Starting phenix.real_space_refine on Thu Mar 5 05:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u0n_20608/03_2026/6u0n_20608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u0n_20608/03_2026/6u0n_20608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u0n_20608/03_2026/6u0n_20608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u0n_20608/03_2026/6u0n_20608.map" model { file = "/net/cci-nas-00/data/ceres_data/6u0n_20608/03_2026/6u0n_20608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u0n_20608/03_2026/6u0n_20608_neut.cif" } resolution = 3.5 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= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 12153 2.51 5 N 3304 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19322 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2774 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 342} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 10, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "C" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2724 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 21, 'TRANS': 341} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 13, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 775 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 967 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 28 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 985 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 4, 'TYS:plan-2': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 786 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 110, 780 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 790 Chain: "P" Number of atoms: 987 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 132, 981 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 997 Chain: "Q" Number of atoms: 792 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 110, 786 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 102} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 796 Chain: "X" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 991 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 22 Chain: "Y" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 940 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "Z" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 927 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 55 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} 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: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASER L 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER L 70 " occ=0.50 residue: pdb=" N ACYS P 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS P 92 " occ=0.50 residue: pdb=" N ASER Q 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER Q 70 " occ=0.50 Time building chain proxies: 5.09, per 1000 atoms: 0.26 Number of scatterers: 19322 At special positions: 0 Unit cell: (146.923, 149.037, 167.006, 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 118 16.00 O 3747 8.00 N 3304 7.00 C 12153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS X 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS Y 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS Z 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 84 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG ACYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG BCYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 598 " - pdb=" SG CYS X 604 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 598 " - pdb=" SG CYS Z 604 " distance=2.02 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 ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 603 " - " ASN A 355 " " NAG A 604 " - " ASN A 339 " " NAG A 605 " - " ASN A 363 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 88 " " NAG A 610 " - " ASN A 234 " " NAG B 601 " - " ASN B 448 " " NAG B 602 " - " ASN B 386 " " NAG B 603 " - " ASN B 88 " " NAG B 604 " - " ASN B 392 " " NAG B 610 " - " ASN B 276 " " NAG B 611 " - " ASN B 295 " " NAG B 612 " - " ASN B 332 " " NAG B 613 " - " ASN B 363 " " NAG B 614 " - " ASN B 339 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 363 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 448 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 88 " " NAG C 614 " - " ASN C 392 " " NAG G 1 " - " ASN A 276 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN B 262 " " NAG O 1 " - " ASN C 262 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 982.3 milliseconds 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4586 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 51 sheets defined 15.5% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.596A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.720A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.586A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.688A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.812A pdb=" N TRP B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 removed outlier: 3.929A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 removed outlier: 3.503A pdb=" N ASN B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'C' and resid 101 through 109 removed outlier: 4.272A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 353 removed outlier: 4.031A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.502A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.738A pdb=" N TRP D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 removed outlier: 3.613A pdb=" N LEU E 61 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP E 62 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 64 removed outlier: 3.573A pdb=" N TRP F 62 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.204A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 96 through 100A removed outlier: 4.257A pdb=" N GLY H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA H 100A" --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 98 through 100A Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.528A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 100 removed outlier: 4.305A pdb=" N GLY P 99 " --> pdb=" O SER P 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.884A pdb=" N ASP Q 82 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 516 through 523 removed outlier: 3.640A pdb=" N LEU X 520 " --> pdb=" O GLY X 516 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU X 523 " --> pdb=" O PHE X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 535 Processing helix chain 'X' and resid 536 through 545 removed outlier: 3.843A pdb=" N ARG X 542 " --> pdb=" O THR X 538 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN X 543 " --> pdb=" O VAL X 539 " (cutoff:3.500A) Processing helix chain 'X' and resid 569 through 574 Processing helix chain 'X' and resid 578 through 594 removed outlier: 3.564A pdb=" N TYR X 586 " --> pdb=" O ALA X 582 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG X 588 " --> pdb=" O GLU X 584 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP X 589 " --> pdb=" O ARG X 585 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN X 590 " --> pdb=" O TYR X 586 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU X 592 " --> pdb=" O ARG X 588 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 622 Processing helix chain 'X' and resid 628 through 633 removed outlier: 4.005A pdb=" N ASP X 632 " --> pdb=" O TRP X 628 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS X 633 " --> pdb=" O LEU X 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 628 through 633' Processing helix chain 'X' and resid 641 through 649 removed outlier: 3.595A pdb=" N GLU X 647 " --> pdb=" O TYR X 643 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU X 648 " --> pdb=" O GLY X 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 529 through 537 removed outlier: 3.706A pdb=" N SER Y 534 " --> pdb=" O MET Y 530 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET Y 535 " --> pdb=" O GLY Y 531 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Y 536 " --> pdb=" O ALA Y 532 " (cutoff:3.500A) Processing helix chain 'Y' and resid 538 through 543 removed outlier: 4.368A pdb=" N ASN Y 543 " --> pdb=" O VAL Y 539 " (cutoff:3.500A) Processing helix chain 'Y' and resid 569 through 574 Processing helix chain 'Y' and resid 576 through 588 removed outlier: 3.504A pdb=" N LEU Y 581 " --> pdb=" O GLN Y 577 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA Y 582 " --> pdb=" O ALA Y 578 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Y 583 " --> pdb=" O ARG Y 579 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR Y 586 " --> pdb=" O ALA Y 582 " (cutoff:3.500A) Processing helix chain 'Y' and resid 589 through 596 removed outlier: 3.532A pdb=" N LEU Y 593 " --> pdb=" O ASP Y 589 " (cutoff:3.500A) Processing helix chain 'Y' and resid 620 through 625 removed outlier: 3.651A pdb=" N ASP Y 624 " --> pdb=" O SER Y 620 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 635 removed outlier: 3.549A pdb=" N GLU Y 634 " --> pdb=" O GLN Y 630 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE Y 635 " --> pdb=" O TRP Y 631 " (cutoff:3.500A) Processing helix chain 'Y' and resid 638 through 658 removed outlier: 3.638A pdb=" N GLY Y 644 " --> pdb=" O GLN Y 640 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU Y 645 " --> pdb=" O ILE Y 641 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Y 646 " --> pdb=" O ILE Y 642 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Y 648 " --> pdb=" O GLY Y 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Y 650 " --> pdb=" O LEU Y 646 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Y 658 " --> pdb=" O GLU Y 654 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 534 Processing helix chain 'Z' and resid 563 through 575 removed outlier: 3.746A pdb=" N LEU Z 568 " --> pdb=" O HIS Z 564 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 569 " --> pdb=" O LEU Z 565 " (cutoff:3.500A) Processing helix chain 'Z' and resid 576 through 596 removed outlier: 3.809A pdb=" N LEU Z 581 " --> pdb=" O GLN Z 577 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR Z 586 " --> pdb=" O ALA Z 582 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 591 " --> pdb=" O LEU Z 587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU Z 592 " --> pdb=" O ARG Z 588 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP Z 596 " --> pdb=" O LEU Z 592 " (cutoff:3.500A) Processing helix chain 'Z' and resid 627 through 635 Processing helix chain 'Z' and resid 638 through 654 removed outlier: 4.023A pdb=" N GLY Z 644 " --> pdb=" O GLN Z 640 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU Z 645 " --> pdb=" O ILE Z 641 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN Z 650 " --> pdb=" O LEU Z 646 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN Z 653 " --> pdb=" O SER Z 649 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 498 through 499 removed outlier: 4.330A pdb=" N VAL A 36 " --> pdb=" O THR X 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.760A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.663A pdb=" N GLN A 432 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.125A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 360 Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 removed outlier: 11.257A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.238A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.036A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS A 296 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 445 " --> pdb=" O CYS A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 414 Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.860A pdb=" N PHE B 53 " --> pdb=" O CYS B 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.591A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 196 through 202 removed outlier: 3.571A pdb=" N THR B 123 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 121 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 120 " --> pdb=" O MET B 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 432 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB4, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.713A pdb=" N ARG B 273 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 467 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 466 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 413 through 418 removed outlier: 3.500A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 413 through 418 removed outlier: 3.500A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 497 removed outlier: 5.733A pdb=" N VAL C 36 " --> pdb=" O THR Z 606 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR Z 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.508A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 83 through 86 removed outlier: 4.874A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.679A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.777A pdb=" N GLN C 432 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'C' and resid 414 through 417 removed outlier: 3.844A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG C 298 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.601A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.801A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 2 through 5 removed outlier: 4.230A pdb=" N LYS D 2 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 94 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 28 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN D 40 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AD1, first strand: chain 'E' and resid 2 through 5 removed outlier: 6.497A pdb=" N LYS E 2 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N LEU E 96 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 4 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS E 84 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU E 85 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS E 27 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP E 28 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 37 " --> pdb=" O TRP E 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 40 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AD3, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.634A pdb=" N LYS F 2 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU F 96 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL F 4 " --> pdb=" O LEU F 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'F' and resid 16 through 17 removed outlier: 3.858A pdb=" N CYS F 16 " --> pdb=" O PHE F 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.766A pdb=" N GLU H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 110 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.515A pdb=" N VAL H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.572A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.512A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY I 50 " --> pdb=" O HIS I 58 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.745A pdb=" N VAL I 102 " --> pdb=" O SER I 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.250A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'J' and resid 19 through 23 removed outlier: 3.580A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE J 75 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.705A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR J 90 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.971A pdb=" N ALA L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AE8, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.752A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.752A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR L 86 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 5 through 6 removed outlier: 3.631A pdb=" N VAL P 20 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 5 through 6 removed outlier: 3.631A pdb=" N VAL P 20 " --> pdb=" O LEU P 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR P 77 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.925A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU P 46 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 23 through 24 Processing sheet with id=AF5, first strand: chain 'Q' and resid 45 through 48 removed outlier: 7.267A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR Q 36 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 45 through 48 removed outlier: 7.267A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR Q 36 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1259 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: 3.55 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6124 1.34 - 1.46: 4779 1.46 - 1.58: 8670 1.58 - 1.70: 6 1.70 - 1.82: 145 Bond restraints: 19724 Sorted by residual: bond pdb=" O3 TYS P 100F" pdb=" S TYS P 100F" ideal model delta sigma weight residual 1.458 1.633 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" O1 TYS I 100F" pdb=" S TYS I 100F" ideal model delta sigma weight residual 1.462 1.634 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" O2 TYS I 100I" pdb=" S TYS I 100I" ideal model delta sigma weight residual 1.461 1.632 -0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" O1 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" O3 TYS P 100I" pdb=" S TYS P 100I" ideal model delta sigma weight residual 1.458 1.627 -0.169 2.00e-02 2.50e+03 7.16e+01 ... (remaining 19719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 25831 2.10 - 4.20: 866 4.20 - 6.30: 117 6.30 - 8.39: 31 8.39 - 10.49: 13 Bond angle restraints: 26858 Sorted by residual: angle pdb=" C GLU J 50 " pdb=" N ASN J 51 " pdb=" CA ASN J 51 " ideal model delta sigma weight residual 121.54 131.04 -9.50 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLU Q 50 " pdb=" N ASN Q 51 " pdb=" CA ASN Q 51 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLU L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N SER C 56 " pdb=" CA SER C 56 " pdb=" C SER C 56 " ideal model delta sigma weight residual 111.02 116.22 -5.20 1.25e+00 6.40e-01 1.73e+01 angle pdb=" C LYS C 335 " pdb=" N ALA C 336 " pdb=" CA ALA C 336 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 26853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 11314 21.85 - 43.70: 786 43.70 - 65.54: 87 65.54 - 87.39: 38 87.39 - 109.24: 14 Dihedral angle restraints: 12239 sinusoidal: 5119 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS X 605 " pdb=" CB CYS X 605 " ideal model delta sinusoidal sigma weight residual -86.00 -12.87 -73.13 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS Z 605 " pdb=" CB CYS Z 605 " ideal model delta sinusoidal sigma weight residual -86.00 -18.96 -67.04 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS B 378 " pdb=" SG CYS B 378 " pdb=" SG CYS B 445 " pdb=" CB CYS B 445 " ideal model delta sinusoidal sigma weight residual -86.00 -139.10 53.10 1 1.00e+01 1.00e-02 3.84e+01 ... (remaining 12236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3142 0.141 - 0.282: 48 0.282 - 0.423: 5 0.423 - 0.564: 1 0.564 - 0.705: 2 Chirality restraints: 3198 Sorted by residual: chirality pdb=" C1 NAG B 613 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 613 " pdb=" O5 NAG B 613 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" C1 NAG C 609 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG C 609 " pdb=" O5 NAG C 609 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 88 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 3195 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 448 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C ASN B 448 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN B 448 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 449 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 75 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C 76 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 243 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C SER A 243 " 0.045 2.00e-02 2.50e+03 pdb=" O SER A 243 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 244 " -0.015 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4080 2.77 - 3.31: 16535 3.31 - 3.84: 31150 3.84 - 4.37: 35387 4.37 - 4.90: 62412 Nonbonded interactions: 149564 Sorted by model distance: nonbonded pdb=" O LYS B 229 " pdb=" OG SER B 241 " model vdw 2.242 3.040 nonbonded pdb=" O SER C 56 " pdb=" OG SER C 56 " model vdw 2.283 3.040 nonbonded pdb=" O LEU B 369 " pdb=" OG1 THR B 373 " model vdw 2.306 3.040 nonbonded pdb=" O SER E 23 " pdb=" OG SER E 23 " model vdw 2.326 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" O ALA A 497 " model vdw 2.328 3.040 ... (remaining 149559 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 35 through 46 or (resid 47 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 77 or (r \ esid 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or \ (resid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 t \ hrough 91 or (resid 92 and (name N or name CA or name C or name O or name CB )) \ or resid 93 through 124 or (resid 125 and (name N or name CA or name C or name O \ or name CB )) or resid 126 or (resid 127 and (name N or name CA or name C or na \ me O or name CB )) or (resid 194 through 195 and (name N or name CA or name C or \ name O or name CB )) or resid 196 through 206 or (resid 207 through 208 and (na \ me N or name CA or name C or name O or name CB )) or resid 209 through 229 or (r \ esid 230 through 232 and (name N or name CA or name C or name O or name CB )) or \ resid 233 through 349 or (resid 350 and (name N or name CA or name C or name O \ or name CB )) or resid 351 through 397 or (resid 412 and (name N or name CA or n \ ame C or name O or name CB )) or resid 413 through 458 or resid 460 through 465 \ or (resid 466 through 467 and (name N or name CA or name C or name O or name CB \ )) or resid 468 through 491 or (resid 492 and (name N or name CA or name C or na \ me O or name CB )) or resid 493 through 499 or (resid 500 and (name N or name CA \ or name C or name O or name CB )) or resid 501 through 502 or resid 603 through \ 610)) selection = (chain 'B' and (resid 35 through 56 or (resid 57 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 or (resid 64 and ( \ name N or name CA or name C or name O or name CB )) or resid 65 through 96 or (r \ esid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 thr \ ough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 through 124 or (resid 125 and (name N or name CA or name C or name \ O or name CB )) or resid 126 through 127 or (resid 194 through 195 and (name N o \ r name CA or name C or name O or name CB )) or resid 196 through 202 or (resid 2 \ 03 through 204 and (name N or name CA or name C or name O or name CB )) or resid \ 205 through 206 or (resid 207 through 208 and (name N or name CA or name C or n \ ame O or name CB )) or resid 209 through 231 or (resid 232 and (name N or name C \ A or name C or name O or name CB )) or resid 233 through 300 or resid 325 throug \ h 357 or (resid 358 and (name N or name CA or name C or name O or name CB )) or \ resid 359 through 369 or (resid 370 and (name N or name CA or name C or name O o \ r name CB )) or resid 371 through 395 or (resid 396 and (name N or name CA or na \ me C or name O or name CB )) or resid 397 through 439 or (resid 440 and (name N \ or name CA or name C or name O or name CB )) or resid 441 through 456 or (resid \ 457 and (name N or name CA or name C or name O or name CB )) or resid 458 or res \ id 463 through 464 or (resid 465 and (name N or name CA or name C or name O or n \ ame CB or name OG1)) or (resid 466 through 467 and (name N or name CA or name C \ or name O or name CB )) or resid 468 through 491 or (resid 492 and (name N or na \ me CA or name C or name O or name CB )) or resid 493 through 499 or (resid 500 a \ nd (name N or name CA or name C or name O or name CB )) or resid 501 through 502 \ or resid 602 through 612)) selection = (chain 'C' and (resid 35 through 56 or (resid 57 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 91 or (resid 92 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 116 or (re \ sid 117 and (name N or name CA or name C or name O or name CB )) or resid 118 th \ rough 229 or (resid 230 through 232 and (name N or name CA or name C or name O o \ r name CB )) or resid 233 through 300 or resid 325 through 349 or (resid 350 and \ (name N or name CA or name C or name O or name CB )) or resid 351 through 357 o \ r (resid 358 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 59 through 397 or (resid 412 and (name N or name CA or name C or name O or name \ CB )) or resid 413 through 439 or (resid 440 and (name N or name CA or name C or \ name O or name CB )) or resid 441 through 458 or resid 460 through 465 or (resi \ d 466 through 467 and (name N or name CA or name C or name O or name CB )) or re \ sid 468 through 502 or resid 607 through 612)) } ncs_group { reference = (chain 'D' and (resid 1 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 23 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid \ 88 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 23 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid \ 88 through 90 or (resid 91 and (name N or name CA or name C or name O or name CB \ )) or resid 92 through 97)) } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = (chain 'H' and (resid 2 through 91 or resid 93 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 112)) selection = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11 or (resid 12 through 13 and (name N or name \ CA or name C or name O or name CB )) or resid 14 through 18 or (resid 19 and (na \ me N or name CA or name C or name O or name CB )) or resid 20 through 91 or resi \ d 93 through 100Q or (resid 101 and (name N or name CA or name C or name O or na \ me CB )) or resid 102 through 112)) selection = (chain 'P' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 91 or resid 93 through 100O or (res \ id 100P and (name N or name CA or name C or name O or name CB )) or resid 100Q o \ r (resid 101 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 02 through 104 or (resid 105 and (name N or name CA or name C or name O or name \ CB )) or resid 106 through 112)) } ncs_group { reference = (chain 'J' and (resid 2 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through \ 69 or resid 71 through 107)) selection = (chain 'L' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 69 or resid 71 through 107)) selection = (chain 'Q' and (resid 2 through 51 or (resid 52 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 through \ 61 and (name N or name CA or name C or name O or name CB )) or resid 62 through \ 69 or resid 71 through 107)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'X' and (resid 521 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 539 or (resid 540 and (name N \ or name CA or name C or name O or name CB )) or (resid 542 and (name N or name C \ A or name C or name O or name CB )) or (resid 560 through 563 and (name N or nam \ e CA or name C or name O or name CB )) or resid 564 through 600 or (resid 601 an \ d (name N or name CA or name C or name O or name CB )) or resid 602 through 606 \ or (resid 607 and (name N or name CA or name C or name O or name CB )) or resid \ 608 through 616 or (resid 617 and (name N or name CA or name C or name O or name \ CB )) or resid 618 through 629 or (resid 630 and (name N or name CA or name C o \ r name O or name CB )) or resid 631 through 632 or (resid 633 and (name N or nam \ e CA or name C or name O or name CB )) or resid 634 through 636 or (resid 637 an \ d (name N or name CA or name C or name O or name CB )) or resid 638 through 639 \ or (resid 640 through 641 and (name N or name CA or name C or name O or name CB \ )) or resid 642 through 647 or (resid 648 and (name N or name CA or name C or na \ me O or name CB )) or resid 649 through 650 or (resid 651 and (name N or name CA \ or name C or name O or name CB )) or resid 652 through 653)) selection = (chain 'Y' and (resid 521 through 528 or (resid 529 and (name N or name CA or na \ me C or name O or name CB )) or resid 530 through 540 or resid 542 or (resid 560 \ through 563 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 64 through 606 or (resid 607 and (name N or name CA or name C or name O or name \ CB )) or resid 608 through 629 or (resid 630 and (name N or name CA or name C or \ name O or name CB )) or resid 631 through 632 or (resid 633 and (name N or name \ CA or name C or name O or name CB )) or resid 634 through 639 or (resid 640 thr \ ough 641 and (name N or name CA or name C or name O or name CB )) or resid 642 t \ hrough 649 or (resid 650 through 651 and (name N or name CA or name C or name O \ or name CB )) or resid 652 or (resid 653 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'Z' and (resid 521 through 557 or resid 560 through 600 or (resid 601 and \ (name N or name CA or name C or name O or name CB )) or resid 602 through 616 o \ r (resid 617 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 18 through 636 or (resid 637 and (name N or name CA or name C or name O or name \ CB )) or resid 638 through 649 or (resid 650 through 651 and (name N or name CA \ or name C or name O or name CB )) or resid 652 through 653)) } 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=0.50 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.810 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.008 0.175 19805 Z= 0.362 Angle : 0.983 23.827 27063 Z= 0.488 Chirality : 0.059 0.705 3198 Planarity : 0.006 0.066 3346 Dihedral : 15.218 109.240 7539 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.58 % Favored : 90.34 % Rotamer: Outliers : 0.56 % Allowed : 6.51 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.29 (0.13), residues: 2420 helix: -4.82 (0.08), residues: 401 sheet: -2.85 (0.17), residues: 736 loop : -3.51 (0.13), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 480 TYR 0.019 0.002 TYR B 484 PHE 0.021 0.002 PHE A 376 TRP 0.019 0.002 TRP X 614 HIS 0.007 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00783 (19724) covalent geometry : angle 0.90837 (26858) SS BOND : bond 0.00490 ( 38) SS BOND : angle 1.63175 ( 76) hydrogen bonds : bond 0.30533 ( 465) hydrogen bonds : angle 11.46122 ( 1259) link_ALPHA1-2 : bond 0.00342 ( 3) link_ALPHA1-2 : angle 2.51316 ( 9) link_ALPHA1-3 : bond 0.00137 ( 3) link_ALPHA1-3 : angle 1.43744 ( 9) link_BETA1-4 : bond 0.01244 ( 8) link_BETA1-4 : angle 3.98813 ( 24) link_NAG-ASN : bond 0.01007 ( 29) link_NAG-ASN : angle 6.18480 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 444 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8648 (mttt) cc_final: 0.8250 (mttp) REVERT: A 62 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7964 (mm-30) REVERT: A 479 TRP cc_start: 0.7378 (m-10) cc_final: 0.7023 (m-10) REVERT: B 340 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7841 (tp30) REVERT: B 377 ASN cc_start: 0.7613 (t0) cc_final: 0.7323 (t0) REVERT: D 89 GLN cc_start: 0.9021 (mt0) cc_final: 0.8364 (mp10) REVERT: F 70 ILE cc_start: 0.8945 (mm) cc_final: 0.8739 (mm) REVERT: F 94 GLN cc_start: 0.8795 (pt0) cc_final: 0.8563 (pm20) REVERT: H 79 TYR cc_start: 0.7890 (m-80) cc_final: 0.7624 (m-10) REVERT: I 10 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8070 (mm-30) REVERT: J 21 ILE cc_start: 0.9191 (mm) cc_final: 0.8973 (mp) REVERT: J 92 ASP cc_start: 0.8236 (t0) cc_final: 0.7605 (p0) REVERT: L 45 LYS cc_start: 0.9028 (ttpt) cc_final: 0.8802 (tttt) REVERT: L 90 THR cc_start: 0.8044 (t) cc_final: 0.7576 (m) REVERT: L 95 LEU cc_start: 0.9257 (mp) cc_final: 0.8841 (tp) REVERT: P 38 ARG cc_start: 0.6821 (ptt180) cc_final: 0.6398 (ptm-80) REVERT: P 61 GLN cc_start: 0.8644 (tp40) cc_final: 0.8303 (tp-100) REVERT: P 66 ARG cc_start: 0.8428 (mtp180) cc_final: 0.8170 (ptm160) REVERT: P 82 ARG cc_start: 0.7052 (ptt-90) cc_final: 0.6771 (mpt180) REVERT: P 82 LEU cc_start: 0.8655 (mt) cc_final: 0.7086 (mp) REVERT: P 101 ASP cc_start: 0.8675 (t70) cc_final: 0.8367 (t0) outliers start: 11 outliers final: 6 residues processed: 452 average time/residue: 0.1451 time to fit residues: 99.7070 Evaluate side-chains 359 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 353 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.0870 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 67 ASN A 279 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 478 ASN B 279 ASN C 72 HIS C 258 GLN C 280 ASN C 422 GLN C 425 ASN D 52 ASN E 27 HIS F 20 GLN F 32 ASN I 6 GLN I 58 HIS I 95 ASN L 31 ASN L 37 GLN P 81 HIS Q 31 ASN Q 37 GLN X 590 GLN X 625 ASN Y 562 GLN Y 564 HIS Y 590 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.113940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082294 restraints weight = 103885.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.084751 restraints weight = 35878.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085579 restraints weight = 22942.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086050 restraints weight = 19711.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086503 restraints weight = 17158.031| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19805 Z= 0.131 Angle : 0.684 18.643 27063 Z= 0.339 Chirality : 0.048 0.602 3198 Planarity : 0.005 0.069 3346 Dihedral : 9.575 81.933 3517 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.97 % Allowed : 14.13 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.44 (0.14), residues: 2420 helix: -3.87 (0.15), residues: 379 sheet: -2.36 (0.17), residues: 784 loop : -3.04 (0.15), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 61 TYR 0.022 0.002 TYR J 87 PHE 0.023 0.001 PHE Q 62 TRP 0.014 0.001 TRP A 479 HIS 0.010 0.001 HIS E 27 Details of bonding type rmsd covalent geometry : bond 0.00287 (19724) covalent geometry : angle 0.62769 (26858) SS BOND : bond 0.00313 ( 38) SS BOND : angle 1.09274 ( 76) hydrogen bonds : bond 0.05007 ( 465) hydrogen bonds : angle 7.12465 ( 1259) link_ALPHA1-2 : bond 0.00178 ( 3) link_ALPHA1-2 : angle 2.25736 ( 9) link_ALPHA1-3 : bond 0.00982 ( 3) link_ALPHA1-3 : angle 2.02299 ( 9) link_BETA1-4 : bond 0.00633 ( 8) link_BETA1-4 : angle 2.51566 ( 24) link_NAG-ASN : bond 0.00700 ( 29) link_NAG-ASN : angle 4.51101 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 389 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8273 (mttt) cc_final: 0.7934 (mttp) REVERT: A 62 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8081 (mm-30) REVERT: A 78 ASP cc_start: 0.8159 (t0) cc_final: 0.7942 (t0) REVERT: A 479 TRP cc_start: 0.7404 (m-10) cc_final: 0.7040 (m-90) REVERT: A 492 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 377 ASN cc_start: 0.7760 (t0) cc_final: 0.7521 (t0) REVERT: C 92 GLU cc_start: 0.7574 (tp30) cc_final: 0.7327 (tp30) REVERT: D 89 GLN cc_start: 0.8771 (mt0) cc_final: 0.7700 (mp10) REVERT: E 23 SER cc_start: 0.8937 (t) cc_final: 0.8715 (p) REVERT: F 70 ILE cc_start: 0.9019 (mm) cc_final: 0.8689 (mt) REVERT: F 94 GLN cc_start: 0.8959 (pt0) cc_final: 0.8600 (pm20) REVERT: H 100 MET cc_start: 0.8359 (pmm) cc_final: 0.8058 (pmm) REVERT: I 10 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8044 (mm-30) REVERT: I 23 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7850 (tm-30) REVERT: I 46 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7633 (tm-30) REVERT: I 62 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8521 (ttpp) REVERT: J 92 ASP cc_start: 0.8345 (t0) cc_final: 0.7392 (p0) REVERT: L 32 ASP cc_start: 0.7733 (p0) cc_final: 0.7504 (p0) REVERT: L 36 TYR cc_start: 0.8029 (m-80) cc_final: 0.7529 (m-80) REVERT: L 45 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8770 (tttt) REVERT: L 90 THR cc_start: 0.8374 (t) cc_final: 0.7973 (m) REVERT: L 95 LEU cc_start: 0.9248 (mp) cc_final: 0.8823 (tp) REVERT: L 103 LYS cc_start: 0.8670 (mppt) cc_final: 0.8428 (tppt) REVERT: P 62 LYS cc_start: 0.8914 (pttm) cc_final: 0.8691 (pttm) REVERT: P 64 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7457 (mtt-85) REVERT: P 82 ARG cc_start: 0.7379 (ptt-90) cc_final: 0.6797 (mpt180) REVERT: P 100 MET cc_start: 0.8450 (mtm) cc_final: 0.8056 (mtt) REVERT: P 101 ASP cc_start: 0.8672 (t70) cc_final: 0.8440 (t0) REVERT: Q 66 LYS cc_start: 0.9227 (ttpp) cc_final: 0.8862 (ttmm) REVERT: Q 72 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7631 (p) outliers start: 39 outliers final: 23 residues processed: 414 average time/residue: 0.1349 time to fit residues: 86.8565 Evaluate side-chains 369 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 345 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 16 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 172 optimal weight: 0.1980 chunk 147 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN C 258 GLN F 32 ASN I 6 GLN J 37 GLN L 17 GLN L 31 ASN L 37 GLN Y 652 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.114166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.080832 restraints weight = 84777.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084335 restraints weight = 36778.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086330 restraints weight = 20978.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086434 restraints weight = 19163.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086177 restraints weight = 16248.901| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19805 Z= 0.305 Angle : 0.759 18.041 27063 Z= 0.374 Chirality : 0.051 0.571 3198 Planarity : 0.005 0.058 3346 Dihedral : 9.066 78.844 3515 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.18 % Allowed : 17.47 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.15), residues: 2420 helix: -3.12 (0.19), residues: 385 sheet: -2.24 (0.18), residues: 787 loop : -2.87 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 617 TYR 0.021 0.002 TYR L 49 PHE 0.016 0.002 PHE A 53 TRP 0.015 0.002 TRP B 45 HIS 0.006 0.001 HIS I 81 Details of bonding type rmsd covalent geometry : bond 0.00706 (19724) covalent geometry : angle 0.70617 (26858) SS BOND : bond 0.00415 ( 38) SS BOND : angle 1.12819 ( 76) hydrogen bonds : bond 0.04761 ( 465) hydrogen bonds : angle 6.65486 ( 1259) link_ALPHA1-2 : bond 0.00217 ( 3) link_ALPHA1-2 : angle 2.12492 ( 9) link_ALPHA1-3 : bond 0.00764 ( 3) link_ALPHA1-3 : angle 2.33674 ( 9) link_BETA1-4 : bond 0.00556 ( 8) link_BETA1-4 : angle 2.67808 ( 24) link_NAG-ASN : bond 0.00649 ( 29) link_NAG-ASN : angle 4.57274 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 359 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8290 (mttt) cc_final: 0.7970 (mttp) REVERT: A 62 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7848 (mm-30) REVERT: A 492 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7728 (mt-10) REVERT: B 342 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8297 (tt) REVERT: B 480 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8512 (ptp-110) REVERT: D 89 GLN cc_start: 0.8793 (mt0) cc_final: 0.8139 (mp10) REVERT: D 91 GLU cc_start: 0.8161 (mp0) cc_final: 0.7823 (mp0) REVERT: E 23 SER cc_start: 0.8904 (t) cc_final: 0.8662 (p) REVERT: F 32 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7759 (t0) REVERT: F 52 ASN cc_start: 0.8170 (t0) cc_final: 0.7946 (m-40) REVERT: F 70 ILE cc_start: 0.9133 (mm) cc_final: 0.8828 (mt) REVERT: F 94 GLN cc_start: 0.8919 (pt0) cc_final: 0.8559 (pm20) REVERT: I 10 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8058 (mm-30) REVERT: I 23 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7798 (tm-30) REVERT: I 46 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7710 (tm-30) REVERT: I 62 LYS cc_start: 0.8824 (ttpp) cc_final: 0.8619 (ttpt) REVERT: J 92 ASP cc_start: 0.8374 (t0) cc_final: 0.7414 (p0) REVERT: L 36 TYR cc_start: 0.8209 (m-80) cc_final: 0.7568 (m-80) REVERT: L 45 LYS cc_start: 0.9112 (ttpt) cc_final: 0.8720 (ttpp) REVERT: L 90 THR cc_start: 0.8411 (t) cc_final: 0.7978 (m) REVERT: L 95 LEU cc_start: 0.9212 (mp) cc_final: 0.8752 (tp) REVERT: P 46 GLU cc_start: 0.7502 (mp0) cc_final: 0.7209 (mp0) REVERT: P 66 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8500 (ptm160) REVERT: P 82 ARG cc_start: 0.7332 (ptt-90) cc_final: 0.6878 (mpt180) REVERT: P 100 MET cc_start: 0.8475 (mtm) cc_final: 0.8193 (mtt) REVERT: P 101 ASP cc_start: 0.8693 (t70) cc_final: 0.8449 (t0) REVERT: Q 66 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8868 (ttmm) REVERT: Q 72 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7694 (p) outliers start: 63 outliers final: 42 residues processed: 398 average time/residue: 0.1315 time to fit residues: 82.6408 Evaluate side-chains 385 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 339 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain L residue 17 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 105 THR Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN H 39 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** L 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.115384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.082325 restraints weight = 83783.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085914 restraints weight = 36070.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.087168 restraints weight = 21499.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087576 restraints weight = 18576.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087372 restraints weight = 15926.726| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19805 Z= 0.189 Angle : 0.683 17.250 27063 Z= 0.334 Chirality : 0.048 0.564 3198 Planarity : 0.004 0.064 3346 Dihedral : 8.156 78.442 3514 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.28 % Allowed : 19.13 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.74 (0.15), residues: 2420 helix: -2.69 (0.21), residues: 389 sheet: -2.02 (0.19), residues: 749 loop : -2.71 (0.15), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 76 TYR 0.015 0.001 TYR B 484 PHE 0.021 0.001 PHE P 63 TRP 0.015 0.001 TRP Z 571 HIS 0.006 0.001 HIS I 81 Details of bonding type rmsd covalent geometry : bond 0.00437 (19724) covalent geometry : angle 0.63032 (26858) SS BOND : bond 0.00326 ( 38) SS BOND : angle 1.15306 ( 76) hydrogen bonds : bond 0.04004 ( 465) hydrogen bonds : angle 6.17513 ( 1259) link_ALPHA1-2 : bond 0.00193 ( 3) link_ALPHA1-2 : angle 2.04244 ( 9) link_ALPHA1-3 : bond 0.00947 ( 3) link_ALPHA1-3 : angle 1.88667 ( 9) link_BETA1-4 : bond 0.00567 ( 8) link_BETA1-4 : angle 2.43544 ( 24) link_NAG-ASN : bond 0.00638 ( 29) link_NAG-ASN : angle 4.31971 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 364 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8230 (mttt) cc_final: 0.7951 (mttp) REVERT: A 62 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 91 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 492 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 342 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 377 ASN cc_start: 0.7816 (t0) cc_final: 0.7508 (p0) REVERT: C 91 GLU cc_start: 0.6861 (tp30) cc_final: 0.6648 (tp30) REVERT: C 92 GLU cc_start: 0.7506 (tp30) cc_final: 0.7164 (tp30) REVERT: D 89 GLN cc_start: 0.8782 (mt0) cc_final: 0.7994 (mp10) REVERT: D 91 GLU cc_start: 0.8159 (mp0) cc_final: 0.7688 (mp0) REVERT: E 23 SER cc_start: 0.8873 (t) cc_final: 0.8614 (p) REVERT: F 52 ASN cc_start: 0.8047 (t0) cc_final: 0.7832 (m-40) REVERT: F 70 ILE cc_start: 0.9146 (mm) cc_final: 0.8809 (mt) REVERT: F 94 GLN cc_start: 0.8954 (pt0) cc_final: 0.8553 (pm20) REVERT: I 10 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8098 (mm-30) REVERT: I 23 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7804 (tm-30) REVERT: I 46 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7662 (tm-30) REVERT: J 92 ASP cc_start: 0.8375 (t0) cc_final: 0.7420 (p0) REVERT: L 32 ASP cc_start: 0.7802 (p0) cc_final: 0.7571 (p0) REVERT: L 36 TYR cc_start: 0.8178 (m-80) cc_final: 0.7726 (m-80) REVERT: L 45 LYS cc_start: 0.9159 (ttpt) cc_final: 0.8800 (ttpp) REVERT: L 90 THR cc_start: 0.8410 (t) cc_final: 0.7957 (m) REVERT: L 95 LEU cc_start: 0.9216 (mp) cc_final: 0.8766 (tp) REVERT: P 66 ARG cc_start: 0.8926 (mtp180) cc_final: 0.8527 (ptm160) REVERT: P 76 ARG cc_start: 0.8639 (ptp-110) cc_final: 0.7688 (ptp-110) REVERT: P 100 MET cc_start: 0.8473 (mtm) cc_final: 0.8168 (mtt) REVERT: P 101 ASP cc_start: 0.8662 (t70) cc_final: 0.8409 (t0) REVERT: Q 72 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7561 (p) outliers start: 65 outliers final: 43 residues processed: 404 average time/residue: 0.1273 time to fit residues: 81.4473 Evaluate side-chains 385 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 83 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 283 ASN D 52 ASN E 40 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN L 17 GLN L 31 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078872 restraints weight = 121877.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083388 restraints weight = 41794.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.086283 restraints weight = 20106.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085803 restraints weight = 16382.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085914 restraints weight = 14973.142| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19805 Z= 0.144 Angle : 0.649 16.559 27063 Z= 0.318 Chirality : 0.047 0.543 3198 Planarity : 0.004 0.062 3346 Dihedral : 7.291 78.310 3514 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.98 % Allowed : 20.39 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.16), residues: 2420 helix: -2.24 (0.23), residues: 381 sheet: -1.78 (0.19), residues: 753 loop : -2.59 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 38 TYR 0.024 0.001 TYR L 49 PHE 0.011 0.001 PHE A 53 TRP 0.019 0.001 TRP A 479 HIS 0.005 0.001 HIS I 81 Details of bonding type rmsd covalent geometry : bond 0.00332 (19724) covalent geometry : angle 0.60042 (26858) SS BOND : bond 0.00278 ( 38) SS BOND : angle 1.08773 ( 76) hydrogen bonds : bond 0.03594 ( 465) hydrogen bonds : angle 5.83659 ( 1259) link_ALPHA1-2 : bond 0.00107 ( 3) link_ALPHA1-2 : angle 1.94651 ( 9) link_ALPHA1-3 : bond 0.01221 ( 3) link_ALPHA1-3 : angle 1.68559 ( 9) link_BETA1-4 : bond 0.00693 ( 8) link_BETA1-4 : angle 2.22073 ( 24) link_NAG-ASN : bond 0.00649 ( 29) link_NAG-ASN : angle 4.09372 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 361 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8258 (mttt) cc_final: 0.7914 (mttp) REVERT: A 91 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 492 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 377 ASN cc_start: 0.7873 (t0) cc_final: 0.7623 (p0) REVERT: C 91 GLU cc_start: 0.6826 (tp30) cc_final: 0.6616 (tp30) REVERT: C 92 GLU cc_start: 0.7474 (tp30) cc_final: 0.7148 (tp30) REVERT: D 89 GLN cc_start: 0.8895 (mt0) cc_final: 0.8173 (mp10) REVERT: D 91 GLU cc_start: 0.8030 (mp0) cc_final: 0.7574 (mp0) REVERT: E 23 SER cc_start: 0.8885 (t) cc_final: 0.8647 (p) REVERT: F 70 ILE cc_start: 0.9115 (mm) cc_final: 0.8777 (mt) REVERT: F 94 GLN cc_start: 0.8947 (pt0) cc_final: 0.8537 (pm20) REVERT: H 4 LEU cc_start: 0.8319 (tp) cc_final: 0.7832 (mt) REVERT: I 10 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8070 (mm-30) REVERT: I 23 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7711 (tm-30) REVERT: I 46 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7827 (tm-30) REVERT: I 62 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8486 (ttpp) REVERT: J 92 ASP cc_start: 0.8320 (t0) cc_final: 0.7356 (p0) REVERT: L 32 ASP cc_start: 0.7749 (p0) cc_final: 0.7524 (p0) REVERT: L 36 TYR cc_start: 0.8379 (m-80) cc_final: 0.7683 (m-80) REVERT: L 45 LYS cc_start: 0.9174 (ttpt) cc_final: 0.8821 (tttt) REVERT: L 90 THR cc_start: 0.8353 (t) cc_final: 0.7892 (m) REVERT: L 95 LEU cc_start: 0.9199 (mp) cc_final: 0.8749 (tp) REVERT: P 46 GLU cc_start: 0.7494 (mp0) cc_final: 0.7229 (mp0) REVERT: P 62 LYS cc_start: 0.8538 (pttp) cc_final: 0.8160 (pttp) REVERT: P 64 ARG cc_start: 0.7974 (ptp90) cc_final: 0.7721 (ptp90) REVERT: P 100 MET cc_start: 0.8411 (mtm) cc_final: 0.8106 (mtt) REVERT: P 101 ASP cc_start: 0.8745 (t70) cc_final: 0.8493 (t0) REVERT: Q 72 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7514 (p) outliers start: 59 outliers final: 45 residues processed: 395 average time/residue: 0.1240 time to fit residues: 77.7440 Evaluate side-chains 392 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 346 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 30 ASN Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 203 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 287 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.115138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.081137 restraints weight = 93751.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085260 restraints weight = 37994.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086785 restraints weight = 19658.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.086908 restraints weight = 19385.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086688 restraints weight = 16569.307| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19805 Z= 0.207 Angle : 0.676 16.316 27063 Z= 0.330 Chirality : 0.048 0.537 3198 Planarity : 0.004 0.058 3346 Dihedral : 7.023 80.142 3514 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.43 % Allowed : 20.75 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.16), residues: 2420 helix: -2.04 (0.24), residues: 381 sheet: -1.79 (0.19), residues: 766 loop : -2.46 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 64 TYR 0.015 0.002 TYR B 484 PHE 0.012 0.001 PHE A 53 TRP 0.014 0.001 TRP X 631 HIS 0.005 0.001 HIS I 81 Details of bonding type rmsd covalent geometry : bond 0.00481 (19724) covalent geometry : angle 0.62871 (26858) SS BOND : bond 0.00343 ( 38) SS BOND : angle 1.08702 ( 76) hydrogen bonds : bond 0.03676 ( 465) hydrogen bonds : angle 5.74998 ( 1259) link_ALPHA1-2 : bond 0.00135 ( 3) link_ALPHA1-2 : angle 1.98369 ( 9) link_ALPHA1-3 : bond 0.00921 ( 3) link_ALPHA1-3 : angle 1.86440 ( 9) link_BETA1-4 : bond 0.00572 ( 8) link_BETA1-4 : angle 2.24162 ( 24) link_NAG-ASN : bond 0.00612 ( 29) link_NAG-ASN : angle 4.09169 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 355 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8245 (mttt) cc_final: 0.7943 (mttp) REVERT: A 492 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7573 (mt-10) REVERT: B 377 ASN cc_start: 0.7862 (t0) cc_final: 0.7500 (p0) REVERT: C 91 GLU cc_start: 0.6955 (tp30) cc_final: 0.6733 (tp30) REVERT: C 92 GLU cc_start: 0.7542 (tp30) cc_final: 0.7229 (tp30) REVERT: D 89 GLN cc_start: 0.8901 (mt0) cc_final: 0.8176 (mp10) REVERT: D 91 GLU cc_start: 0.8057 (mp0) cc_final: 0.7618 (mp0) REVERT: E 23 SER cc_start: 0.8921 (t) cc_final: 0.8698 (p) REVERT: F 70 ILE cc_start: 0.9132 (mm) cc_final: 0.8805 (mt) REVERT: F 94 GLN cc_start: 0.8951 (pt0) cc_final: 0.8588 (pm20) REVERT: H 4 LEU cc_start: 0.8274 (tp) cc_final: 0.7836 (mt) REVERT: I 10 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8130 (mm-30) REVERT: I 23 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7649 (tm-30) REVERT: J 92 ASP cc_start: 0.8332 (t0) cc_final: 0.7381 (p0) REVERT: L 32 ASP cc_start: 0.7801 (p0) cc_final: 0.7565 (p0) REVERT: L 36 TYR cc_start: 0.8381 (m-80) cc_final: 0.7670 (m-80) REVERT: L 45 LYS cc_start: 0.9174 (ttpt) cc_final: 0.8827 (ttpp) REVERT: L 90 THR cc_start: 0.8422 (t) cc_final: 0.7944 (m) REVERT: P 46 GLU cc_start: 0.7388 (mp0) cc_final: 0.7144 (mp0) REVERT: P 76 ARG cc_start: 0.8716 (ptp-110) cc_final: 0.7750 (ptp-110) REVERT: P 101 ASP cc_start: 0.8701 (t70) cc_final: 0.8465 (t0) REVERT: Q 72 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7552 (p) REVERT: Z 585 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7940 (mtt180) outliers start: 68 outliers final: 51 residues processed: 397 average time/residue: 0.1316 time to fit residues: 82.7732 Evaluate side-chains 397 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Y residue 646 LEU Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 0.0770 chunk 17 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 287 GLN ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.112940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.078375 restraints weight = 99239.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.082411 restraints weight = 37933.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084389 restraints weight = 19500.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084297 restraints weight = 16933.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.084291 restraints weight = 15226.132| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19805 Z= 0.183 Angle : 0.665 15.951 27063 Z= 0.325 Chirality : 0.048 0.538 3198 Planarity : 0.004 0.058 3346 Dihedral : 6.708 80.389 3514 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.48 % Allowed : 21.91 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.16), residues: 2420 helix: -1.85 (0.25), residues: 384 sheet: -1.58 (0.19), residues: 745 loop : -2.45 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 64 TYR 0.023 0.001 TYR L 49 PHE 0.020 0.001 PHE P 63 TRP 0.014 0.001 TRP Z 571 HIS 0.005 0.001 HIS I 81 Details of bonding type rmsd covalent geometry : bond 0.00427 (19724) covalent geometry : angle 0.61917 (26858) SS BOND : bond 0.00339 ( 38) SS BOND : angle 1.24131 ( 76) hydrogen bonds : bond 0.03527 ( 465) hydrogen bonds : angle 5.64008 ( 1259) link_ALPHA1-2 : bond 0.00132 ( 3) link_ALPHA1-2 : angle 2.00620 ( 9) link_ALPHA1-3 : bond 0.01003 ( 3) link_ALPHA1-3 : angle 1.74641 ( 9) link_BETA1-4 : bond 0.00558 ( 8) link_BETA1-4 : angle 2.10649 ( 24) link_NAG-ASN : bond 0.00615 ( 29) link_NAG-ASN : angle 4.01059 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 356 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8268 (mttt) cc_final: 0.7915 (mttp) REVERT: A 62 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 91 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 492 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7663 (mt-10) REVERT: B 377 ASN cc_start: 0.7950 (t0) cc_final: 0.7620 (p0) REVERT: C 92 GLU cc_start: 0.7545 (tp30) cc_final: 0.7209 (tp30) REVERT: C 479 TRP cc_start: 0.7970 (m-10) cc_final: 0.7584 (m-90) REVERT: D 89 GLN cc_start: 0.8934 (mt0) cc_final: 0.8209 (mp10) REVERT: D 91 GLU cc_start: 0.8058 (mp0) cc_final: 0.7618 (mp0) REVERT: E 23 SER cc_start: 0.8934 (t) cc_final: 0.8725 (p) REVERT: F 70 ILE cc_start: 0.9127 (mm) cc_final: 0.8799 (mt) REVERT: F 94 GLN cc_start: 0.9022 (pt0) cc_final: 0.8541 (pm20) REVERT: H 4 LEU cc_start: 0.8284 (tp) cc_final: 0.7887 (mt) REVERT: I 10 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8166 (mm-30) REVERT: I 23 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7570 (tm-30) REVERT: I 62 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8434 (ttpp) REVERT: J 92 ASP cc_start: 0.8355 (t0) cc_final: 0.7352 (p0) REVERT: L 32 ASP cc_start: 0.7841 (p0) cc_final: 0.7583 (p0) REVERT: L 36 TYR cc_start: 0.8390 (m-80) cc_final: 0.7606 (m-80) REVERT: L 45 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8826 (ttpp) REVERT: L 90 THR cc_start: 0.8417 (t) cc_final: 0.7923 (m) REVERT: L 95 LEU cc_start: 0.9207 (mp) cc_final: 0.8595 (tp) REVERT: P 45 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8230 (mm) REVERT: P 62 LYS cc_start: 0.8592 (pttp) cc_final: 0.8276 (pttp) REVERT: P 76 ARG cc_start: 0.8695 (ptp-110) cc_final: 0.7695 (ptp-110) REVERT: P 101 ASP cc_start: 0.8730 (t70) cc_final: 0.8503 (t0) REVERT: Q 66 LYS cc_start: 0.9162 (ttpp) cc_final: 0.8872 (ttmm) REVERT: Q 72 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7558 (p) REVERT: Z 585 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7919 (mtt180) outliers start: 69 outliers final: 52 residues processed: 396 average time/residue: 0.1265 time to fit residues: 79.8784 Evaluate side-chains 402 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 81 HIS Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 604 CYS Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Chi-restraints excluded: chain Z residue 652 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 35 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN I 61 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078888 restraints weight = 110636.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.083586 restraints weight = 40723.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084388 restraints weight = 19234.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084596 restraints weight = 18982.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084663 restraints weight = 16655.639| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19805 Z= 0.140 Angle : 0.645 15.438 27063 Z= 0.317 Chirality : 0.047 0.526 3198 Planarity : 0.004 0.057 3346 Dihedral : 6.331 80.334 3514 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.93 % Allowed : 22.31 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.16), residues: 2420 helix: -1.62 (0.26), residues: 376 sheet: -1.57 (0.19), residues: 765 loop : -2.33 (0.16), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 38 TYR 0.015 0.001 TYR B 484 PHE 0.020 0.001 PHE P 63 TRP 0.020 0.001 TRP A 96 HIS 0.004 0.001 HIS I 81 Details of bonding type rmsd covalent geometry : bond 0.00327 (19724) covalent geometry : angle 0.60199 (26858) SS BOND : bond 0.00301 ( 38) SS BOND : angle 1.05818 ( 76) hydrogen bonds : bond 0.03323 ( 465) hydrogen bonds : angle 5.47606 ( 1259) link_ALPHA1-2 : bond 0.00119 ( 3) link_ALPHA1-2 : angle 1.94395 ( 9) link_ALPHA1-3 : bond 0.01044 ( 3) link_ALPHA1-3 : angle 1.36593 ( 9) link_BETA1-4 : bond 0.00584 ( 8) link_BETA1-4 : angle 1.95924 ( 24) link_NAG-ASN : bond 0.00617 ( 29) link_NAG-ASN : angle 3.85531 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 358 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8241 (mttt) cc_final: 0.7887 (mttp) REVERT: A 62 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7823 (mm-30) REVERT: A 91 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 377 ASN cc_start: 0.7930 (t0) cc_final: 0.7575 (p0) REVERT: C 92 GLU cc_start: 0.7466 (tp30) cc_final: 0.7126 (tp30) REVERT: D 89 GLN cc_start: 0.8925 (mt0) cc_final: 0.8173 (mp10) REVERT: D 91 GLU cc_start: 0.8019 (mp0) cc_final: 0.7592 (mp0) REVERT: E 23 SER cc_start: 0.8934 (t) cc_final: 0.8734 (p) REVERT: E 58 ARG cc_start: 0.7937 (mtp-110) cc_final: 0.7636 (ttm110) REVERT: F 70 ILE cc_start: 0.9126 (mm) cc_final: 0.8786 (mt) REVERT: F 94 GLN cc_start: 0.8980 (pt0) cc_final: 0.8577 (pm20) REVERT: H 4 LEU cc_start: 0.8290 (tp) cc_final: 0.7838 (mt) REVERT: I 10 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7956 (mm-30) REVERT: I 23 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7552 (tm-30) REVERT: J 92 ASP cc_start: 0.8345 (t0) cc_final: 0.7352 (p0) REVERT: L 32 ASP cc_start: 0.7833 (p0) cc_final: 0.7552 (p0) REVERT: L 36 TYR cc_start: 0.8409 (m-80) cc_final: 0.7590 (m-80) REVERT: L 45 LYS cc_start: 0.9177 (ttpt) cc_final: 0.8850 (ptmt) REVERT: L 90 THR cc_start: 0.8406 (t) cc_final: 0.7933 (m) REVERT: L 95 LEU cc_start: 0.9183 (mp) cc_final: 0.8561 (tp) REVERT: P 62 LYS cc_start: 0.8607 (pttp) cc_final: 0.8351 (pttp) REVERT: P 63 PHE cc_start: 0.7979 (m-10) cc_final: 0.7616 (m-10) REVERT: P 76 ARG cc_start: 0.8648 (ptp-110) cc_final: 0.8011 (ptp-110) REVERT: P 101 ASP cc_start: 0.8717 (t70) cc_final: 0.8514 (t0) REVERT: Q 66 LYS cc_start: 0.9151 (ttpp) cc_final: 0.8862 (ttmm) REVERT: Q 72 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7700 (p) REVERT: Z 585 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7915 (mtt180) outliers start: 58 outliers final: 47 residues processed: 395 average time/residue: 0.1244 time to fit residues: 78.3368 Evaluate side-chains 395 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 346 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.113629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.078844 restraints weight = 101378.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082757 restraints weight = 38151.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085336 restraints weight = 19483.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084904 restraints weight = 16297.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085071 restraints weight = 15085.982| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19805 Z= 0.160 Angle : 0.652 15.114 27063 Z= 0.321 Chirality : 0.047 0.517 3198 Planarity : 0.004 0.057 3346 Dihedral : 6.203 81.220 3514 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.73 % Allowed : 22.56 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.16), residues: 2420 helix: -1.54 (0.26), residues: 378 sheet: -1.45 (0.20), residues: 747 loop : -2.35 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 64 TYR 0.022 0.001 TYR L 49 PHE 0.016 0.001 PHE P 63 TRP 0.014 0.001 TRP Z 571 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00372 (19724) covalent geometry : angle 0.61081 (26858) SS BOND : bond 0.00312 ( 38) SS BOND : angle 1.07727 ( 76) hydrogen bonds : bond 0.03339 ( 465) hydrogen bonds : angle 5.43565 ( 1259) link_ALPHA1-2 : bond 0.00119 ( 3) link_ALPHA1-2 : angle 1.92085 ( 9) link_ALPHA1-3 : bond 0.00958 ( 3) link_ALPHA1-3 : angle 1.41871 ( 9) link_BETA1-4 : bond 0.00567 ( 8) link_BETA1-4 : angle 1.94471 ( 24) link_NAG-ASN : bond 0.00604 ( 29) link_NAG-ASN : angle 3.81574 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8223 (mttt) cc_final: 0.7911 (mttp) REVERT: A 62 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 91 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 377 ASN cc_start: 0.7944 (t0) cc_final: 0.7602 (p0) REVERT: C 479 TRP cc_start: 0.7922 (m-10) cc_final: 0.7607 (m-90) REVERT: D 89 GLN cc_start: 0.8902 (mt0) cc_final: 0.8189 (mp10) REVERT: D 91 GLU cc_start: 0.8017 (mp0) cc_final: 0.7615 (mp0) REVERT: E 23 SER cc_start: 0.8950 (t) cc_final: 0.8740 (p) REVERT: F 70 ILE cc_start: 0.9109 (mm) cc_final: 0.8766 (mt) REVERT: F 94 GLN cc_start: 0.9021 (pt0) cc_final: 0.8552 (pm20) REVERT: H 4 LEU cc_start: 0.8256 (tp) cc_final: 0.8046 (mt) REVERT: I 10 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7922 (mm-30) REVERT: I 23 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7445 (tm-30) REVERT: I 46 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7829 (pm20) REVERT: I 83 ARG cc_start: 0.8500 (ptp-170) cc_final: 0.8184 (ptp90) REVERT: J 92 ASP cc_start: 0.8355 (t0) cc_final: 0.7339 (p0) REVERT: L 32 ASP cc_start: 0.7829 (p0) cc_final: 0.7551 (p0) REVERT: L 36 TYR cc_start: 0.8404 (m-80) cc_final: 0.7584 (m-80) REVERT: L 45 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8873 (ptmt) REVERT: L 90 THR cc_start: 0.8396 (t) cc_final: 0.7897 (m) REVERT: L 95 LEU cc_start: 0.9137 (mp) cc_final: 0.8505 (tp) REVERT: P 45 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8087 (mm) REVERT: P 62 LYS cc_start: 0.8567 (pttp) cc_final: 0.8182 (pttp) REVERT: P 66 ARG cc_start: 0.8195 (ptm160) cc_final: 0.7947 (ptm160) REVERT: P 76 ARG cc_start: 0.8631 (ptp-110) cc_final: 0.8005 (ptp-110) REVERT: P 101 ASP cc_start: 0.8696 (t70) cc_final: 0.8491 (t0) REVERT: Q 66 LYS cc_start: 0.9167 (ttpp) cc_final: 0.8867 (ttmm) REVERT: Q 72 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7684 (p) REVERT: Z 585 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7891 (mtt180) outliers start: 54 outliers final: 47 residues processed: 383 average time/residue: 0.1227 time to fit residues: 74.7493 Evaluate side-chains 395 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 345 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 0.0370 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.114661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079624 restraints weight = 113097.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.084458 restraints weight = 40513.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085253 restraints weight = 19071.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085409 restraints weight = 18876.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085527 restraints weight = 16635.702| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19805 Z= 0.129 Angle : 0.635 14.712 27063 Z= 0.313 Chirality : 0.047 0.505 3198 Planarity : 0.004 0.058 3346 Dihedral : 5.903 81.508 3514 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.42 % Allowed : 23.02 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.17), residues: 2420 helix: -1.35 (0.26), residues: 379 sheet: -1.30 (0.20), residues: 739 loop : -2.28 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 58 TYR 0.016 0.001 TYR H 79 PHE 0.017 0.001 PHE P 63 TRP 0.016 0.001 TRP A 479 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00302 (19724) covalent geometry : angle 0.59532 (26858) SS BOND : bond 0.00265 ( 38) SS BOND : angle 0.99958 ( 76) hydrogen bonds : bond 0.03144 ( 465) hydrogen bonds : angle 5.26219 ( 1259) link_ALPHA1-2 : bond 0.00135 ( 3) link_ALPHA1-2 : angle 1.82829 ( 9) link_ALPHA1-3 : bond 0.00973 ( 3) link_ALPHA1-3 : angle 1.15645 ( 9) link_BETA1-4 : bond 0.00571 ( 8) link_BETA1-4 : angle 1.81841 ( 24) link_NAG-ASN : bond 0.00608 ( 29) link_NAG-ASN : angle 3.68713 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 356 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 492 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 377 ASN cc_start: 0.7960 (t0) cc_final: 0.7639 (p0) REVERT: D 89 GLN cc_start: 0.8889 (mt0) cc_final: 0.8165 (mp10) REVERT: D 91 GLU cc_start: 0.8058 (mp0) cc_final: 0.7642 (mp0) REVERT: E 23 SER cc_start: 0.8951 (t) cc_final: 0.8734 (p) REVERT: F 70 ILE cc_start: 0.9102 (mm) cc_final: 0.8753 (mt) REVERT: F 94 GLN cc_start: 0.8970 (pt0) cc_final: 0.8599 (pm20) REVERT: H 4 LEU cc_start: 0.8263 (tp) cc_final: 0.8052 (mt) REVERT: I 10 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7950 (mm-30) REVERT: I 23 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7312 (tm-30) REVERT: I 46 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7915 (pm20) REVERT: I 83 ARG cc_start: 0.8513 (ptp-170) cc_final: 0.8198 (ptp90) REVERT: J 92 ASP cc_start: 0.8340 (t0) cc_final: 0.7337 (p0) REVERT: L 32 ASP cc_start: 0.7820 (p0) cc_final: 0.7529 (p0) REVERT: L 36 TYR cc_start: 0.8388 (m-80) cc_final: 0.7561 (m-80) REVERT: L 45 LYS cc_start: 0.9133 (ttpt) cc_final: 0.8811 (ptmt) REVERT: L 90 THR cc_start: 0.8376 (t) cc_final: 0.7894 (m) REVERT: L 95 LEU cc_start: 0.9163 (mp) cc_final: 0.8557 (tp) REVERT: P 45 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8047 (mm) REVERT: P 62 LYS cc_start: 0.8600 (pttp) cc_final: 0.8240 (pttp) REVERT: P 66 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7957 (ptm160) REVERT: P 76 ARG cc_start: 0.8588 (ptp-110) cc_final: 0.7986 (ptp-110) REVERT: P 100 MET cc_start: 0.8354 (mtm) cc_final: 0.8096 (mtt) REVERT: Q 66 LYS cc_start: 0.9157 (ttpp) cc_final: 0.8853 (ttmm) REVERT: Q 72 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7676 (p) REVERT: Z 585 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7908 (mtt180) outliers start: 48 outliers final: 45 residues processed: 385 average time/residue: 0.1225 time to fit residues: 74.5116 Evaluate side-chains 396 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain E residue 24 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain X residue 540 GLN Chi-restraints excluded: chain X residue 606 THR Chi-restraints excluded: chain Y residue 641 ILE Chi-restraints excluded: chain Z residue 523 LEU Chi-restraints excluded: chain Z residue 573 ILE Chi-restraints excluded: chain Z residue 585 ARG Chi-restraints excluded: chain Z residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 59 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 236 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 196 optimal weight: 0.4980 chunk 140 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 30 optimal weight: 0.0270 chunk 208 optimal weight: 3.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.114474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079491 restraints weight = 105852.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083605 restraints weight = 38690.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086346 restraints weight = 19395.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.085839 restraints weight = 16219.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086004 restraints weight = 14907.846| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19805 Z= 0.139 Angle : 0.635 14.525 27063 Z= 0.314 Chirality : 0.047 0.497 3198 Planarity : 0.004 0.058 3346 Dihedral : 5.813 82.357 3513 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.32 % Allowed : 23.12 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.17), residues: 2420 helix: -1.19 (0.27), residues: 379 sheet: -1.26 (0.20), residues: 739 loop : -2.25 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.022 0.001 TYR L 49 PHE 0.015 0.001 PHE P 63 TRP 0.018 0.001 TRP A 479 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00324 (19724) covalent geometry : angle 0.59699 (26858) SS BOND : bond 0.00294 ( 38) SS BOND : angle 1.00486 ( 76) hydrogen bonds : bond 0.03148 ( 465) hydrogen bonds : angle 5.15953 ( 1259) link_ALPHA1-2 : bond 0.00130 ( 3) link_ALPHA1-2 : angle 1.82808 ( 9) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 1.22372 ( 9) link_BETA1-4 : bond 0.00571 ( 8) link_BETA1-4 : angle 1.82983 ( 24) link_NAG-ASN : bond 0.00592 ( 29) link_NAG-ASN : angle 3.63934 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.54 seconds wall clock time: 69 minutes 23.90 seconds (4163.90 seconds total)