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 129 through 130 Processing sheet with id=AD9, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE1, first strand: chain 'I' and resid 201 through 203 removed outlier: 6.519A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 259 through 261 current: chain 'I' and resid 284 through 307 removed outlier: 5.717A pdb=" N THR I 305 " --> pdb=" O THR I 320 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR I 320 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE I 307 " --> pdb=" O TYR I 318 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TYR I 318 " --> pdb=" O ILE I 307 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 317 through 323 current: chain 'I' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 381 through 385 current: chain 'I' and resid 463 through 468 Processing sheet with id=AE3, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.575A pdb=" N TYR K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER K 21 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET K 80 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR K 70 " --> pdb=" O TYR K 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100E through 103 Processing sheet with id=AE5, first strand: chain 'K' and resid 120 through 124 removed outlier: 3.951A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 135 through 145 current: chain 'K' and resid 176 through 185 Processing sheet with id=AE6, first strand: chain 'K' and resid 151 through 154 Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.567A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.530A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.181A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1500 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.60 Time building geometry restraints manager: 8.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7646 1.35 - 1.47: 6103 1.47 - 1.59: 10613 1.59 - 1.71: 0 1.71 - 1.83: 187 Bond restraints: 24549 Sorted by residual: bond pdb=" C6 BMA R 3 " pdb=" O6 BMA R 3 " ideal model delta sigma weight residual 1.411 1.468 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C6 BMA d 3 " pdb=" O6 BMA d 3 " ideal model delta sigma weight residual 1.411 1.466 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C6 BMA X 3 " pdb=" O6 BMA X 3 " ideal model delta sigma weight residual 1.411 1.464 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" C3 BMA R 3 " pdb=" O3 BMA R 3 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C3 BMA d 3 " pdb=" O3 BMA d 3 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.63e+00 ... (remaining 24544 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 31728 1.66 - 3.32: 1233 3.32 - 4.99: 276 4.99 - 6.65: 73 6.65 - 8.31: 12 Bond angle restraints: 33322 Sorted by residual: angle pdb=" N HIS G 100D" pdb=" CA HIS G 100D" pdb=" C HIS G 100D" ideal model delta sigma weight residual 110.35 116.06 -5.71 1.40e+00 5.10e-01 1.66e+01 angle pdb=" N ASN A 133 " pdb=" CA ASN A 133 " pdb=" C ASN A 133 " ideal model delta sigma weight residual 110.91 115.65 -4.74 1.17e+00 7.31e-01 1.64e+01 angle pdb=" N SER B 615 " pdb=" CA SER B 615 " pdb=" CB SER B 615 " ideal model delta sigma weight residual 114.17 109.97 4.20 1.14e+00 7.69e-01 1.36e+01 angle pdb=" C LEU G 100C" pdb=" N HIS G 100D" pdb=" CA HIS G 100D" ideal model delta sigma weight residual 121.31 126.26 -4.95 1.49e+00 4.50e-01 1.10e+01 angle pdb=" N ASN I 133 " pdb=" CA ASN I 133 " pdb=" C ASN I 133 " ideal model delta sigma weight residual 110.91 114.72 -3.81 1.17e+00 7.31e-01 1.06e+01 ... (remaining 33317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 14578 21.83 - 43.67: 766 43.67 - 65.50: 108 65.50 - 87.33: 106 87.33 - 109.17: 54 Dihedral angle restraints: 15612 sinusoidal: 6993 harmonic: 8619 Sorted by residual: dihedral pdb=" CB CYS I 54 " pdb=" SG CYS I 54 " pdb=" SG CYS I 74 " pdb=" CB CYS I 74 " ideal model delta sinusoidal sigma weight residual -86.00 -171.20 85.20 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual -86.00 -131.23 45.23 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -131.08 45.08 1 1.00e+01 1.00e-02 2.82e+01 ... (remaining 15609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 3921 0.146 - 0.292: 28 0.292 - 0.437: 2 0.437 - 0.583: 0 0.583 - 0.729: 3 Chirality restraints: 3954 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN I 262 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN E 262 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 3951 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 93 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASN L 93 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN L 93 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP L 94 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 203 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO L 204 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 204 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 204 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 125 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO K 126 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO K 126 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 126 " 0.025 5.00e-02 4.00e+02 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 271 2.61 - 3.18: 21530 3.18 - 3.75: 35538 3.75 - 4.33: 49818 4.33 - 4.90: 83335 Nonbonded interactions: 190492 Sorted by model distance: nonbonded pdb=" O ASN B 625 " pdb=" OG1 THR B 627 " model vdw 2.036 3.040 nonbonded pdb=" OG1 THR I 37 " pdb=" O CYS J 604 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR G 84 " pdb=" O GLN G 171 " model vdw 2.191 3.040 nonbonded pdb=" O MET A 145 " pdb=" N CYS A 157 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR C 84 " pdb=" O GLN C 171 " model vdw 2.201 3.040 ... (remaining 190487 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' and (resid 32 through 144 or resid 157 through 503 or resid 601 throu \ gh 602)) selection = (chain 'E' and (resid 32 through 309 or resid 314 through 503 or resid 601 throu \ gh 602)) selection = (chain 'I' and (resid 32 through 144 or resid 157 through 503 or resid 601 throu \ gh 602)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'S' selection = chain 'W' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'Z' selection = chain 'b' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'X' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 57.340 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 : 0.005 0.057 24651 Z= 0.227 Angle : 0.911 14.279 33592 Z= 0.442 Chirality : 0.053 0.729 3954 Planarity : 0.004 0.046 4158 Dihedral : 16.296 109.168 9954 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 0.08 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.22 (0.15), residues: 2916 helix: 1.21 (0.28), residues: 378 sheet: -1.21 (0.16), residues: 957 loop : -1.00 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 427 HIS 0.011 0.001 HIS K 100D PHE 0.022 0.002 PHE A 210 TYR 0.019 0.001 TYR D 91 ARG 0.005 0.001 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 24) link_NAG-ASN : angle 3.78191 ( 72) link_ALPHA1-6 : bond 0.01778 ( 6) link_ALPHA1-6 : angle 6.46499 ( 18) link_BETA1-4 : bond 0.01105 ( 33) link_BETA1-4 : angle 5.35887 ( 99) link_ALPHA1-3 : bond 0.01477 ( 3) link_ALPHA1-3 : angle 5.69527 ( 9) hydrogen bonds : bond 0.20933 ( 578) hydrogen bonds : angle 8.64478 ( 1500) SS BOND : bond 0.00412 ( 36) SS BOND : angle 1.41961 ( 72) covalent geometry : bond 0.00465 (24549) covalent geometry : angle 0.82702 (33322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7474 (mtt) cc_final: 0.7147 (mmp) REVERT: I 84 MET cc_start: 0.7647 (mpp) cc_final: 0.7404 (mpp) REVERT: K 89 MET cc_start: 0.7659 (ppp) cc_final: 0.7314 (ppp) outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.4134 time to fit residues: 50.1023 Evaluate side-chains 54 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain I residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 30.0000 chunk 140 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS A 321AGLN A 422 GLN B 625 ASN C 6 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 246 GLN E 321AGLN E 422 GLN F 625 ASN F 651 ASN G 164 HIS H 32 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN H 137 ASN I 216 HIS I 321AGLN I 357 ASN I 422 GLN K 164 HIS L 32 ASN L 92 ASN L 137 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.042832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.032950 restraints weight = 205352.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.033825 restraints weight = 103950.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.034347 restraints weight = 69846.579| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 24651 Z= 0.296 Angle : 0.898 12.291 33592 Z= 0.432 Chirality : 0.053 0.520 3954 Planarity : 0.006 0.066 4158 Dihedral : 11.449 79.342 4557 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.14 % Rotamer: Outliers : 0.54 % Allowed : 5.36 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.47 (0.15), residues: 2916 helix: 1.23 (0.28), residues: 378 sheet: -1.23 (0.16), residues: 982 loop : -1.33 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP I 427 HIS 0.016 0.002 HIS G 100D PHE 0.029 0.003 PHE F 519 TYR 0.031 0.003 TYR H 49 ARG 0.007 0.001 ARG C 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 24) link_NAG-ASN : angle 4.51031 ( 72) link_ALPHA1-6 : bond 0.00823 ( 6) link_ALPHA1-6 : angle 2.62775 ( 18) link_BETA1-4 : bond 0.01100 ( 33) link_BETA1-4 : angle 4.13505 ( 99) link_ALPHA1-3 : bond 0.01579 ( 3) link_ALPHA1-3 : angle 3.09960 ( 9) hydrogen bonds : bond 0.04758 ( 578) hydrogen bonds : angle 6.22606 ( 1500) SS BOND : bond 0.00532 ( 36) SS BOND : angle 1.60185 ( 72) covalent geometry : bond 0.00671 (24549) covalent geometry : angle 0.84004 (33322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 473 MET cc_start: 0.9189 (tpp) cc_final: 0.8876 (tpp) REVERT: I 426 MET cc_start: 0.7478 (tpt) cc_final: 0.7270 (tpp) REVERT: L 96 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.6851 (m-10) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.3599 time to fit residues: 40.8187 Evaluate side-chains 58 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 218 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 266 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS E 246 GLN H 38 HIS I 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.042614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032736 restraints weight = 212163.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033604 restraints weight = 107670.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034138 restraints weight = 73019.311| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24651 Z= 0.168 Angle : 0.684 11.713 33592 Z= 0.325 Chirality : 0.046 0.443 3954 Planarity : 0.004 0.043 4158 Dihedral : 10.328 76.781 4557 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 0.93 % Allowed : 7.87 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.15 (0.16), residues: 2916 helix: 1.36 (0.28), residues: 402 sheet: -1.06 (0.16), residues: 994 loop : -1.08 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 631 HIS 0.005 0.001 HIS K 100D PHE 0.021 0.001 PHE F 519 TYR 0.024 0.001 TYR L 49 ARG 0.003 0.000 ARG C 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 24) link_NAG-ASN : angle 4.02404 ( 72) link_ALPHA1-6 : bond 0.00806 ( 6) link_ALPHA1-6 : angle 1.56832 ( 18) link_BETA1-4 : bond 0.01064 ( 33) link_BETA1-4 : angle 3.57483 ( 99) link_ALPHA1-3 : bond 0.01153 ( 3) link_ALPHA1-3 : angle 1.69959 ( 9) hydrogen bonds : bond 0.04274 ( 578) hydrogen bonds : angle 5.78024 ( 1500) SS BOND : bond 0.00445 ( 36) SS BOND : angle 1.07286 ( 72) covalent geometry : bond 0.00376 (24549) covalent geometry : angle 0.62755 (33322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7801 (mt-10) REVERT: H 96 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.6882 (m100) outliers start: 24 outliers final: 14 residues processed: 72 average time/residue: 0.3617 time to fit residues: 47.3229 Evaluate side-chains 67 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 5.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 89 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 113 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN E 334 ASN H 77 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 658 GLN K 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.040562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.030740 restraints weight = 214153.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.031541 restraints weight = 110846.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.032045 restraints weight = 76479.992| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 24651 Z= 0.293 Angle : 0.835 11.282 33592 Z= 0.403 Chirality : 0.050 0.485 3954 Planarity : 0.006 0.045 4158 Dihedral : 10.308 70.836 4557 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.10 % Favored : 92.87 % Rotamer: Outliers : 2.35 % Allowed : 9.88 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.43 (0.16), residues: 2916 helix: 1.44 (0.29), residues: 378 sheet: -1.25 (0.16), residues: 994 loop : -1.31 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 631 HIS 0.015 0.002 HIS G 100D PHE 0.025 0.002 PHE D 87 TYR 0.023 0.002 TYR L 49 ARG 0.005 0.001 ARG C 3 Details of bonding type rmsd link_NAG-ASN : bond 0.00774 ( 24) link_NAG-ASN : angle 4.10633 ( 72) link_ALPHA1-6 : bond 0.00766 ( 6) link_ALPHA1-6 : angle 2.44638 ( 18) link_BETA1-4 : bond 0.01113 ( 33) link_BETA1-4 : angle 3.70308 ( 99) link_ALPHA1-3 : bond 0.01199 ( 3) link_ALPHA1-3 : angle 2.42414 ( 9) hydrogen bonds : bond 0.04656 ( 578) hydrogen bonds : angle 6.02749 ( 1500) SS BOND : bond 0.00972 ( 36) SS BOND : angle 1.57425 ( 72) covalent geometry : bond 0.00666 (24549) covalent geometry : angle 0.78476 (33322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 52 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 626 MET cc_start: 0.7335 (mpp) cc_final: 0.6875 (mpp) REVERT: C 75 MET cc_start: 0.8666 (mtm) cc_final: 0.8427 (mtp) REVERT: G 75 MET cc_start: 0.8453 (mtm) cc_final: 0.8185 (mtp) REVERT: H 96 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.6655 (m-10) REVERT: I 426 MET cc_start: 0.7720 (tpt) cc_final: 0.7433 (tpp) REVERT: K 89 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7731 (tmm) REVERT: L 96 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.7392 (m-10) outliers start: 61 outliers final: 32 residues processed: 108 average time/residue: 0.3011 time to fit residues: 58.7005 Evaluate side-chains 86 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 51 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 59 TYR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 38 HIS Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 42 VAL Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 59 TYR Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 70 optimal weight: 0.0010 chunk 134 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 overall best weight: 5.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.040570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.030788 restraints weight = 212000.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.031601 restraints weight = 109142.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.032103 restraints weight = 74814.903| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24651 Z= 0.234 Angle : 0.732 12.196 33592 Z= 0.350 Chirality : 0.047 0.448 3954 Planarity : 0.004 0.039 4158 Dihedral : 9.899 69.817 4557 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 2.35 % Allowed : 11.30 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.31 (0.16), residues: 2916 helix: 1.46 (0.29), residues: 396 sheet: -1.24 (0.16), residues: 994 loop : -1.20 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 628 HIS 0.007 0.001 HIS I 72 PHE 0.016 0.002 PHE D 87 TYR 0.025 0.002 TYR L 49 ARG 0.003 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 24) link_NAG-ASN : angle 4.24701 ( 72) link_ALPHA1-6 : bond 0.00555 ( 6) link_ALPHA1-6 : angle 1.98832 ( 18) link_BETA1-4 : bond 0.01006 ( 33) link_BETA1-4 : angle 3.41479 ( 99) link_ALPHA1-3 : bond 0.01099 ( 3) link_ALPHA1-3 : angle 1.61800 ( 9) hydrogen bonds : bond 0.04005 ( 578) hydrogen bonds : angle 5.82394 ( 1500) SS BOND : bond 0.00694 ( 36) SS BOND : angle 1.34898 ( 72) covalent geometry : bond 0.00534 (24549) covalent geometry : angle 0.67854 (33322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 51 time to evaluate : 5.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 584 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7392 (mt-10) REVERT: B 626 MET cc_start: 0.7325 (mpp) cc_final: 0.6888 (mpp) REVERT: H 96 TRP cc_start: 0.8169 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: L 48 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8146 (mm) REVERT: L 96 TRP cc_start: 0.8435 (OUTLIER) cc_final: 0.7447 (m-10) outliers start: 61 outliers final: 37 residues processed: 106 average time/residue: 0.4789 time to fit residues: 91.2302 Evaluate side-chains 91 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 51 time to evaluate : 5.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 281 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 276 optimal weight: 4.9990 chunk 166 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 242 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN D 77 ASN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.040060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.030276 restraints weight = 215933.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.031057 restraints weight = 113880.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.031525 restraints weight = 79100.106| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24651 Z= 0.284 Angle : 0.777 11.268 33592 Z= 0.372 Chirality : 0.048 0.454 3954 Planarity : 0.005 0.052 4158 Dihedral : 9.959 67.472 4557 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.85 % Favored : 92.11 % Rotamer: Outliers : 2.62 % Allowed : 11.92 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.48 (0.16), residues: 2916 helix: 1.18 (0.28), residues: 411 sheet: -1.32 (0.17), residues: 976 loop : -1.31 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 631 HIS 0.009 0.002 HIS G 100D PHE 0.021 0.002 PHE L 87 TYR 0.023 0.002 TYR L 49 ARG 0.004 0.000 ARG I 467 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 24) link_NAG-ASN : angle 4.07047 ( 72) link_ALPHA1-6 : bond 0.00578 ( 6) link_ALPHA1-6 : angle 2.24043 ( 18) link_BETA1-4 : bond 0.01049 ( 33) link_BETA1-4 : angle 3.46018 ( 99) link_ALPHA1-3 : bond 0.01153 ( 3) link_ALPHA1-3 : angle 1.87293 ( 9) hydrogen bonds : bond 0.04155 ( 578) hydrogen bonds : angle 5.89911 ( 1500) SS BOND : bond 0.00567 ( 36) SS BOND : angle 1.57249 ( 72) covalent geometry : bond 0.00649 (24549) covalent geometry : angle 0.72699 (33322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 50 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7623 (pp) REVERT: B 584 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7436 (mt-10) REVERT: B 626 MET cc_start: 0.7330 (mpp) cc_final: 0.6864 (mpp) REVERT: G 75 MET cc_start: 0.8545 (mtm) cc_final: 0.8317 (mtp) REVERT: H 96 TRP cc_start: 0.8180 (OUTLIER) cc_final: 0.7283 (m-10) REVERT: J 529 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7488 (t) REVERT: L 48 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8236 (mm) REVERT: L 96 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.7559 (m-10) outliers start: 68 outliers final: 51 residues processed: 111 average time/residue: 0.2947 time to fit residues: 58.1759 Evaluate side-chains 106 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 50 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 494 VAL Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 120 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 274 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS J 653 GLN K 100DHIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.040702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.030921 restraints weight = 213666.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.031745 restraints weight = 109767.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.032239 restraints weight = 75394.191| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24651 Z= 0.129 Angle : 0.664 11.910 33592 Z= 0.312 Chirality : 0.045 0.413 3954 Planarity : 0.004 0.037 4158 Dihedral : 9.303 65.202 4557 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.16 % Allowed : 12.38 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.14 (0.16), residues: 2916 helix: 1.60 (0.29), residues: 393 sheet: -1.07 (0.17), residues: 961 loop : -1.13 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.036 0.001 HIS A 72 PHE 0.012 0.001 PHE A 210 TYR 0.024 0.001 TYR L 49 ARG 0.003 0.000 ARG E 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00621 ( 24) link_NAG-ASN : angle 4.03371 ( 72) link_ALPHA1-6 : bond 0.00641 ( 6) link_ALPHA1-6 : angle 1.70230 ( 18) link_BETA1-4 : bond 0.01008 ( 33) link_BETA1-4 : angle 3.26351 ( 99) link_ALPHA1-3 : bond 0.01293 ( 3) link_ALPHA1-3 : angle 1.58571 ( 9) hydrogen bonds : bond 0.03396 ( 578) hydrogen bonds : angle 5.46442 ( 1500) SS BOND : bond 0.00397 ( 36) SS BOND : angle 1.23630 ( 72) covalent geometry : bond 0.00287 (24549) covalent geometry : angle 0.60951 (33322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 51 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7676 (pp) REVERT: B 584 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7422 (mt-10) REVERT: B 626 MET cc_start: 0.7257 (mpp) cc_final: 0.6881 (mpp) REVERT: G 75 MET cc_start: 0.8576 (mtm) cc_final: 0.8321 (mtp) REVERT: H 96 TRP cc_start: 0.8006 (OUTLIER) cc_final: 0.7063 (m100) REVERT: K 89 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7810 (tmm) REVERT: L 48 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8163 (mm) REVERT: L 96 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7653 (m-10) outliers start: 56 outliers final: 35 residues processed: 101 average time/residue: 0.3164 time to fit residues: 55.7100 Evaluate side-chains 90 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 50 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 35 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 277 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 200 optimal weight: 40.0000 chunk 201 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.040096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.030330 restraints weight = 215061.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.031131 restraints weight = 111900.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.031618 restraints weight = 77070.326| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24651 Z= 0.232 Angle : 0.719 11.450 33592 Z= 0.341 Chirality : 0.047 0.435 3954 Planarity : 0.004 0.045 4158 Dihedral : 9.465 63.958 4557 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.31 % Allowed : 12.35 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.19 (0.16), residues: 2916 helix: 1.59 (0.29), residues: 399 sheet: -1.08 (0.17), residues: 938 loop : -1.21 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 96 HIS 0.008 0.001 HIS G 100D PHE 0.019 0.002 PHE D 87 TYR 0.021 0.002 TYR L 49 ARG 0.003 0.000 ARG E 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 24) link_NAG-ASN : angle 3.99118 ( 72) link_ALPHA1-6 : bond 0.00508 ( 6) link_ALPHA1-6 : angle 2.05106 ( 18) link_BETA1-4 : bond 0.01038 ( 33) link_BETA1-4 : angle 3.30668 ( 99) link_ALPHA1-3 : bond 0.01185 ( 3) link_ALPHA1-3 : angle 1.71994 ( 9) hydrogen bonds : bond 0.03759 ( 578) hydrogen bonds : angle 5.59531 ( 1500) SS BOND : bond 0.00499 ( 36) SS BOND : angle 1.29501 ( 72) covalent geometry : bond 0.00531 (24549) covalent geometry : angle 0.66939 (33322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 50 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7572 (pp) REVERT: B 584 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7411 (mt-10) REVERT: G 75 MET cc_start: 0.8609 (mtm) cc_final: 0.8360 (mtp) REVERT: H 96 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: J 530 MET cc_start: 0.6058 (pmm) cc_final: 0.5688 (pmm) REVERT: L 48 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8179 (mm) REVERT: L 96 TRP cc_start: 0.8495 (OUTLIER) cc_final: 0.7678 (m-10) outliers start: 60 outliers final: 54 residues processed: 103 average time/residue: 0.3051 time to fit residues: 56.0424 Evaluate side-chains 108 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 50 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 145 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 289 optimal weight: 30.0000 chunk 247 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 222 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 256 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.040817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.030980 restraints weight = 215403.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.031813 restraints weight = 110460.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032321 restraints weight = 75842.556| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 24651 Z= 0.121 Angle : 0.637 11.873 33592 Z= 0.299 Chirality : 0.045 0.402 3954 Planarity : 0.004 0.041 4158 Dihedral : 8.837 60.776 4557 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.20 % Allowed : 12.42 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.92 (0.16), residues: 2916 helix: 1.89 (0.29), residues: 384 sheet: -0.91 (0.17), residues: 959 loop : -1.02 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 96 HIS 0.003 0.001 HIS I 374 PHE 0.009 0.001 PHE A 176 TYR 0.021 0.001 TYR L 49 ARG 0.003 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 24) link_NAG-ASN : angle 3.96855 ( 72) link_ALPHA1-6 : bond 0.00511 ( 6) link_ALPHA1-6 : angle 1.55448 ( 18) link_BETA1-4 : bond 0.00986 ( 33) link_BETA1-4 : angle 3.14497 ( 99) link_ALPHA1-3 : bond 0.01315 ( 3) link_ALPHA1-3 : angle 1.49264 ( 9) hydrogen bonds : bond 0.03111 ( 578) hydrogen bonds : angle 5.19726 ( 1500) SS BOND : bond 0.00382 ( 36) SS BOND : angle 1.11236 ( 72) covalent geometry : bond 0.00267 (24549) covalent geometry : angle 0.58377 (33322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 54 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7641 (pp) REVERT: B 626 MET cc_start: 0.7252 (mpp) cc_final: 0.6883 (mpp) REVERT: E 424 ILE cc_start: 0.8883 (mm) cc_final: 0.8632 (tp) REVERT: G 75 MET cc_start: 0.8530 (mtm) cc_final: 0.8247 (mtp) REVERT: H 96 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.7467 (m-10) REVERT: J 530 MET cc_start: 0.5753 (pmm) cc_final: 0.5420 (pmm) REVERT: L 96 TRP cc_start: 0.8377 (OUTLIER) cc_final: 0.7723 (m-10) outliers start: 57 outliers final: 42 residues processed: 106 average time/residue: 0.3097 time to fit residues: 58.5804 Evaluate side-chains 96 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 51 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 107 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 125 optimal weight: 0.0030 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.040444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.030630 restraints weight = 216372.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.031444 restraints weight = 111530.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.031937 restraints weight = 76675.732| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24651 Z= 0.165 Angle : 0.659 11.494 33592 Z= 0.310 Chirality : 0.045 0.411 3954 Planarity : 0.004 0.045 4158 Dihedral : 8.847 58.817 4557 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.77 % Allowed : 13.00 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -0.91 (0.16), residues: 2916 helix: 1.78 (0.29), residues: 402 sheet: -0.87 (0.17), residues: 984 loop : -1.03 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 628 HIS 0.006 0.001 HIS G 100D PHE 0.013 0.001 PHE D 87 TYR 0.022 0.001 TYR L 49 ARG 0.005 0.000 ARG J 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 24) link_NAG-ASN : angle 3.88599 ( 72) link_ALPHA1-6 : bond 0.00467 ( 6) link_ALPHA1-6 : angle 1.75417 ( 18) link_BETA1-4 : bond 0.01017 ( 33) link_BETA1-4 : angle 3.16001 ( 99) link_ALPHA1-3 : bond 0.01214 ( 3) link_ALPHA1-3 : angle 1.61445 ( 9) hydrogen bonds : bond 0.03286 ( 578) hydrogen bonds : angle 5.20320 ( 1500) SS BOND : bond 0.00408 ( 36) SS BOND : angle 1.12202 ( 72) covalent geometry : bond 0.00375 (24549) covalent geometry : angle 0.60820 (33322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5832 Ramachandran restraints generated. 2916 Oldfield, 0 Emsley, 2916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 50 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7617 (pp) REVERT: B 626 MET cc_start: 0.7321 (mpp) cc_final: 0.6848 (mpp) REVERT: G 75 MET cc_start: 0.8539 (mtm) cc_final: 0.8284 (mtp) REVERT: H 96 TRP cc_start: 0.8152 (OUTLIER) cc_final: 0.7427 (m-10) REVERT: J 530 MET cc_start: 0.5876 (pmm) cc_final: 0.5545 (pmm) REVERT: K 89 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7812 (tmm) REVERT: L 96 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.7690 (m-10) outliers start: 46 outliers final: 41 residues processed: 92 average time/residue: 0.3389 time to fit residues: 55.4804 Evaluate side-chains 94 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 49 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 427 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 197 ASN Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 315 GLN Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 497 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 96 TRP Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 145 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.040018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.030400 restraints weight = 215916.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.031383 restraints weight = 118702.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.031565 restraints weight = 72039.819| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24651 Z= 0.223 Angle : 0.710 11.093 33592 Z= 0.338 Chirality : 0.046 0.429 3954 Planarity : 0.004 0.041 4158 Dihedral : 9.149 57.599 4557 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.97 % Allowed : 13.00 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: -1.04 (0.16), residues: 2916 helix: 1.88 (0.29), residues: 387 sheet: -0.97 (0.17), residues: 979 loop : -1.13 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 628 HIS 0.007 0.001 HIS G 100D PHE 0.017 0.002 PHE L 87 TYR 0.021 0.002 TYR L 49 ARG 0.004 0.000 ARG J 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 24) link_NAG-ASN : angle 3.87000 ( 72) link_ALPHA1-6 : bond 0.00539 ( 6) link_ALPHA1-6 : angle 2.03228 ( 18) link_BETA1-4 : bond 0.01035 ( 33) link_BETA1-4 : angle 3.22294 ( 99) link_ALPHA1-3 : bond 0.01160 ( 3) link_ALPHA1-3 : angle 1.70619 ( 9) hydrogen bonds : bond 0.03672 ( 578) hydrogen bonds : angle 5.40208 ( 1500) SS BOND : bond 0.00478 ( 36) SS BOND : angle 1.24307 ( 72) covalent geometry : bond 0.00504 (24549) covalent geometry : angle 0.66222 (33322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6832.28 seconds wall clock time: 123 minutes 4.97 seconds (7384.97 seconds total)