Starting phenix.real_space_refine on Fri Mar 6 05:39:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9t_25767/03_2026/7t9t_25767_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9t_25767/03_2026/7t9t_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t9t_25767/03_2026/7t9t_25767_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9t_25767/03_2026/7t9t_25767_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t9t_25767/03_2026/7t9t_25767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9t_25767/03_2026/7t9t_25767.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.29, per 1000 atoms: 0.22 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: 1.99 Conformation dependent library (CDL) restraints added in 787.8 milliseconds 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: 0.86 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: 3.92 Time building geometry restraints manager: 2.57 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 602)) selection = (chain 'E' and (resid 32 through 309 or resid 314 through 602)) selection = (chain 'I' and (resid 32 through 144 or resid 157 through 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.540 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- 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 : 2.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.005 0.001 ARG C 66 TYR 0.019 0.001 TYR D 91 PHE 0.022 0.002 PHE A 210 TRP 0.027 0.001 TRP E 427 HIS 0.011 0.001 HIS K 100D Details of bonding type rmsd covalent geometry : bond 0.00465 (24549) covalent geometry : angle 0.82702 (33322) SS BOND : bond 0.00412 ( 36) SS BOND : angle 1.41961 ( 72) hydrogen bonds : bond 0.20933 ( 578) hydrogen bonds : angle 8.64478 ( 1500) link_ALPHA1-3 : bond 0.01477 ( 3) link_ALPHA1-3 : angle 5.69527 ( 9) 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_NAG-ASN : bond 0.00826 ( 24) link_NAG-ASN : angle 3.78191 ( 72) *********************** 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 : 0.843 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: 0.1629 time to fit residues: 19.5739 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 : 0.911 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 D 38 HIS D 137 ASN E 133 ASN E 246 GLN E 476 ASN H 137 ASN K 164 HIS L 32 ASN L 92 ASN L 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.046996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.037481 restraints weight = 203861.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.038443 restraints weight = 100723.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.039060 restraints weight = 66191.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.039402 restraints weight = 51486.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.039633 restraints weight = 44786.960| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24651 Z= 0.134 Angle : 0.705 12.298 33592 Z= 0.330 Chirality : 0.047 0.431 3954 Planarity : 0.004 0.045 4158 Dihedral : 11.310 80.861 4557 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 94.99 % Rotamer: Outliers : 0.19 % Allowed : 3.63 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2916 helix: 1.49 (0.28), residues: 390 sheet: -0.82 (0.16), residues: 987 loop : -0.92 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 588 TYR 0.022 0.001 TYR H 49 PHE 0.031 0.001 PHE F 519 TRP 0.022 0.001 TRP I 427 HIS 0.005 0.001 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00284 (24549) covalent geometry : angle 0.64010 (33322) SS BOND : bond 0.00341 ( 36) SS BOND : angle 1.12548 ( 72) hydrogen bonds : bond 0.03438 ( 578) hydrogen bonds : angle 5.84574 ( 1500) link_ALPHA1-3 : bond 0.01438 ( 3) link_ALPHA1-3 : angle 2.86450 ( 9) link_ALPHA1-6 : bond 0.01091 ( 6) link_ALPHA1-6 : angle 1.63359 ( 18) link_BETA1-4 : bond 0.01052 ( 33) link_BETA1-4 : angle 3.94212 ( 99) link_NAG-ASN : bond 0.00615 ( 24) link_NAG-ASN : angle 4.23976 ( 72) *********************** 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 61 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 473 MET cc_start: 0.9172 (tpp) cc_final: 0.8760 (tpp) REVERT: H 49 TYR cc_start: 0.8342 (p90) cc_final: 0.8141 (p90) REVERT: K 89 MET cc_start: 0.7407 (ppp) cc_final: 0.7161 (ppp) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.1459 time to fit residues: 15.0227 Evaluate side-chains 57 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 152 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 chunk 246 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 chunk 280 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 195 ASN A 422 GLN B 625 ASN E 216 HIS E 246 GLN F 625 ASN F 651 ASN G 164 HIS H 32 ASN H 38 HIS H 92 ASN ** I 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 357 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.033243 restraints weight = 204965.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.034141 restraints weight = 102315.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.034690 restraints weight = 68341.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.035022 restraints weight = 54301.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.035209 restraints weight = 47549.154| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24651 Z= 0.228 Angle : 0.750 11.742 33592 Z= 0.360 Chirality : 0.048 0.461 3954 Planarity : 0.005 0.044 4158 Dihedral : 10.255 77.772 4557 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 0.85 % Allowed : 6.60 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.16), residues: 2916 helix: 1.64 (0.28), residues: 384 sheet: -0.89 (0.16), residues: 1001 loop : -0.99 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 588 TYR 0.028 0.002 TYR L 49 PHE 0.022 0.002 PHE L 87 TRP 0.030 0.002 TRP A 427 HIS 0.010 0.002 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00519 (24549) covalent geometry : angle 0.69933 (33322) SS BOND : bond 0.00544 ( 36) SS BOND : angle 1.30555 ( 72) hydrogen bonds : bond 0.04533 ( 578) hydrogen bonds : angle 5.73568 ( 1500) link_ALPHA1-3 : bond 0.00993 ( 3) link_ALPHA1-3 : angle 1.89045 ( 9) link_ALPHA1-6 : bond 0.00552 ( 6) link_ALPHA1-6 : angle 1.67636 ( 18) link_BETA1-4 : bond 0.01040 ( 33) link_BETA1-4 : angle 3.61658 ( 99) link_NAG-ASN : bond 0.00699 ( 24) link_NAG-ASN : angle 3.94741 ( 72) *********************** 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 75 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7285 (tpp) cc_final: 0.6949 (tmm) REVERT: E 473 MET cc_start: 0.9277 (tpp) cc_final: 0.8957 (tpp) REVERT: I 426 MET cc_start: 0.7070 (tpp) cc_final: 0.6385 (tmm) REVERT: L 96 TRP cc_start: 0.8352 (OUTLIER) cc_final: 0.7067 (m-10) outliers start: 22 outliers final: 10 residues processed: 71 average time/residue: 0.1371 time to fit residues: 17.6369 Evaluate side-chains 63 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 333 ILE Chi-restraints excluded: chain C residue 51 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 245 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 105 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** A 321AGLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 321AGLN E 422 GLN G 6 GLN I 216 HIS I 280 ASN I 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.041506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.031630 restraints weight = 213639.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.032473 restraints weight = 109553.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.033003 restraints weight = 74740.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.033301 restraints weight = 60008.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.033462 restraints weight = 53178.934| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4203 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= 0.229 Angle : 0.739 11.793 33592 Z= 0.356 Chirality : 0.048 0.463 3954 Planarity : 0.005 0.046 4158 Dihedral : 9.847 67.965 4557 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.20 % Rotamer: Outliers : 1.85 % Allowed : 8.10 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.16), residues: 2916 helix: 1.54 (0.29), residues: 396 sheet: -1.03 (0.16), residues: 987 loop : -1.08 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 3 TYR 0.023 0.002 TYR K 50 PHE 0.019 0.002 PHE L 87 TRP 0.026 0.002 TRP J 623 HIS 0.008 0.001 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00521 (24549) covalent geometry : angle 0.68535 (33322) SS BOND : bond 0.00501 ( 36) SS BOND : angle 1.26090 ( 72) hydrogen bonds : bond 0.03955 ( 578) hydrogen bonds : angle 5.62774 ( 1500) link_ALPHA1-3 : bond 0.01261 ( 3) link_ALPHA1-3 : angle 1.97467 ( 9) link_ALPHA1-6 : bond 0.00678 ( 6) link_ALPHA1-6 : angle 2.08629 ( 18) link_BETA1-4 : bond 0.00941 ( 33) link_BETA1-4 : angle 3.56361 ( 99) link_NAG-ASN : bond 0.00632 ( 24) link_NAG-ASN : angle 4.12868 ( 72) *********************** 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 100 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 52 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7570 (mmt) cc_final: 0.7316 (mmp) REVERT: G 75 MET cc_start: 0.8429 (mtm) cc_final: 0.8200 (mtp) REVERT: H 96 TRP cc_start: 0.8065 (OUTLIER) cc_final: 0.7118 (m100) REVERT: J 626 MET cc_start: 0.7124 (ptm) cc_final: 0.6863 (ptm) REVERT: L 96 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.7191 (m-10) outliers start: 48 outliers final: 21 residues processed: 92 average time/residue: 0.1281 time to fit residues: 21.2146 Evaluate side-chains 73 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 261 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain H residue 22 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 I residue 455 THR 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 75 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 240 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 97 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 263 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- 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 133 ASN ** 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 = 0.3432 r_free = 0.3432 target = 0.041865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.032007 restraints weight = 211748.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032868 restraints weight = 107227.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033396 restraints weight = 72918.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.033691 restraints weight = 58528.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.033875 restraints weight = 52006.931| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24651 Z= 0.125 Angle : 0.640 11.782 33592 Z= 0.302 Chirality : 0.045 0.416 3954 Planarity : 0.004 0.039 4158 Dihedral : 9.349 67.265 4557 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.23 % Allowed : 9.45 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2916 helix: 1.68 (0.28), residues: 402 sheet: -0.84 (0.16), residues: 992 loop : -0.90 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 298 TYR 0.025 0.001 TYR L 49 PHE 0.011 0.001 PHE F 519 TRP 0.013 0.001 TRP B 628 HIS 0.008 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00276 (24549) covalent geometry : angle 0.58578 (33322) SS BOND : bond 0.00527 ( 36) SS BOND : angle 1.06101 ( 72) hydrogen bonds : bond 0.03298 ( 578) hydrogen bonds : angle 5.31702 ( 1500) link_ALPHA1-3 : bond 0.01247 ( 3) link_ALPHA1-3 : angle 1.49840 ( 9) link_ALPHA1-6 : bond 0.00593 ( 6) link_ALPHA1-6 : angle 1.64248 ( 18) link_BETA1-4 : bond 0.01023 ( 33) link_BETA1-4 : angle 3.28347 ( 99) link_NAG-ASN : bond 0.00666 ( 24) link_NAG-ASN : angle 3.91150 ( 72) *********************** 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 82 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 50 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7622 (mmt) cc_final: 0.7242 (mmp) REVERT: E 473 MET cc_start: 0.9042 (tpp) cc_final: 0.8783 (tpp) REVERT: G 75 MET cc_start: 0.8440 (mtm) cc_final: 0.8210 (mtp) REVERT: H 96 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7024 (m100) REVERT: J 626 MET cc_start: 0.7484 (ptm) cc_final: 0.7036 (ptm) REVERT: L 96 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7201 (m-10) outliers start: 32 outliers final: 22 residues processed: 75 average time/residue: 0.1310 time to fit residues: 17.6362 Evaluate side-chains 74 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 B residue 529 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 96 TRP Chi-restraints excluded: chain I residue 100 MET 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 51 ILE Chi-restraints excluded: chain K residue 89 MET Chi-restraints excluded: chain K residue 197 ASN Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 205 optimal weight: 20.0000 chunk 288 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** H 77 ASN ** 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 = 0.3394 r_free = 0.3394 target = 0.040832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.030989 restraints weight = 212721.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.031820 restraints weight = 108577.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.032329 restraints weight = 74166.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.032625 restraints weight = 59751.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.032779 restraints weight = 52916.610| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24651 Z= 0.222 Angle : 0.711 12.806 33592 Z= 0.338 Chirality : 0.047 0.437 3954 Planarity : 0.005 0.055 4158 Dihedral : 9.501 64.724 4557 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.93 % Allowed : 9.57 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2916 helix: 1.77 (0.29), residues: 396 sheet: -0.97 (0.17), residues: 979 loop : -1.03 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 273 TYR 0.024 0.002 TYR L 49 PHE 0.020 0.002 PHE D 87 TRP 0.014 0.002 TRP J 631 HIS 0.009 0.002 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00503 (24549) covalent geometry : angle 0.65894 (33322) SS BOND : bond 0.00590 ( 36) SS BOND : angle 1.35977 ( 72) hydrogen bonds : bond 0.03790 ( 578) hydrogen bonds : angle 5.48050 ( 1500) link_ALPHA1-3 : bond 0.01198 ( 3) link_ALPHA1-3 : angle 1.63894 ( 9) link_ALPHA1-6 : bond 0.00541 ( 6) link_ALPHA1-6 : angle 2.05153 ( 18) link_BETA1-4 : bond 0.01065 ( 33) link_BETA1-4 : angle 3.36279 ( 99) link_NAG-ASN : bond 0.00617 ( 24) link_NAG-ASN : angle 4.04711 ( 72) *********************** 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 99 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 49 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 529 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6931 (t) REVERT: B 626 MET cc_start: 0.7655 (mmt) cc_final: 0.7314 (mmp) REVERT: E 473 MET cc_start: 0.9024 (tpp) cc_final: 0.8798 (tpp) REVERT: G 75 MET cc_start: 0.8460 (mtm) cc_final: 0.8097 (mtp) REVERT: H 96 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7173 (m-10) REVERT: J 626 MET cc_start: 0.7511 (ptm) cc_final: 0.7000 (ptm) REVERT: L 96 TRP cc_start: 0.8341 (OUTLIER) cc_final: 0.7290 (m-10) outliers start: 50 outliers final: 31 residues processed: 92 average time/residue: 0.1278 time to fit residues: 21.1527 Evaluate side-chains 82 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 48 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 197 ASN 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 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 197 ASN Chi-restraints excluded: chain E residue 100 MET 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 G residue 51 ILE 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 I residue 197 ASN Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 427 TRP Chi-restraints excluded: chain I residue 455 THR 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 K residue 197 ASN Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 96 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 88 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 overall best weight: 3.6986 ------------------------------------------------------------------------------- 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** ** 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 = 0.040933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.031164 restraints weight = 210150.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.032002 restraints weight = 106476.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032525 restraints weight = 72480.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032794 restraints weight = 58099.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.032983 restraints weight = 51711.874| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24651 Z= 0.168 Angle : 0.665 11.926 33592 Z= 0.314 Chirality : 0.045 0.421 3954 Planarity : 0.004 0.038 4158 Dihedral : 9.268 63.444 4557 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.70 % Allowed : 10.30 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2916 helix: 1.86 (0.29), residues: 396 sheet: -0.92 (0.17), residues: 997 loop : -0.96 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 108 TYR 0.023 0.001 TYR L 49 PHE 0.014 0.001 PHE L 87 TRP 0.033 0.001 TRP B 628 HIS 0.030 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00382 (24549) covalent geometry : angle 0.61025 (33322) SS BOND : bond 0.00540 ( 36) SS BOND : angle 1.35338 ( 72) hydrogen bonds : bond 0.03405 ( 578) hydrogen bonds : angle 5.31929 ( 1500) link_ALPHA1-3 : bond 0.01238 ( 3) link_ALPHA1-3 : angle 1.51396 ( 9) link_ALPHA1-6 : bond 0.00539 ( 6) link_ALPHA1-6 : angle 1.85670 ( 18) link_BETA1-4 : bond 0.01004 ( 33) link_BETA1-4 : angle 3.26214 ( 99) link_NAG-ASN : bond 0.00565 ( 24) link_NAG-ASN : angle 4.03008 ( 72) *********************** 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 92 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 48 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.7493 (mmt) cc_final: 0.7190 (mmp) REVERT: G 75 MET cc_start: 0.8448 (mtm) cc_final: 0.8096 (mtp) REVERT: G 89 MET cc_start: 0.7949 (ttt) cc_final: 0.7591 (ttm) REVERT: H 96 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7132 (m100) REVERT: I 426 MET cc_start: 0.7174 (tpp) cc_final: 0.5528 (tmm) REVERT: J 626 MET cc_start: 0.7636 (ptm) cc_final: 0.7173 (ptm) REVERT: L 96 TRP cc_start: 0.8281 (OUTLIER) cc_final: 0.7331 (m-10) outliers start: 44 outliers final: 32 residues processed: 87 average time/residue: 0.1253 time to fit residues: 19.4633 Evaluate side-chains 82 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 48 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 455 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain E residue 100 MET 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 583 VAL Chi-restraints excluded: chain G residue 51 ILE 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 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 427 TRP 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 96 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 65 optimal weight: 2.9990 chunk 169 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 254 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.040464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030692 restraints weight = 212614.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.031521 restraints weight = 108473.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.032024 restraints weight = 73996.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.032293 restraints weight = 59708.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.032479 restraints weight = 53192.462| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24651 Z= 0.212 Angle : 0.697 11.446 33592 Z= 0.331 Chirality : 0.046 0.431 3954 Planarity : 0.004 0.044 4158 Dihedral : 9.338 61.237 4557 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 1.93 % Allowed : 10.57 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2916 helix: 1.84 (0.29), residues: 396 sheet: -0.96 (0.17), residues: 977 loop : -1.02 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 273 TYR 0.022 0.002 TYR L 49 PHE 0.019 0.002 PHE D 87 TRP 0.027 0.002 TRP B 628 HIS 0.008 0.002 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00482 (24549) covalent geometry : angle 0.64663 (33322) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.35511 ( 72) hydrogen bonds : bond 0.03599 ( 578) hydrogen bonds : angle 5.39557 ( 1500) link_ALPHA1-3 : bond 0.01228 ( 3) link_ALPHA1-3 : angle 1.58080 ( 9) link_ALPHA1-6 : bond 0.00553 ( 6) link_ALPHA1-6 : angle 2.02989 ( 18) link_BETA1-4 : bond 0.01041 ( 33) link_BETA1-4 : angle 3.26227 ( 99) link_NAG-ASN : bond 0.00579 ( 24) link_NAG-ASN : angle 3.94043 ( 72) *********************** 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 98 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 48 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 MET cc_start: 0.8487 (mtm) cc_final: 0.8212 (mtp) REVERT: G 89 MET cc_start: 0.7830 (ttt) cc_final: 0.7387 (ttm) REVERT: H 96 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.7415 (m-10) REVERT: J 626 MET cc_start: 0.7597 (ptm) cc_final: 0.7080 (ptm) REVERT: L 96 TRP cc_start: 0.8361 (OUTLIER) cc_final: 0.7429 (m-10) outliers start: 50 outliers final: 43 residues processed: 90 average time/residue: 0.1304 time to fit residues: 21.1862 Evaluate side-chains 93 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 48 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 196 CYS Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 242 VAL 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 455 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 93 VAL 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 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 583 VAL Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 51 ILE 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 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 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 96 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 260 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 230 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 176 optimal weight: 0.0470 overall best weight: 2.7682 ------------------------------------------------------------------------------- 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 H 32 ASN ** I 133 ASN ** 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 = 0.3397 r_free = 0.3397 target = 0.040787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.031198 restraints weight = 213831.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.032214 restraints weight = 117722.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.032307 restraints weight = 70006.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032417 restraints weight = 68471.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032469 restraints weight = 62835.835| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24651 Z= 0.138 Angle : 0.648 11.841 33592 Z= 0.304 Chirality : 0.045 0.410 3954 Planarity : 0.004 0.038 4158 Dihedral : 9.035 59.814 4557 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.66 % Allowed : 11.03 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2916 helix: 1.91 (0.29), residues: 396 sheet: -0.87 (0.17), residues: 997 loop : -0.92 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 467 TYR 0.024 0.001 TYR L 49 PHE 0.011 0.001 PHE L 87 TRP 0.021 0.001 TRP B 628 HIS 0.024 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00308 (24549) covalent geometry : angle 0.59546 (33322) SS BOND : bond 0.00404 ( 36) SS BOND : angle 1.19880 ( 72) hydrogen bonds : bond 0.03217 ( 578) hydrogen bonds : angle 5.17172 ( 1500) link_ALPHA1-3 : bond 0.01208 ( 3) link_ALPHA1-3 : angle 1.47003 ( 9) link_ALPHA1-6 : bond 0.00563 ( 6) link_ALPHA1-6 : angle 1.74708 ( 18) link_BETA1-4 : bond 0.01001 ( 33) link_BETA1-4 : angle 3.17955 ( 99) link_NAG-ASN : bond 0.00586 ( 24) link_NAG-ASN : angle 3.92466 ( 72) *********************** 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 92 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 49 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 MET cc_start: 0.8531 (mtm) cc_final: 0.8183 (mtp) REVERT: G 89 MET cc_start: 0.7888 (ttt) cc_final: 0.7553 (ttm) REVERT: H 96 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.7143 (m100) REVERT: J 626 MET cc_start: 0.7638 (ptm) cc_final: 0.7055 (ptm) REVERT: L 96 TRP cc_start: 0.8294 (OUTLIER) cc_final: 0.7424 (m-10) outliers start: 43 outliers final: 36 residues processed: 88 average time/residue: 0.1336 time to fit residues: 21.1834 Evaluate side-chains 86 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 48 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 260 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 576 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 VAL 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 196 CYS 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 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 583 VAL 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 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 427 TRP 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 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 285 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 225 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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** D 77 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 461 ASN K 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.040334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.030728 restraints weight = 215460.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.031862 restraints weight = 120521.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.031863 restraints weight = 69428.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.031961 restraints weight = 68442.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.032014 restraints weight = 63677.624| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24651 Z= 0.205 Angle : 0.688 11.774 33592 Z= 0.326 Chirality : 0.046 0.428 3954 Planarity : 0.004 0.043 4158 Dihedral : 9.103 58.137 4557 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.66 % Allowed : 10.92 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2916 helix: 1.82 (0.29), residues: 402 sheet: -0.90 (0.17), residues: 990 loop : -1.00 (0.16), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 588 TYR 0.023 0.001 TYR L 49 PHE 0.018 0.002 PHE D 87 TRP 0.018 0.002 TRP A 427 HIS 0.007 0.001 HIS G 100D Details of bonding type rmsd covalent geometry : bond 0.00464 (24549) covalent geometry : angle 0.63869 (33322) SS BOND : bond 0.00467 ( 36) SS BOND : angle 1.25998 ( 72) hydrogen bonds : bond 0.03507 ( 578) hydrogen bonds : angle 5.30232 ( 1500) link_ALPHA1-3 : bond 0.01190 ( 3) link_ALPHA1-3 : angle 1.55840 ( 9) link_ALPHA1-6 : bond 0.00508 ( 6) link_ALPHA1-6 : angle 1.98673 ( 18) link_BETA1-4 : bond 0.01034 ( 33) link_BETA1-4 : angle 3.20371 ( 99) link_NAG-ASN : bond 0.00558 ( 24) link_NAG-ASN : angle 3.91108 ( 72) ********************** 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 91 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 48 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 MET cc_start: 0.8969 (ttp) cc_final: 0.8697 (ptm) REVERT: G 75 MET cc_start: 0.8529 (mtm) cc_final: 0.8288 (mtp) REVERT: G 89 MET cc_start: 0.7785 (ttt) cc_final: 0.7576 (ttm) REVERT: H 96 TRP cc_start: 0.8143 (OUTLIER) cc_final: 0.7454 (m-10) REVERT: J 626 MET cc_start: 0.7636 (ptm) cc_final: 0.7081 (ptm) REVERT: L 96 TRP cc_start: 0.8413 (OUTLIER) cc_final: 0.7527 (m-10) outliers start: 43 outliers final: 40 residues processed: 87 average time/residue: 0.1352 time to fit residues: 21.0981 Evaluate side-chains 90 residues out of total 2595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 48 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS 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 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 576 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 VAL 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 196 CYS 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 434 MET Chi-restraints excluded: chain E residue 482 TYR Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain G residue 51 ILE 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 260 LEU Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 427 TRP 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 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 148 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 267 optimal weight: 30.0000 chunk 111 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100DHIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.040251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.030651 restraints weight = 214742.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.031781 restraints weight = 120250.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.031772 restraints weight = 69557.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.031884 restraints weight = 68482.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.031927 restraints weight = 63518.582| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 24651 Z= 0.213 Angle : 0.692 11.582 33592 Z= 0.328 Chirality : 0.046 0.424 3954 Planarity : 0.004 0.039 4158 Dihedral : 9.106 57.549 4557 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.74 % Allowed : 10.84 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2916 helix: 1.87 (0.29), residues: 399 sheet: -0.91 (0.17), residues: 990 loop : -1.00 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 588 TYR 0.023 0.002 TYR L 49 PHE 0.018 0.002 PHE D 87 TRP 0.016 0.002 TRP A 427 HIS 0.022 0.002 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00486 (24549) covalent geometry : angle 0.64270 (33322) SS BOND : bond 0.00467 ( 36) SS BOND : angle 1.26599 ( 72) hydrogen bonds : bond 0.03528 ( 578) hydrogen bonds : angle 5.32247 ( 1500) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 1.52637 ( 9) link_ALPHA1-6 : bond 0.00501 ( 6) link_ALPHA1-6 : angle 1.99164 ( 18) link_BETA1-4 : bond 0.01018 ( 33) link_BETA1-4 : angle 3.19329 ( 99) link_NAG-ASN : bond 0.00542 ( 24) link_NAG-ASN : angle 3.91062 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.13 seconds wall clock time: 60 minutes 5.19 seconds (3605.19 seconds total)