Starting phenix.real_space_refine on Thu Mar 5 05:50:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u0l_20605/03_2026/6u0l_20605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u0l_20605/03_2026/6u0l_20605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u0l_20605/03_2026/6u0l_20605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u0l_20605/03_2026/6u0l_20605_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u0l_20605/03_2026/6u0l_20605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u0l_20605/03_2026/6u0l_20605.map" } resolution = 3.3 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= 0.004 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 120 5.16 5 C 12319 2.51 5 N 3336 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19611 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2791 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2781 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 345} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 12, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2814 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 21, 'TRANS': 343} Chain breaks: 4 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1008 Chain: "I" Number of atoms: 998 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1008 Chain: "J" Number of atoms: 812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} bond proxies already assigned to first conformer: 803 Chain: "L" Number of atoms: 806 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} bond proxies already assigned to first conformer: 810 Chain: "P" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 128} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 3, 'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 11 Chain: "Q" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "X" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 984 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "Y" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1012 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 33 Chain: "Z" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 46 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: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "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 Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ACYS H 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 92 " occ=0.50 residue: pdb=" N ACYS I 92 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 92 " occ=0.50 residue: pdb=" N ASER J 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER J 70 " occ=0.50 residue: pdb=" N ACYS J 88 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 88 " occ=0.50 residue: pdb=" N ASER L 70 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER L 70 " occ=0.50 residue: pdb=" C1 NAG B 604 " occ=0.69 ... (12 atoms not shown) pdb=" O7 NAG B 604 " occ=0.69 Time building chain proxies: 4.90, per 1000 atoms: 0.25 Number of scatterers: 19611 At special positions: 0 Unit cell: (149.037, 150.094, 154.322, 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 120 16.00 O 3836 8.00 N 3336 7.00 C 12319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS Y 605 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 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 ACYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG BCYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG ACYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG BCYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG ACYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG BCYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS 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=2.03 Simple disulfide: pdb=" SG CYS Y 598 " - pdb=" SG CYS Y 604 " distance=2.02 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 K 4 " - " MAN K 5 " " MAN O 4 " - " MAN O 5 " " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA O 3 " - " MAN O 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG A 601 " - " ASN A 363 " " NAG A 604 " - " ASN A 448 " " NAG A 612 " - " ASN A 339 " " NAG A 613 " - " ASN A 88 " " NAG A 614 " - " ASN A 234 " " NAG A 615 " - " ASN A 355 " " NAG B 601 " - " ASN B 339 " " NAG B 604 " - " ASN B 234 " " NAG B 605 " - " ASN B 448 " " NAG B 615 " - " ASN B 332 " " NAG B 616 " - " ASN B 363 " " NAG C 601 " - " ASN C 448 " " NAG C 607 " - " ASN C 276 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 332 " " NAG C 610 " - " ASN C 339 " " NAG C 611 " - " ASN C 386 " " NAG C 612 " - " ASN C 88 " " NAG C 613 " - " ASN C 363 " " NAG C 614 " - " ASN C 392 " " NAG G 1 " - " ASN A 386 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN B 386 " " NAG O 1 " - " ASN B 262 " " NAG R 1 " - " ASN B 276 " " NAG S 1 " - " ASN C 262 " " NAG X 701 " - " ASN X 637 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 937.7 milliseconds 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 46 sheets defined 18.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.678A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.748A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.613A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.999A pdb=" N THR B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS B 72 " --> pdb=" O VAL B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.804A pdb=" N ARG B 350 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.819A pdb=" N TRP C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.611A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 353 removed outlier: 3.798A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.595A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 480 removed outlier: 3.849A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.506A pdb=" N LEU D 61 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP D 62 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 64 removed outlier: 3.504A pdb=" N LEU E 61 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP E 62 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 64 removed outlier: 3.505A pdb=" N LEU F 61 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP F 62 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 100 through 100D removed outlier: 3.531A pdb=" N GLY H 100D" --> pdb=" O ALA H 100A" (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.631A pdb=" N ASP I 86 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'I' and resid 98 through 100A removed outlier: 3.594A pdb=" N ALA I 100A" --> pdb=" O ALA I 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 98 through 100A' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.616A pdb=" N ASP P 86 " --> pdb=" O ARG P 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 83 through 87' Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'X' and resid 516 through 522 removed outlier: 3.711A pdb=" N LEU X 520 " --> pdb=" O GLY X 516 " (cutoff:3.500A) Processing helix chain 'X' and resid 529 through 544 removed outlier: 3.598A pdb=" N THR X 536 " --> pdb=" O ALA X 532 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR X 538 " --> pdb=" O SER X 534 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL X 539 " --> pdb=" O MET X 535 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA X 541 " --> pdb=" O LEU X 537 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG X 542 " --> pdb=" O THR X 538 " (cutoff:3.500A) Processing helix chain 'X' and resid 560 through 574 removed outlier: 3.682A pdb=" N LEU X 568 " --> pdb=" O HIS X 564 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP X 571 " --> pdb=" O LYS X 567 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY X 572 " --> pdb=" O LEU X 568 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE X 573 " --> pdb=" O THR X 569 " (cutoff:3.500A) Processing helix chain 'X' and resid 578 through 591 removed outlier: 3.540A pdb=" N ALA X 582 " --> pdb=" O ALA X 578 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG X 588 " --> pdb=" O GLU X 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP X 589 " --> pdb=" O ARG X 585 " (cutoff:3.500A) Processing helix chain 'X' and resid 591 through 597 removed outlier: 3.676A pdb=" N TRP X 596 " --> pdb=" O LEU X 592 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 624 Processing helix chain 'X' and resid 627 through 636 removed outlier: 3.644A pdb=" N GLU X 634 " --> pdb=" O GLN X 630 " (cutoff:3.500A) Processing helix chain 'X' and resid 638 through 653 removed outlier: 3.566A pdb=" N LEU X 645 " --> pdb=" O ILE X 641 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU X 647 " --> pdb=" O TYR X 643 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 516 No H-bonds generated for 'chain 'Y' and resid 514 through 516' Processing helix chain 'Y' and resid 517 through 522 removed outlier: 3.519A pdb=" N GLY Y 521 " --> pdb=" O ALA Y 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE Y 522 " --> pdb=" O VAL Y 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 517 through 522' Processing helix chain 'Y' and resid 523 through 526 Processing helix chain 'Y' and resid 529 through 544 removed outlier: 3.519A pdb=" N MET Y 535 " --> pdb=" O GLY Y 531 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR Y 538 " --> pdb=" O SER Y 534 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL Y 539 " --> pdb=" O MET Y 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Y 542 " --> pdb=" O THR Y 538 " (cutoff:3.500A) Processing helix chain 'Y' and resid 561 through 566 removed outlier: 4.403A pdb=" N LEU Y 566 " --> pdb=" O GLN Y 562 " (cutoff:3.500A) Processing helix chain 'Y' and resid 569 through 577 removed outlier: 3.512A pdb=" N LYS Y 574 " --> pdb=" O VAL Y 570 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN Y 575 " --> pdb=" O TRP Y 571 " (cutoff:3.500A) Processing helix chain 'Y' and resid 580 through 596 removed outlier: 3.670A pdb=" N TYR Y 586 " --> pdb=" O ALA Y 582 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU Y 592 " --> pdb=" O ARG Y 588 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY Y 594 " --> pdb=" O GLN Y 590 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP Y 596 " --> pdb=" O LEU Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 627 through 636 removed outlier: 4.019A pdb=" N TRP Y 631 " --> pdb=" O THR Y 627 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP Y 632 " --> pdb=" O TRP Y 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS Y 633 " --> pdb=" O LEU Y 629 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER Y 636 " --> pdb=" O ASP Y 632 " (cutoff:3.500A) Processing helix chain 'Y' and resid 638 through 653 removed outlier: 3.583A pdb=" N TYR Y 643 " --> pdb=" O THR Y 639 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN Y 650 " --> pdb=" O LEU Y 646 " (cutoff:3.500A) Processing helix chain 'Z' and resid 529 through 541 removed outlier: 3.630A pdb=" N ALA Z 541 " --> pdb=" O LEU Z 537 " (cutoff:3.500A) Processing helix chain 'Z' and resid 564 through 597 removed outlier: 3.935A pdb=" N LEU Z 568 " --> pdb=" O HIS Z 564 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN Z 575 " --> pdb=" O TRP Z 571 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG Z 579 " --> pdb=" O GLN Z 575 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR Z 586 " --> pdb=" O ALA Z 582 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN Z 591 " --> pdb=" O LEU Z 587 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU Z 592 " --> pdb=" O ARG Z 588 " (cutoff:3.500A) Processing helix chain 'Z' and resid 628 through 635 removed outlier: 4.190A pdb=" N ASP Z 632 " --> pdb=" O TRP Z 628 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Z 633 " --> pdb=" O LEU Z 629 " (cutoff:3.500A) Processing helix chain 'Z' and resid 638 through 657 removed outlier: 3.831A pdb=" N GLN Z 650 " --> pdb=" O LEU Z 646 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 653 " --> pdb=" O SER Z 649 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Z 655 " --> pdb=" O ASN Z 651 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 removed outlier: 3.637A pdb=" N ALA A 497 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 4.391A 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 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202 Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.812A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.812A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 382 through 384 removed outlier: 4.468A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA9, first strand: chain 'B' and resid 494 through 495 removed outlier: 4.483A pdb=" N VAL B 36 " --> pdb=" O THR Y 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 93 removed outlier: 3.739A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AB5, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AB6, first strand: chain 'B' and resid 272 through 273 Processing sheet with id=AB7, first strand: chain 'B' and resid 272 through 273 removed outlier: 12.076A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.571A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 447 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 359 through 360 removed outlier: 3.570A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 375 removed outlier: 4.629A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AC2, first strand: chain 'C' and resid 54 through 56 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'C' and resid 197 through 202 removed outlier: 3.678A pdb=" N VAL C 120 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AC7, first strand: chain 'C' and resid 383 through 384 removed outlier: 3.742A pdb=" N ILE C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.843A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 2 through 5 removed outlier: 6.865A pdb=" N TRP D 28 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 12 through 17 removed outlier: 3.630A pdb=" N VAL D 12 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N CYS D 16 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 2 through 5 removed outlier: 6.866A pdb=" N TRP E 28 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 12 through 17 removed outlier: 3.630A pdb=" N VAL E 12 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS E 16 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 2 through 5 removed outlier: 6.866A pdb=" N TRP F 28 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 12 through 17 removed outlier: 3.629A pdb=" N VAL F 12 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.805A 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 removed outlier: 3.745A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.033A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.543A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN I 95 " --> pdb=" O ALA I 33 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.513A pdb=" N VAL J 11 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA J 13 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 18 through 24 Processing sheet with id=AE3, first strand: chain 'J' and resid 90 through 92 Processing sheet with id=AE4, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AE5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.660A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE7, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.765A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 10 through 13 removed outlier: 7.109A pdb=" N VAL Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TYR Q 49 " --> pdb=" O VAL Q 33 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'Q' and resid 19 through 24 601 hydrogen bonds defined for protein. 1555 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: 3.57 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6267 1.34 - 1.48: 5419 1.48 - 1.62: 8179 1.62 - 1.76: 10 1.76 - 1.89: 143 Bond restraints: 20018 Sorted by residual: bond pdb=" O1 TYS I 100F" pdb=" S TYS I 100F" ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" O3 TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.458 1.631 -0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" O1 TYS P 100F" pdb=" S TYS P 100F" ideal model delta sigma weight residual 1.462 1.632 -0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" O2 TYS P 100I" pdb=" S TYS P 100I" ideal model delta sigma weight residual 1.461 1.627 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" O3 TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.458 1.624 -0.166 2.00e-02 2.50e+03 6.86e+01 ... (remaining 20013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 26405 2.64 - 5.27: 738 5.27 - 7.91: 86 7.91 - 10.54: 20 10.54 - 13.18: 3 Bond angle restraints: 27252 Sorted by residual: angle pdb=" N ARG X 542 " pdb=" CA ARG X 542 " pdb=" C ARG X 542 " ideal model delta sigma weight residual 113.43 105.11 8.32 1.26e+00 6.30e-01 4.36e+01 angle pdb=" C GLU L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 132.96 -11.42 1.91e+00 2.74e-01 3.58e+01 angle pdb=" N LEU X 544 " pdb=" CA LEU X 544 " pdb=" C LEU X 544 " ideal model delta sigma weight residual 108.99 117.15 -8.16 1.57e+00 4.06e-01 2.70e+01 angle pdb=" CA GLU L 50 " pdb=" CB GLU L 50 " pdb=" CG GLU L 50 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" C TYR H 100O" pdb=" N ASP H 100P" pdb=" CA ASP H 100P" ideal model delta sigma weight residual 122.46 129.42 -6.96 1.41e+00 5.03e-01 2.44e+01 ... (remaining 27247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 11391 21.34 - 42.68: 868 42.68 - 64.02: 153 64.02 - 85.36: 45 85.36 - 106.71: 16 Dihedral angle restraints: 12473 sinusoidal: 5311 harmonic: 7162 Sorted by residual: 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 -1.26 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CA ILE A 277 " pdb=" C ILE A 277 " pdb=" N THR A 278 " pdb=" CA THR A 278 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA ALA B 336 " pdb=" C ALA B 336 " pdb=" N THR B 337 " pdb=" CA THR B 337 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 12470 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 3216 0.220 - 0.439: 18 0.439 - 0.659: 2 0.659 - 0.878: 0 0.878 - 1.098: 2 Chirality restraints: 3238 Sorted by residual: chirality pdb=" C1 NAG C 611 " pdb=" ND2 ASN C 386 " pdb=" C2 NAG C 611 " pdb=" O5 NAG C 611 " both_signs ideal model delta sigma weight residual False -2.40 -1.30 -1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" C1 NAG B 605 " pdb=" ND2 ASN B 448 " pdb=" C2 NAG B 605 " pdb=" O5 NAG B 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG B 616 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 616 " pdb=" O5 NAG B 616 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 3235 not shown) Planarity restraints: 3430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 102 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C VAL P 102 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL P 102 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP P 103 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 102 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C VAL I 102 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL I 102 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP I 103 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 614 " -0.031 2.00e-02 2.50e+03 2.53e-02 8.02e+00 pdb=" C7 NAG C 614 " 0.008 2.00e-02 2.50e+03 pdb=" C8 NAG C 614 " -0.024 2.00e-02 2.50e+03 pdb=" N2 NAG C 614 " 0.040 2.00e-02 2.50e+03 pdb=" O7 NAG C 614 " 0.006 2.00e-02 2.50e+03 ... (remaining 3427 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 546 2.66 - 3.22: 17266 3.22 - 3.78: 29709 3.78 - 4.34: 38940 4.34 - 4.90: 66368 Nonbonded interactions: 152829 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.106 3.040 nonbonded pdb=" CB SER C 388 " pdb=" O7 NAG C 611 " model vdw 2.203 3.440 nonbonded pdb=" OD1 ASP P 72 " pdb=" OG SER P 74 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 37 " pdb=" OG1 THR B 499 " model vdw 2.292 3.040 nonbonded pdb=" OG SER B 334 " pdb=" OG1 THR B 337 " model vdw 2.299 3.040 ... (remaining 152824 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 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 86 or (r \ esid 87 and (name N or name CA or name C or name O or name CB )) or resid 88 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 126 or resid 194 through 202 or (resid 203 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 name O or name CB )) \ or resid 209 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB )) or resid 242 through 251 or (resid 252 and (name N or name CA o \ r name C or name O or name CB )) or resid 253 through 266 or (resid 267 through \ 269 and (name N or name CA or name C or name O or name CB )) or resid 270 throug \ h 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 name C or name O o \ r name CB )) or resid 413 through 456 or (resid 457 and (name N or name CA or na \ me C or name O or name CB )) or resid 458 or (resid 460 and (name N or name CA o \ r name C or name O or name CB )) or resid 464 or (resid 465 and (name N or name \ CA or name C or name O or name CB or name OG1)) or (resid 466 and (name N or nam \ e CA or name C or name O or name CB )) or resid 467 through 501 or resid 604 thr \ ough 615)) selection = (chain 'B' and (resid 35 through 55 or (resid 56 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 79 or (resid 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 89 or (res \ id 90 through 91 and (name N or name CA or name C or name O or name CB )) or res \ id 92 through 126 or resid 194 through 240 or (resid 241 and (name N or name CA \ or name C or name O or name CB )) or resid 242 through 245 or (resid 246 and (na \ me N or name CA or name C or name O or name CB )) or resid 247 through 349 or (r \ esid 350 and (name N or name CA or name C or name O or name CB )) or resid 351 t \ hrough 359 or (resid 360 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name NE )) or resid 361 through 397 or (resid 412 and (n \ ame N or name CA or name C or name O or name CB )) or resid 413 through 458 or ( \ resid 460 and (name N or name CA or name C or name O or name CB )) or resid 464 \ through 499 or (resid 500 and (name N or name CA or name C or name O or name CB \ )) or resid 501 or resid 601 through 616)) selection = (chain 'C' and (resid 35 through 45 or (resid 46 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 through 55 or (resid 56 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 (name N or name CA or name C or name O or name CB )) or res \ id 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or r \ esid 65 through 77 or (resid 78 and (name N or name CA or name C or name O or na \ me 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 through 89 or (resid 90 through 91 and (name N or name CA \ or name C or name O or name CB )) or resid 92 through 96 or (resid 97 and (name \ N or name CA or name C or name O or name CB )) or resid 98 through 116 or (resi \ d 117 and (name N or name CA or name C or name O or name CB )) or resid 118 thro \ ugh 202 or (resid 203 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 nam \ e CA or name C or name O or name CB )) or resid 209 through 245 or (resid 246 an \ d (name N or name CA or name C or name O or name CB )) or resid 247 through 251 \ or (resid 252 and (name N or name CA or name C or name O or name CB )) or resid \ 253 through 266 or (resid 267 through 269 and (name N or name CA or name C or na \ me O or name CB )) or resid 270 through 300 or resid 325 through 359 or (resid 3 \ 60 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name NE )) or resid 361 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 456 or (resid 457 and (name N \ or name CA or name C or name O or name CB )) or resid 458 or resid 463 through 4 \ 64 or (resid 465 and (name N or name CA or name C or name O or name CB or name O \ G1)) or resid 466 through 473 or (resid 474 and (name N or name CA or name C or \ name O or name CB )) or resid 475 through 499 or (resid 500 and (name N or name \ CA or name C or name O or name CB )) or resid 501 or resid 610 through 614)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 2 through 91 or resid 93 through 112)) selection = (chain 'I' and (resid 2 through 91 or resid 93 through 112)) selection = (chain 'P' and (resid 2 through 91 or resid 93 through 112)) } ncs_group { reference = (chain 'J' and (resid 2 through 69 or resid 71 through 87 or resid 89 through 10 \ 7)) selection = (chain 'L' and (resid 2 through 69 or resid 71 through 87 or resid 89 through 10 \ 7)) selection = (chain 'Q' and (resid 2 through 69 or resid 71 through 87 or resid 89 through 10 \ 7)) } ncs_group { reference = chain 'K' selection = chain 'S' } ncs_group { reference = (chain 'X' and ((resid 519 and (name N or name CA or name C or name O or name CB \ )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or n \ ame O or name CB )) or resid 524 through 542 or (resid 563 and (name N or name C \ A or name C or name O or name CB )) or resid 564 or (resid 565 and (name N or na \ me CA or name C or name O or name CB )) or resid 566 through 600 or (resid 601 a \ nd (name N or name CA or name C or name O or name CB )) or resid 602 through 636 \ or (resid 637 and (name N or name CA or name C or name O or name CB )) or resid \ 638 through 647 or (resid 648 and (name N or name CA or name C or name O or nam \ e CB )) or resid 649 through 651 or (resid 652 through 654 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'Y' and ((resid 519 and (name N or name CA or name C or name O or name CB \ )) or resid 520 through 522 or (resid 523 and (name N or name CA or name C or n \ ame O or name CB )) or resid 524 through 539 or (resid 540 through 542 and (name \ N or name CA or name C or name O or name CB )) or resid 563 through 564 or (res \ id 565 and (name N or name CA or name C or name O or name CB )) or resid 566 thr \ ough 598 or (resid 599 and (name N or name CA or name C or name O or name CB )) \ or resid 600 or (resid 601 and (name N or name CA or name C or name O or name CB \ )) or resid 602 through 615 or (resid 616 through 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 or name O or name CB )) or resid 631 through 632 or (res \ id 633 and (name N or name CA or name C or name O or name CB )) or resid 634 thr \ ough 636 or (resid 637 and (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 nam \ e C or name O or name CB )) or resid 642 through 646 or (resid 647 through 648 a \ nd (name N or name CA or name C or name O or name CB )) or resid 649 through 650 \ or (resid 651 through 654 and (name N or name CA or name C or name O or name CB \ )))) selection = (chain 'Z' and (resid 519 through 541 or (resid 542 through 563 and (name N or n \ ame CA or name C or name O or name CB )) or resid 564 through 598 or (resid 599 \ and (name N or name CA or name C or name O or name CB )) or resid 600 through 61 \ 5 or (resid 616 through 617 and (name N or name CA or name C or name O or name C \ B )) or resid 618 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 thro \ ugh 641 and (name N or name CA or name C or name O or name CB )) or resid 642 th \ rough 646 or (resid 647 through 648 and (name N or name CA or name C or name O o \ r name CB )) or resid 649 or (resid 650 through 654 and (name N or name CA or na \ me C or name O or name CB )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.640 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.011 0.315 20104 Z= 0.501 Angle : 1.135 24.694 27470 Z= 0.583 Chirality : 0.069 1.098 3238 Planarity : 0.007 0.064 3402 Dihedral : 15.944 106.706 7743 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 2.41 % Allowed : 9.65 % Favored : 87.94 % Cbeta Deviations : 0.04 % 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: -5.02 (0.13), residues: 2438 helix: -4.72 (0.09), residues: 439 sheet: -2.62 (0.17), residues: 758 loop : -3.25 (0.13), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 480 TYR 0.025 0.003 TYR A 217 PHE 0.023 0.003 PHE B 376 TRP 0.025 0.003 TRP A 45 HIS 0.008 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.01077 (20018) covalent geometry : angle 1.05746 (27252) SS BOND : bond 0.00788 ( 40) SS BOND : angle 1.93198 ( 80) hydrogen bonds : bond 0.27084 ( 591) hydrogen bonds : angle 10.24304 ( 1555) link_ALPHA1-2 : bond 0.00484 ( 3) link_ALPHA1-2 : angle 2.99940 ( 9) link_ALPHA1-3 : bond 0.00407 ( 4) link_ALPHA1-3 : angle 2.10507 ( 12) link_ALPHA1-6 : bond 0.00388 ( 1) link_ALPHA1-6 : angle 3.15187 ( 3) link_BETA1-4 : bond 0.01297 ( 10) link_BETA1-4 : angle 3.95453 ( 30) link_NAG-ASN : bond 0.06009 ( 28) link_NAG-ASN : angle 6.88289 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 462 time to evaluate : 0.796 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: B 435 TYR cc_start: 0.8524 (m-80) cc_final: 0.8284 (m-80) REVERT: C 279 ASN cc_start: 0.7022 (t0) cc_final: 0.6761 (t0) REVERT: C 368 ASP cc_start: 0.7454 (t70) cc_final: 0.7172 (t0) REVERT: E 63 ASP cc_start: 0.7538 (t70) cc_final: 0.7068 (t0) REVERT: E 81 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7908 (m) REVERT: E 85 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7315 (mp0) REVERT: E 94 GLN cc_start: 0.7357 (pp30) cc_final: 0.7087 (tm-30) REVERT: F 63 ASP cc_start: 0.7790 (t70) cc_final: 0.7568 (t0) REVERT: H 63 PHE cc_start: 0.8261 (m-80) cc_final: 0.8035 (m-80) REVERT: H 91 TYR cc_start: 0.7401 (m-80) cc_final: 0.6742 (m-10) REVERT: J 95 LEU cc_start: 0.9203 (mm) cc_final: 0.8968 (mm) REVERT: L 32 ASP cc_start: 0.8592 (p0) cc_final: 0.8204 (p0) REVERT: L 54 ARG cc_start: 0.7732 (mtm110) cc_final: 0.7479 (mtm-85) REVERT: L 78 LEU cc_start: 0.8666 (mm) cc_final: 0.7489 (tt) outliers start: 48 outliers final: 11 residues processed: 488 average time/residue: 0.1561 time to fit residues: 113.1342 Evaluate side-chains 341 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 329 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Z residue 606 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 235 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 99 ASN A 295 ASN A 348 GLN A 352 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN A 440 GLN B 279 ASN B 374 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 197 ASN C 258 GLN C 280 ASN C 293 GLN C 478 ASN D 27 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS E 94 GLN F 27 HIS I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN P 6 GLN P 12 ASN Q 7 GLN Q 37 GLN X 607 ASN X 618 ASN Y 543 ASN Y 625 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.138436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101471 restraints weight = 99697.646| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 5.33 r_work: 0.3265 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20104 Z= 0.151 Angle : 0.726 18.564 27470 Z= 0.360 Chirality : 0.048 0.544 3238 Planarity : 0.005 0.059 3402 Dihedral : 9.765 77.979 3608 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.46 % Allowed : 16.35 % Favored : 81.19 % 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: -4.04 (0.15), residues: 2438 helix: -3.46 (0.16), residues: 439 sheet: -1.91 (0.19), residues: 756 loop : -2.88 (0.14), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 76 TYR 0.030 0.002 TYR J 36 PHE 0.014 0.001 PHE B 361 TRP 0.017 0.001 TRP A 479 HIS 0.004 0.001 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00336 (20018) covalent geometry : angle 0.67664 (27252) SS BOND : bond 0.00419 ( 40) SS BOND : angle 1.15588 ( 80) hydrogen bonds : bond 0.04669 ( 591) hydrogen bonds : angle 6.62356 ( 1555) link_ALPHA1-2 : bond 0.00195 ( 3) link_ALPHA1-2 : angle 2.33110 ( 9) link_ALPHA1-3 : bond 0.01259 ( 4) link_ALPHA1-3 : angle 2.27544 ( 12) link_ALPHA1-6 : bond 0.00381 ( 1) link_ALPHA1-6 : angle 1.81642 ( 3) link_BETA1-4 : bond 0.00909 ( 10) link_BETA1-4 : angle 2.62060 ( 30) link_NAG-ASN : bond 0.00589 ( 28) link_NAG-ASN : angle 4.32780 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 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: C 475 MET cc_start: 0.7790 (mmt) cc_final: 0.6968 (mmt) REVERT: C 479 TRP cc_start: 0.7627 (m-10) cc_final: 0.7368 (m-90) REVERT: D 88 ASP cc_start: 0.8572 (p0) cc_final: 0.8338 (p0) REVERT: E 63 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.7898 (t0) REVERT: E 85 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7121 (mp0) REVERT: E 94 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: F 63 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8026 (t0) REVERT: F 67 PHE cc_start: 0.8646 (m-80) cc_final: 0.8405 (m-10) REVERT: H 4 LEU cc_start: 0.7497 (mt) cc_final: 0.6884 (tp) REVERT: H 23 GLN cc_start: 0.8649 (tt0) cc_final: 0.8399 (mm-40) REVERT: H 53 ILE cc_start: 0.9146 (tp) cc_final: 0.8858 (tp) REVERT: H 63 PHE cc_start: 0.8854 (m-80) cc_final: 0.8200 (m-80) REVERT: H 64 ARG cc_start: 0.8400 (mmm160) cc_final: 0.8060 (tpp80) REVERT: H 91 TYR cc_start: 0.7945 (m-80) cc_final: 0.7699 (m-10) REVERT: I 61 GLN cc_start: 0.7687 (pm20) cc_final: 0.7219 (pm20) REVERT: J 37 GLN cc_start: 0.7623 (tp40) cc_final: 0.6941 (tp40) REVERT: J 86 TYR cc_start: 0.8331 (m-80) cc_final: 0.8051 (m-10) REVERT: J 95 LEU cc_start: 0.9503 (mm) cc_final: 0.9285 (mm) REVERT: L 53 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8251 (mm-30) REVERT: L 54 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7707 (mtm-85) REVERT: L 66 LYS cc_start: 0.7870 (ttpp) cc_final: 0.7490 (ttpp) REVERT: Q 36 TYR cc_start: 0.7102 (m-80) cc_final: 0.6696 (m-80) REVERT: Q 53 GLU cc_start: 0.9342 (mm-30) cc_final: 0.8957 (mm-30) REVERT: Q 54 ARG cc_start: 0.8482 (ptp-110) cc_final: 0.7818 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7120 (m-80) cc_final: 0.6783 (m-80) REVERT: Z 626 MET cc_start: 0.7482 (ttm) cc_final: 0.6617 (ttm) REVERT: Z 630 GLN cc_start: 0.8239 (mt0) cc_final: 0.7943 (mt0) outliers start: 49 outliers final: 32 residues processed: 413 average time/residue: 0.1374 time to fit residues: 87.1297 Evaluate side-chains 377 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN P 12 ASN Y 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.138732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099780 restraints weight = 89939.351| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 5.18 r_work: 0.3279 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20104 Z= 0.141 Angle : 0.670 16.018 27470 Z= 0.328 Chirality : 0.046 0.495 3238 Planarity : 0.004 0.061 3402 Dihedral : 8.692 66.050 3599 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.10 % Allowed : 18.02 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.15), residues: 2438 helix: -2.62 (0.20), residues: 443 sheet: -1.68 (0.19), residues: 758 loop : -2.63 (0.15), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 83 TYR 0.028 0.001 TYR L 49 PHE 0.016 0.001 PHE D 26 TRP 0.016 0.001 TRP A 479 HIS 0.009 0.001 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00321 (20018) covalent geometry : angle 0.62927 (27252) SS BOND : bond 0.00643 ( 40) SS BOND : angle 0.97966 ( 80) hydrogen bonds : bond 0.03748 ( 591) hydrogen bonds : angle 6.04226 ( 1555) link_ALPHA1-2 : bond 0.00201 ( 3) link_ALPHA1-2 : angle 2.01762 ( 9) link_ALPHA1-3 : bond 0.01180 ( 4) link_ALPHA1-3 : angle 1.87498 ( 12) link_ALPHA1-6 : bond 0.00530 ( 1) link_ALPHA1-6 : angle 1.63062 ( 3) link_BETA1-4 : bond 0.00877 ( 10) link_BETA1-4 : angle 2.40395 ( 30) link_NAG-ASN : bond 0.00477 ( 28) link_NAG-ASN : angle 3.77912 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 365 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.7546 (m-10) cc_final: 0.7007 (m-90) REVERT: B 104 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8717 (ttm) REVERT: C 479 TRP cc_start: 0.7491 (m-10) cc_final: 0.7241 (m-90) REVERT: D 80 ASP cc_start: 0.7609 (p0) cc_final: 0.7123 (p0) REVERT: E 63 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.7947 (t0) REVERT: E 85 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7094 (mp0) REVERT: E 94 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7090 (pp30) REVERT: F 63 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8156 (t0) REVERT: F 67 PHE cc_start: 0.8713 (m-80) cc_final: 0.8438 (m-10) REVERT: H 23 GLN cc_start: 0.8630 (tt0) cc_final: 0.8333 (mm-40) REVERT: H 39 GLN cc_start: 0.7170 (tt0) cc_final: 0.6740 (tt0) REVERT: H 53 ILE cc_start: 0.9183 (tp) cc_final: 0.8920 (tp) REVERT: H 63 PHE cc_start: 0.8904 (m-80) cc_final: 0.8357 (m-80) REVERT: H 64 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8082 (tpp80) REVERT: H 76 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7914 (mtm110) REVERT: I 10 GLU cc_start: 0.7408 (tp30) cc_final: 0.6886 (tp30) REVERT: I 61 GLN cc_start: 0.7736 (pm20) cc_final: 0.7329 (pm20) REVERT: I 76 ARG cc_start: 0.8913 (mtp-110) cc_final: 0.8673 (mtm-85) REVERT: J 37 GLN cc_start: 0.7712 (tp40) cc_final: 0.6832 (tp40) REVERT: J 49 TYR cc_start: 0.7991 (p90) cc_final: 0.7778 (p90) REVERT: L 54 ARG cc_start: 0.8254 (mtm110) cc_final: 0.7640 (mtm-85) REVERT: L 66 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7599 (ttpp) REVERT: L 92 ASP cc_start: 0.8728 (t0) cc_final: 0.8124 (t0) REVERT: Q 36 TYR cc_start: 0.7281 (m-80) cc_final: 0.6694 (m-80) REVERT: Q 45 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8745 (tmtt) REVERT: Q 53 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8862 (mm-30) REVERT: Q 54 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.7709 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7131 (m-80) cc_final: 0.6796 (m-80) REVERT: Z 626 MET cc_start: 0.7533 (ttm) cc_final: 0.6720 (ttm) REVERT: Z 630 GLN cc_start: 0.8182 (mt0) cc_final: 0.7898 (mt0) outliers start: 61 outliers final: 41 residues processed: 397 average time/residue: 0.1383 time to fit residues: 84.5254 Evaluate side-chains 390 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 345 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 647 GLU Chi-restraints excluded: chain Z residue 584 GLU Chi-restraints excluded: chain Z residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** A 440 GLN B 103 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 27 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Q 17 GLN Y 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097698 restraints weight = 90802.197| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 5.13 r_work: 0.3246 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20104 Z= 0.186 Angle : 0.675 14.665 27470 Z= 0.330 Chirality : 0.047 0.534 3238 Planarity : 0.004 0.064 3402 Dihedral : 8.174 61.502 3599 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.40 % Allowed : 19.55 % Favored : 77.06 % 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: -3.21 (0.16), residues: 2438 helix: -2.10 (0.22), residues: 433 sheet: -1.57 (0.19), residues: 749 loop : -2.49 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 83 TYR 0.026 0.002 TYR L 49 PHE 0.012 0.001 PHE B 53 TRP 0.017 0.001 TRP A 479 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00430 (20018) covalent geometry : angle 0.63618 (27252) SS BOND : bond 0.00496 ( 40) SS BOND : angle 1.06532 ( 80) hydrogen bonds : bond 0.03630 ( 591) hydrogen bonds : angle 5.77117 ( 1555) link_ALPHA1-2 : bond 0.00182 ( 3) link_ALPHA1-2 : angle 2.03812 ( 9) link_ALPHA1-3 : bond 0.01138 ( 4) link_ALPHA1-3 : angle 2.07987 ( 12) link_ALPHA1-6 : bond 0.00559 ( 1) link_ALPHA1-6 : angle 1.58147 ( 3) link_BETA1-4 : bond 0.00901 ( 10) link_BETA1-4 : angle 2.39169 ( 30) link_NAG-ASN : bond 0.00418 ( 28) link_NAG-ASN : angle 3.64099 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 354 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 347 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7793 (ttpp) REVERT: C 479 TRP cc_start: 0.7573 (m-10) cc_final: 0.6988 (m-90) REVERT: D 27 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7466 (t-90) REVERT: D 80 ASP cc_start: 0.7733 (p0) cc_final: 0.7231 (p0) REVERT: E 36 ILE cc_start: 0.8692 (mm) cc_final: 0.8394 (tt) REVERT: E 63 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.7966 (t0) REVERT: E 85 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7009 (mp0) REVERT: E 94 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7416 (pp30) REVERT: F 63 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8309 (t0) REVERT: H 12 ASN cc_start: 0.8055 (m-40) cc_final: 0.7441 (t0) REVERT: H 53 ILE cc_start: 0.9188 (tp) cc_final: 0.8949 (tp) REVERT: H 63 PHE cc_start: 0.8937 (m-80) cc_final: 0.8444 (m-80) REVERT: I 10 GLU cc_start: 0.7543 (tp30) cc_final: 0.7029 (tp30) REVERT: I 76 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8759 (mtm-85) REVERT: J 37 GLN cc_start: 0.7637 (tp40) cc_final: 0.7339 (tp40) REVERT: L 50 GLU cc_start: 0.7821 (tp30) cc_final: 0.7443 (tp30) REVERT: L 54 ARG cc_start: 0.8291 (mtm110) cc_final: 0.7703 (mtm-85) REVERT: L 66 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7531 (ttpp) REVERT: P 23 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7935 (tm-30) REVERT: P 72 ASP cc_start: 0.8204 (t0) cc_final: 0.7910 (t0) REVERT: Q 21 ILE cc_start: 0.8511 (mt) cc_final: 0.8157 (pt) REVERT: Q 36 TYR cc_start: 0.7473 (m-80) cc_final: 0.6613 (m-80) REVERT: Q 45 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8742 (tmtt) REVERT: Q 53 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9028 (mm-30) REVERT: Q 54 ARG cc_start: 0.8540 (ptp-110) cc_final: 0.7894 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7195 (m-80) cc_final: 0.6797 (m-80) REVERT: X 530 MET cc_start: 0.7462 (mtt) cc_final: 0.7139 (mtt) REVERT: X 545 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6153 (tp) REVERT: Z 630 GLN cc_start: 0.8292 (mt0) cc_final: 0.7995 (mt0) outliers start: 67 outliers final: 44 residues processed: 390 average time/residue: 0.1307 time to fit residues: 78.4466 Evaluate side-chains 385 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 584 GLU Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 75 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 27 HIS I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.100135 restraints weight = 111351.674| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 5.44 r_work: 0.3249 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20104 Z= 0.131 Angle : 0.631 13.516 27470 Z= 0.308 Chirality : 0.046 0.461 3238 Planarity : 0.004 0.062 3402 Dihedral : 7.529 57.940 3599 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.50 % Allowed : 19.99 % Favored : 76.51 % 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: -2.91 (0.16), residues: 2438 helix: -1.64 (0.23), residues: 437 sheet: -1.39 (0.19), residues: 751 loop : -2.39 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 83 TYR 0.023 0.001 TYR L 49 PHE 0.008 0.001 PHE B 53 TRP 0.017 0.001 TRP B 96 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00303 (20018) covalent geometry : angle 0.59624 (27252) SS BOND : bond 0.00346 ( 40) SS BOND : angle 0.92935 ( 80) hydrogen bonds : bond 0.03243 ( 591) hydrogen bonds : angle 5.46251 ( 1555) link_ALPHA1-2 : bond 0.00197 ( 3) link_ALPHA1-2 : angle 1.88505 ( 9) link_ALPHA1-3 : bond 0.01219 ( 4) link_ALPHA1-3 : angle 1.71394 ( 12) link_ALPHA1-6 : bond 0.00641 ( 1) link_ALPHA1-6 : angle 1.46663 ( 3) link_BETA1-4 : bond 0.00834 ( 10) link_BETA1-4 : angle 2.24541 ( 30) link_NAG-ASN : bond 0.00489 ( 28) link_NAG-ASN : angle 3.37159 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 365 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.7518 (m-10) cc_final: 0.7070 (m-90) REVERT: B 91 GLU cc_start: 0.7834 (tp30) cc_final: 0.7220 (tp30) REVERT: C 479 TRP cc_start: 0.7421 (m-10) cc_final: 0.7155 (m-90) REVERT: D 27 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: D 80 ASP cc_start: 0.7759 (p0) cc_final: 0.7286 (p0) REVERT: E 36 ILE cc_start: 0.8679 (mm) cc_final: 0.8360 (tt) REVERT: E 56 ASP cc_start: 0.7845 (t70) cc_final: 0.7575 (m-30) REVERT: E 63 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.7919 (t0) REVERT: E 85 GLU cc_start: 0.7804 (mt-10) cc_final: 0.6973 (mp0) REVERT: E 94 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: F 63 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8449 (t0) REVERT: F 67 PHE cc_start: 0.8783 (m-80) cc_final: 0.8464 (m-10) REVERT: F 86 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7441 (t) REVERT: H 4 LEU cc_start: 0.7820 (mt) cc_final: 0.7583 (tp) REVERT: H 12 ASN cc_start: 0.7997 (m-40) cc_final: 0.7379 (t0) REVERT: H 53 ILE cc_start: 0.9166 (tp) cc_final: 0.8915 (tp) REVERT: H 63 PHE cc_start: 0.8967 (m-80) cc_final: 0.8640 (m-80) REVERT: H 105 GLN cc_start: 0.8827 (pm20) cc_final: 0.8488 (pp30) REVERT: I 10 GLU cc_start: 0.7606 (tp30) cc_final: 0.7098 (tp30) REVERT: J 95 LEU cc_start: 0.9376 (mm) cc_final: 0.9095 (tp) REVERT: L 50 GLU cc_start: 0.7715 (tp30) cc_final: 0.7345 (tp30) REVERT: L 54 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7660 (mtm-85) REVERT: L 66 LYS cc_start: 0.7822 (ttpp) cc_final: 0.7515 (ttpp) REVERT: P 23 GLN cc_start: 0.8518 (tm-30) cc_final: 0.7926 (tm-30) REVERT: P 72 ASP cc_start: 0.8308 (t0) cc_final: 0.7976 (t0) REVERT: P 73 GLU cc_start: 0.8721 (pm20) cc_final: 0.8402 (pm20) REVERT: Q 21 ILE cc_start: 0.8522 (mt) cc_final: 0.8164 (pt) REVERT: Q 36 TYR cc_start: 0.7493 (m-80) cc_final: 0.6750 (m-80) REVERT: Q 45 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8823 (tmtt) REVERT: Q 53 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9011 (mm-30) REVERT: Q 54 ARG cc_start: 0.8521 (ptp-110) cc_final: 0.7823 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7115 (m-80) cc_final: 0.6612 (m-80) REVERT: X 520 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8577 (tp) REVERT: X 530 MET cc_start: 0.7292 (mtt) cc_final: 0.6978 (mtt) REVERT: X 545 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6129 (tp) REVERT: Z 630 GLN cc_start: 0.8266 (mt0) cc_final: 0.8001 (mt0) outliers start: 69 outliers final: 45 residues processed: 405 average time/residue: 0.1357 time to fit residues: 85.3701 Evaluate side-chains 397 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 345 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain X residue 520 LEU Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 23 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 64 optimal weight: 0.3980 chunk 244 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 208 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS I 81 HIS ** L 7 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 = 0.4034 r_free = 0.4034 target = 0.137869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097656 restraints weight = 84086.915| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 4.97 r_work: 0.3262 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20104 Z= 0.132 Angle : 0.625 12.826 27470 Z= 0.306 Chirality : 0.046 0.437 3238 Planarity : 0.004 0.062 3402 Dihedral : 7.090 54.589 3598 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.20 % Allowed : 20.43 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.71 (0.16), residues: 2438 helix: -1.30 (0.24), residues: 436 sheet: -1.28 (0.19), residues: 751 loop : -2.32 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 83 TYR 0.023 0.001 TYR L 49 PHE 0.012 0.001 PHE B 376 TRP 0.014 0.001 TRP I 103 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00308 (20018) covalent geometry : angle 0.59182 (27252) SS BOND : bond 0.00376 ( 40) SS BOND : angle 1.15693 ( 80) hydrogen bonds : bond 0.03089 ( 591) hydrogen bonds : angle 5.32018 ( 1555) link_ALPHA1-2 : bond 0.00200 ( 3) link_ALPHA1-2 : angle 1.84284 ( 9) link_ALPHA1-3 : bond 0.01213 ( 4) link_ALPHA1-3 : angle 1.65333 ( 12) link_ALPHA1-6 : bond 0.00675 ( 1) link_ALPHA1-6 : angle 1.43188 ( 3) link_BETA1-4 : bond 0.00831 ( 10) link_BETA1-4 : angle 2.20646 ( 30) link_NAG-ASN : bond 0.00452 ( 28) link_NAG-ASN : angle 3.22509 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 368 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.7493 (m-10) cc_final: 0.7046 (m-90) REVERT: B 91 GLU cc_start: 0.7799 (tp30) cc_final: 0.7196 (tp30) REVERT: C 479 TRP cc_start: 0.7343 (m-10) cc_final: 0.7087 (m-90) REVERT: D 27 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7464 (t-90) REVERT: D 80 ASP cc_start: 0.7634 (p0) cc_final: 0.7134 (p0) REVERT: E 36 ILE cc_start: 0.8689 (mm) cc_final: 0.8368 (tt) REVERT: E 56 ASP cc_start: 0.7841 (t70) cc_final: 0.7549 (m-30) REVERT: E 63 ASP cc_start: 0.8734 (t70) cc_final: 0.7897 (t0) REVERT: E 85 GLU cc_start: 0.7781 (mt-10) cc_final: 0.6927 (mp0) REVERT: E 94 GLN cc_start: 0.7833 (pp30) cc_final: 0.7536 (pm20) REVERT: F 63 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8421 (t0) REVERT: F 86 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7644 (t) REVERT: H 4 LEU cc_start: 0.7812 (mt) cc_final: 0.7606 (tp) REVERT: H 12 ASN cc_start: 0.8026 (m-40) cc_final: 0.7405 (t0) REVERT: H 48 MET cc_start: 0.8351 (ttm) cc_final: 0.8080 (ttm) REVERT: H 53 ILE cc_start: 0.9151 (tp) cc_final: 0.8907 (tp) REVERT: H 63 PHE cc_start: 0.9026 (m-80) cc_final: 0.8718 (m-80) REVERT: H 91 TYR cc_start: 0.7878 (m-10) cc_final: 0.7542 (m-10) REVERT: H 105 GLN cc_start: 0.8786 (pm20) cc_final: 0.8500 (pp30) REVERT: I 10 GLU cc_start: 0.7632 (tp30) cc_final: 0.7192 (tp30) REVERT: L 54 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7662 (mtm-85) REVERT: L 66 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7473 (ttpp) REVERT: L 79 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8086 (mm-40) REVERT: P 23 GLN cc_start: 0.8484 (tm-30) cc_final: 0.7889 (tm-30) REVERT: P 46 GLU cc_start: 0.8010 (tt0) cc_final: 0.7236 (pt0) REVERT: P 72 ASP cc_start: 0.8286 (t0) cc_final: 0.7926 (t0) REVERT: P 73 GLU cc_start: 0.8700 (pm20) cc_final: 0.8416 (pm20) REVERT: Q 21 ILE cc_start: 0.8500 (mt) cc_final: 0.8151 (pt) REVERT: Q 36 TYR cc_start: 0.7520 (m-80) cc_final: 0.6949 (m-80) REVERT: Q 45 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8793 (tmtt) REVERT: Q 46 LEU cc_start: 0.8713 (tt) cc_final: 0.8481 (tp) REVERT: Q 53 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8966 (mm-30) REVERT: Q 54 ARG cc_start: 0.8503 (ptp-110) cc_final: 0.7785 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7089 (m-80) cc_final: 0.6612 (m-80) REVERT: X 520 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8539 (tp) REVERT: X 530 MET cc_start: 0.7332 (mtt) cc_final: 0.7006 (mtt) REVERT: X 545 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5982 (tp) REVERT: X 632 ASP cc_start: 0.9110 (t70) cc_final: 0.8872 (m-30) REVERT: Z 629 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8046 (mm) REVERT: Z 630 GLN cc_start: 0.8275 (mt0) cc_final: 0.7962 (mt0) outliers start: 63 outliers final: 44 residues processed: 407 average time/residue: 0.1392 time to fit residues: 88.2486 Evaluate side-chains 393 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 343 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain X residue 520 LEU Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 518 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 639 THR Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 209 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 139 optimal weight: 0.0980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 27 HIS F 64 GLN I 32 HIS I 39 GLN I 81 HIS J 38 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN Z 616 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092919 restraints weight = 97707.245| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 5.10 r_work: 0.3185 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 20104 Z= 0.355 Angle : 0.809 12.152 27470 Z= 0.397 Chirality : 0.052 0.432 3238 Planarity : 0.005 0.071 3402 Dihedral : 7.911 59.544 3598 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.19 % Allowed : 20.43 % Favored : 75.38 % 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: 2438 helix: -1.58 (0.23), residues: 429 sheet: -1.45 (0.19), residues: 750 loop : -2.43 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 83 TYR 0.021 0.002 TYR C 217 PHE 0.022 0.003 PHE B 223 TRP 0.026 0.003 TRP Y 610 HIS 0.007 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00829 (20018) covalent geometry : angle 0.77424 (27252) SS BOND : bond 0.00622 ( 40) SS BOND : angle 1.65746 ( 80) hydrogen bonds : bond 0.04076 ( 591) hydrogen bonds : angle 5.80176 ( 1555) link_ALPHA1-2 : bond 0.00280 ( 3) link_ALPHA1-2 : angle 2.38539 ( 9) link_ALPHA1-3 : bond 0.01036 ( 4) link_ALPHA1-3 : angle 2.43029 ( 12) link_ALPHA1-6 : bond 0.00576 ( 1) link_ALPHA1-6 : angle 1.48090 ( 3) link_BETA1-4 : bond 0.00742 ( 10) link_BETA1-4 : angle 2.41321 ( 30) link_NAG-ASN : bond 0.00586 ( 28) link_NAG-ASN : angle 3.64784 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 349 time to evaluate : 0.768 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: B 96 TRP cc_start: 0.8491 (m100) cc_final: 0.8174 (m100) REVERT: C 479 TRP cc_start: 0.7571 (m-10) cc_final: 0.7004 (m-90) REVERT: D 27 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7665 (t70) REVERT: D 80 ASP cc_start: 0.7399 (p0) cc_final: 0.6866 (p0) REVERT: D 88 ASP cc_start: 0.8536 (p0) cc_final: 0.8311 (p0) REVERT: E 36 ILE cc_start: 0.8809 (mm) cc_final: 0.8484 (tt) REVERT: E 63 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7963 (t0) REVERT: E 94 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: F 63 ASP cc_start: 0.8790 (t70) cc_final: 0.8485 (t0) REVERT: F 73 ASN cc_start: 0.7413 (t0) cc_final: 0.7191 (t0) REVERT: H 4 LEU cc_start: 0.8089 (mt) cc_final: 0.7850 (tp) REVERT: H 12 ASN cc_start: 0.8099 (m-40) cc_final: 0.7498 (t0) REVERT: H 23 GLN cc_start: 0.8850 (tp40) cc_final: 0.8623 (mm110) REVERT: H 72 ASP cc_start: 0.8060 (t0) cc_final: 0.7708 (t0) REVERT: H 105 GLN cc_start: 0.8722 (pm20) cc_final: 0.8473 (pp30) REVERT: J 38 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: L 50 GLU cc_start: 0.7898 (tp30) cc_final: 0.7592 (tp30) REVERT: L 54 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7604 (mtm-85) REVERT: L 66 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7668 (ttpp) REVERT: L 79 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8301 (mm-40) REVERT: P 46 GLU cc_start: 0.8117 (tt0) cc_final: 0.7644 (pm20) REVERT: P 72 ASP cc_start: 0.8224 (t0) cc_final: 0.7814 (t0) REVERT: Q 36 TYR cc_start: 0.7618 (m-80) cc_final: 0.6948 (m-80) REVERT: Q 53 GLU cc_start: 0.9259 (mm-30) cc_final: 0.9034 (mm-30) REVERT: Q 54 ARG cc_start: 0.8567 (ptp-110) cc_final: 0.7909 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7250 (m-80) cc_final: 0.6639 (m-80) REVERT: X 530 MET cc_start: 0.7718 (mtt) cc_final: 0.7345 (mtt) REVERT: Z 629 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8205 (mm) outliers start: 83 outliers final: 56 residues processed: 397 average time/residue: 0.1370 time to fit residues: 85.1817 Evaluate side-chains 392 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 331 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain J residue 38 GLN Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 538 THR Chi-restraints excluded: chain X residue 545 LEU Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 66 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 167 optimal weight: 20.0000 chunk 74 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 27 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.136590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096307 restraints weight = 84792.055| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 4.95 r_work: 0.3244 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20104 Z= 0.137 Angle : 0.663 11.935 27470 Z= 0.323 Chirality : 0.046 0.423 3238 Planarity : 0.004 0.064 3402 Dihedral : 7.224 53.728 3598 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.40 % Allowed : 21.57 % Favored : 75.04 % 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: -2.62 (0.16), residues: 2438 helix: -1.19 (0.24), residues: 431 sheet: -1.21 (0.19), residues: 752 loop : -2.29 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 83 TYR 0.023 0.001 TYR L 49 PHE 0.017 0.001 PHE C 233 TRP 0.017 0.001 TRP B 96 HIS 0.003 0.001 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00320 (20018) covalent geometry : angle 0.63305 (27252) SS BOND : bond 0.00361 ( 40) SS BOND : angle 1.13825 ( 80) hydrogen bonds : bond 0.03190 ( 591) hydrogen bonds : angle 5.42397 ( 1555) link_ALPHA1-2 : bond 0.00157 ( 3) link_ALPHA1-2 : angle 1.98157 ( 9) link_ALPHA1-3 : bond 0.01310 ( 4) link_ALPHA1-3 : angle 1.44664 ( 12) link_ALPHA1-6 : bond 0.00739 ( 1) link_ALPHA1-6 : angle 1.32495 ( 3) link_BETA1-4 : bond 0.00809 ( 10) link_BETA1-4 : angle 2.13692 ( 30) link_NAG-ASN : bond 0.00467 ( 28) link_NAG-ASN : angle 3.18544 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 364 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.7550 (m-10) cc_final: 0.7062 (m-90) REVERT: B 91 GLU cc_start: 0.7826 (tp30) cc_final: 0.7459 (tp30) REVERT: D 27 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7430 (t-90) REVERT: D 80 ASP cc_start: 0.7498 (p0) cc_final: 0.7002 (p0) REVERT: E 36 ILE cc_start: 0.8710 (mm) cc_final: 0.8392 (tt) REVERT: E 63 ASP cc_start: 0.8753 (t70) cc_final: 0.7964 (t0) REVERT: E 85 GLU cc_start: 0.7787 (mt-10) cc_final: 0.6872 (mp0) REVERT: F 50 LYS cc_start: 0.8510 (mppt) cc_final: 0.8292 (mptt) REVERT: F 63 ASP cc_start: 0.8765 (t70) cc_final: 0.8448 (t0) REVERT: F 73 ASN cc_start: 0.7371 (t0) cc_final: 0.7151 (t0) REVERT: H 12 ASN cc_start: 0.8047 (m-40) cc_final: 0.7409 (t0) REVERT: H 72 ASP cc_start: 0.8060 (t0) cc_final: 0.7718 (t0) REVERT: H 91 TYR cc_start: 0.7875 (m-10) cc_final: 0.7504 (m-10) REVERT: I 10 GLU cc_start: 0.7288 (tp30) cc_final: 0.6955 (tp30) REVERT: J 53 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7332 (mt-10) REVERT: L 50 GLU cc_start: 0.7766 (tp30) cc_final: 0.7473 (tp30) REVERT: L 54 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7532 (mtm-85) REVERT: L 66 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7483 (ttpp) REVERT: L 79 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8370 (mm-40) REVERT: P 23 GLN cc_start: 0.8533 (tm-30) cc_final: 0.7903 (tm-30) REVERT: P 46 GLU cc_start: 0.8055 (tt0) cc_final: 0.7666 (pt0) REVERT: P 72 ASP cc_start: 0.8302 (t0) cc_final: 0.7899 (t0) REVERT: P 73 GLU cc_start: 0.8741 (pm20) cc_final: 0.8460 (pm20) REVERT: Q 21 ILE cc_start: 0.8526 (mt) cc_final: 0.8164 (pt) REVERT: Q 36 TYR cc_start: 0.7472 (m-80) cc_final: 0.6998 (m-80) REVERT: Q 53 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8981 (mm-30) REVERT: Q 54 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.7836 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7166 (m-80) cc_final: 0.6593 (m-80) REVERT: X 632 ASP cc_start: 0.9127 (t70) cc_final: 0.8885 (m-30) REVERT: Z 629 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8044 (mm) outliers start: 67 outliers final: 51 residues processed: 404 average time/residue: 0.1315 time to fit residues: 83.8787 Evaluate side-chains 397 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 19 LYS Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 626 MET Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 9 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS I 81 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.093792 restraints weight = 93955.201| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.92 r_work: 0.3202 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20104 Z= 0.277 Angle : 0.762 11.912 27470 Z= 0.372 Chirality : 0.050 0.415 3238 Planarity : 0.005 0.069 3402 Dihedral : 7.422 53.677 3596 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.10 % Allowed : 22.45 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.16), residues: 2438 helix: -1.40 (0.24), residues: 440 sheet: -1.27 (0.19), residues: 747 loop : -2.36 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG P 83 TYR 0.021 0.002 TYR L 49 PHE 0.017 0.002 PHE B 223 TRP 0.029 0.002 TRP I 47 HIS 0.007 0.001 HIS P 81 Details of bonding type rmsd covalent geometry : bond 0.00647 (20018) covalent geometry : angle 0.73222 (27252) SS BOND : bond 0.00500 ( 40) SS BOND : angle 1.37530 ( 80) hydrogen bonds : bond 0.03709 ( 591) hydrogen bonds : angle 5.65325 ( 1555) link_ALPHA1-2 : bond 0.00205 ( 3) link_ALPHA1-2 : angle 2.15347 ( 9) link_ALPHA1-3 : bond 0.01066 ( 4) link_ALPHA1-3 : angle 2.03814 ( 12) link_ALPHA1-6 : bond 0.00646 ( 1) link_ALPHA1-6 : angle 1.43142 ( 3) link_BETA1-4 : bond 0.00697 ( 10) link_BETA1-4 : angle 2.25859 ( 30) link_NAG-ASN : bond 0.00483 ( 28) link_NAG-ASN : angle 3.32727 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 351 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 GLU cc_start: 0.7945 (tp30) cc_final: 0.7235 (tp30) REVERT: C 475 MET cc_start: 0.7675 (mmt) cc_final: 0.7449 (mmt) REVERT: D 27 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7639 (t70) REVERT: D 80 ASP cc_start: 0.7394 (p0) cc_final: 0.6880 (p0) REVERT: E 36 ILE cc_start: 0.8791 (mm) cc_final: 0.8463 (tt) REVERT: E 63 ASP cc_start: 0.8749 (t70) cc_final: 0.7996 (t0) REVERT: F 50 LYS cc_start: 0.8547 (mppt) cc_final: 0.8327 (mptt) REVERT: F 63 ASP cc_start: 0.8762 (t70) cc_final: 0.8452 (t0) REVERT: F 66 ASN cc_start: 0.8010 (t0) cc_final: 0.7803 (m-40) REVERT: F 73 ASN cc_start: 0.7391 (t0) cc_final: 0.7186 (t0) REVERT: H 12 ASN cc_start: 0.8114 (m-40) cc_final: 0.7487 (t0) REVERT: H 72 ASP cc_start: 0.8107 (t0) cc_final: 0.7820 (t0) REVERT: H 91 TYR cc_start: 0.7918 (m-10) cc_final: 0.7494 (m-10) REVERT: I 10 GLU cc_start: 0.7303 (tp30) cc_final: 0.6967 (tp30) REVERT: L 50 GLU cc_start: 0.7858 (tp30) cc_final: 0.7560 (tp30) REVERT: L 54 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7600 (mtm-85) REVERT: L 66 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7619 (ttpp) REVERT: L 79 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8409 (mm-40) REVERT: P 23 GLN cc_start: 0.8561 (tm-30) cc_final: 0.7871 (tm-30) REVERT: P 46 GLU cc_start: 0.8219 (tt0) cc_final: 0.7703 (pm20) REVERT: P 72 ASP cc_start: 0.8256 (t0) cc_final: 0.7861 (t0) REVERT: P 73 GLU cc_start: 0.8774 (pm20) cc_final: 0.8383 (pm20) REVERT: Q 21 ILE cc_start: 0.8492 (mt) cc_final: 0.8099 (pt) REVERT: Q 36 TYR cc_start: 0.7615 (m-80) cc_final: 0.7221 (m-80) REVERT: Q 53 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8985 (mm-30) REVERT: Q 54 ARG cc_start: 0.8528 (ptp-110) cc_final: 0.7834 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7321 (m-80) cc_final: 0.6750 (m-80) REVERT: Q 79 GLN cc_start: 0.7265 (mp10) cc_final: 0.6955 (mp10) REVERT: Z 595 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8540 (mm) REVERT: Z 622 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7139 (tt) REVERT: Z 629 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8108 (mm) outliers start: 61 outliers final: 50 residues processed: 392 average time/residue: 0.1310 time to fit residues: 80.9677 Evaluate side-chains 395 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 ARG Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain X residue 638 TYR Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 604 CYS Chi-restraints excluded: chain Y residue 616 ASN Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 622 ILE Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 87 optimal weight: 0.7980 chunk 239 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.137337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096592 restraints weight = 91116.602| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 5.05 r_work: 0.3262 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20104 Z= 0.135 Angle : 0.675 11.435 27470 Z= 0.331 Chirality : 0.046 0.406 3238 Planarity : 0.004 0.064 3402 Dihedral : 6.909 53.135 3596 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.56 % Allowed : 23.19 % Favored : 74.25 % 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: -2.47 (0.16), residues: 2438 helix: -1.02 (0.25), residues: 432 sheet: -1.13 (0.19), residues: 748 loop : -2.20 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P 83 TYR 0.022 0.001 TYR L 49 PHE 0.014 0.001 PHE H 63 TRP 0.048 0.002 TRP B 96 HIS 0.014 0.001 HIS P 81 Details of bonding type rmsd covalent geometry : bond 0.00317 (20018) covalent geometry : angle 0.64930 (27252) SS BOND : bond 0.00332 ( 40) SS BOND : angle 1.03526 ( 80) hydrogen bonds : bond 0.03199 ( 591) hydrogen bonds : angle 5.38420 ( 1555) link_ALPHA1-2 : bond 0.00191 ( 3) link_ALPHA1-2 : angle 1.85241 ( 9) link_ALPHA1-3 : bond 0.01242 ( 4) link_ALPHA1-3 : angle 1.37479 ( 12) link_ALPHA1-6 : bond 0.00753 ( 1) link_ALPHA1-6 : angle 1.29897 ( 3) link_BETA1-4 : bond 0.00794 ( 10) link_BETA1-4 : angle 2.08282 ( 30) link_NAG-ASN : bond 0.00450 ( 28) link_NAG-ASN : angle 3.00814 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4876 Ramachandran restraints generated. 2438 Oldfield, 0 Emsley, 2438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TRP cc_start: 0.7509 (m-10) cc_final: 0.7048 (m-90) REVERT: B 91 GLU cc_start: 0.7833 (tp30) cc_final: 0.7469 (tp30) REVERT: D 27 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7441 (t-90) REVERT: D 80 ASP cc_start: 0.7428 (p0) cc_final: 0.6928 (p0) REVERT: E 36 ILE cc_start: 0.8773 (mm) cc_final: 0.8430 (tt) REVERT: E 63 ASP cc_start: 0.8755 (t70) cc_final: 0.7982 (t0) REVERT: E 85 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7053 (mp0) REVERT: F 50 LYS cc_start: 0.8509 (mppt) cc_final: 0.8308 (mptt) REVERT: F 63 ASP cc_start: 0.8738 (t70) cc_final: 0.8421 (t0) REVERT: F 73 ASN cc_start: 0.7351 (t0) cc_final: 0.7139 (t0) REVERT: H 12 ASN cc_start: 0.8083 (m-40) cc_final: 0.7447 (t0) REVERT: H 63 PHE cc_start: 0.8890 (m-80) cc_final: 0.8543 (m-80) REVERT: H 72 ASP cc_start: 0.8064 (t0) cc_final: 0.7819 (t0) REVERT: H 91 TYR cc_start: 0.7797 (m-10) cc_final: 0.7433 (m-10) REVERT: I 10 GLU cc_start: 0.7358 (tp30) cc_final: 0.7044 (tp30) REVERT: L 50 GLU cc_start: 0.7747 (tp30) cc_final: 0.7430 (tp30) REVERT: L 54 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7557 (mtm-85) REVERT: L 66 LYS cc_start: 0.7829 (ttpp) cc_final: 0.7622 (ttpp) REVERT: L 79 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8409 (mm-40) REVERT: P 23 GLN cc_start: 0.8512 (tm-30) cc_final: 0.7892 (tm-30) REVERT: P 43 GLN cc_start: 0.8731 (pm20) cc_final: 0.8437 (pm20) REVERT: P 46 GLU cc_start: 0.8098 (tt0) cc_final: 0.7728 (pt0) REVERT: P 72 ASP cc_start: 0.8333 (t0) cc_final: 0.7937 (t0) REVERT: P 73 GLU cc_start: 0.8740 (pm20) cc_final: 0.8464 (pm20) REVERT: Q 21 ILE cc_start: 0.8524 (mt) cc_final: 0.8175 (pt) REVERT: Q 36 TYR cc_start: 0.7535 (m-80) cc_final: 0.7148 (m-80) REVERT: Q 53 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8951 (mm-30) REVERT: Q 54 ARG cc_start: 0.8499 (ptp-110) cc_final: 0.7772 (ptp-110) REVERT: Q 62 PHE cc_start: 0.7294 (m-80) cc_final: 0.6745 (m-80) REVERT: X 632 ASP cc_start: 0.9125 (t70) cc_final: 0.8914 (m-30) REVERT: Z 629 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8006 (mm) outliers start: 50 outliers final: 43 residues processed: 393 average time/residue: 0.1295 time to fit residues: 80.5204 Evaluate side-chains 395 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 350 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 296 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 ASN Chi-restraints excluded: chain P residue 100 ASP Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain X residue 566 LEU Chi-restraints excluded: chain X residue 573 ILE Chi-restraints excluded: chain Y residue 570 VAL Chi-restraints excluded: chain Y residue 595 ILE Chi-restraints excluded: chain Y residue 652 GLN Chi-restraints excluded: chain Z residue 595 ILE Chi-restraints excluded: chain Z residue 606 THR Chi-restraints excluded: chain Z residue 629 LEU Chi-restraints excluded: chain Z residue 631 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 125 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 202 optimal weight: 0.0050 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** P 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 540 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 = 0.4025 r_free = 0.4025 target = 0.137231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097040 restraints weight = 84885.587| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.98 r_work: 0.3254 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 20104 Z= 0.167 Angle : 0.813 59.199 27470 Z= 0.437 Chirality : 0.047 0.396 3238 Planarity : 0.004 0.064 3402 Dihedral : 6.910 53.086 3596 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.46 % Allowed : 23.19 % Favored : 74.35 % 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: -2.46 (0.16), residues: 2438 helix: -1.01 (0.25), residues: 432 sheet: -1.12 (0.19), residues: 748 loop : -2.19 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG P 83 TYR 0.022 0.001 TYR L 49 PHE 0.009 0.001 PHE C 233 TRP 0.036 0.002 TRP B 96 HIS 0.009 0.001 HIS P 81 Details of bonding type rmsd covalent geometry : bond 0.00380 (20018) covalent geometry : angle 0.79140 (27252) SS BOND : bond 0.00341 ( 40) SS BOND : angle 1.13071 ( 80) hydrogen bonds : bond 0.03206 ( 591) hydrogen bonds : angle 5.38408 ( 1555) link_ALPHA1-2 : bond 0.00241 ( 3) link_ALPHA1-2 : angle 1.90284 ( 9) link_ALPHA1-3 : bond 0.01669 ( 4) link_ALPHA1-3 : angle 1.59419 ( 12) link_ALPHA1-6 : bond 0.00759 ( 1) link_ALPHA1-6 : angle 1.30318 ( 3) link_BETA1-4 : bond 0.01036 ( 10) link_BETA1-4 : angle 2.20215 ( 30) link_NAG-ASN : bond 0.00409 ( 28) link_NAG-ASN : angle 3.04865 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5866.73 seconds wall clock time: 101 minutes 2.66 seconds (6062.66 seconds total)