Starting phenix.real_space_refine on Sun Nov 17 10:02:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/11_2024/8j8r_36078.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/11_2024/8j8r_36078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/11_2024/8j8r_36078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/11_2024/8j8r_36078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/11_2024/8j8r_36078.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/11_2024/8j8r_36078.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.121 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 27 5.16 5 C 8522 2.51 5 N 2304 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13424 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2691 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2695 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2693 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 798 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 911 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.25, per 1000 atoms: 0.61 Number of scatterers: 13424 At special positions: 0 Unit cell: (148.664, 141.47, 91.1164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 9 15.00 O 2562 8.00 N 2304 7.00 C 8522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.04 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 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 32 sheets defined 4.1% alpha, 48.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.754A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.080A pdb=" N ARG A 283 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'C' and resid 45 through 50 Processing helix chain 'C' and resid 99 through 110 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.877A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.885A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 removed outlier: 3.921A pdb=" N THR M 94 " --> pdb=" O ALA M 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.793A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 27 through 29 removed outlier: 3.793A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 9.899A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU A 141 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.656A pdb=" N SER A 197 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 224 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.547A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 319 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 240 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 321 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN A 238 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG A 323 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 236 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 325 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 234 " --> pdb=" O LYS A 325 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 327 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE A 232 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL A 329 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE A 232 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU A 258 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL A 234 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN A 256 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 236 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 113 through 118 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.762A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 144 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B 54 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLN B 86 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 56 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASN B 84 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 58 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 82 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 60 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 29 removed outlier: 3.762A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS B 171 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N VAL B 143 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU B 141 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 184 through 189 removed outlier: 3.501A pdb=" N LEU B 200 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.990A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 344 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N VAL B 320 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 329 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 231 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE B 232 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLU B 258 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 234 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN B 256 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 236 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AB3, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.834A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 54 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 86 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL C 56 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN C 84 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 58 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 82 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 60 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.834A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LYS C 171 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N VAL C 143 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 141 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 184 through 190 removed outlier: 3.715A pdb=" N SER C 197 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN C 224 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 208 through 209 removed outlier: 3.967A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C 344 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 320 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.557A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.217A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 removed outlier: 6.217A pdb=" N GLY D 13 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.641A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.894A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.894A pdb=" N LEU E 12 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 98 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AC5, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.483A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 13 through 15 removed outlier: 6.483A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AC8, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.673A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 85 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.673A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 85 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 6 through 10 Processing sheet with id=AD2, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.434A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N SER M 35 " --> pdb=" O SER M 55 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER M 55 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE M 37 " --> pdb=" O SER M 53 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP M 39 " --> pdb=" O VAL M 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.434A pdb=" N GLY M 13 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR M 112 " --> pdb=" O ARG M 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 6 through 8 removed outlier: 3.535A pdb=" N VAL N 20 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.819A pdb=" N LEU N 12 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR N 50 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1398 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: 5.06 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4326 1.34 - 1.46: 3188 1.46 - 1.58: 6151 1.58 - 1.70: 31 1.70 - 1.81: 39 Bond restraints: 13735 Sorted by residual: bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO V 349 " pdb=" P TPO V 349 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OG1 TPO U 307 " pdb=" P TPO U 307 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO G 363 " pdb=" P TPO G 363 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" OG1 TPO U 310 " pdb=" P TPO U 310 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.89e+01 ... (remaining 13730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 18485 2.56 - 5.12: 160 5.12 - 7.68: 29 7.68 - 10.24: 7 10.24 - 12.80: 5 Bond angle restraints: 18686 Sorted by residual: angle pdb=" C CYS B 69 " pdb=" N ASP B 70 " pdb=" CA ASP B 70 " ideal model delta sigma weight residual 123.03 115.87 7.16 1.34e+00 5.57e-01 2.85e+01 angle pdb=" C VAL B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta sigma weight residual 122.93 115.81 7.12 1.45e+00 4.76e-01 2.41e+01 angle pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" CD PRO C 97 " ideal model delta sigma weight residual 112.00 105.27 6.73 1.40e+00 5.10e-01 2.31e+01 angle pdb=" N VAL B 71 " pdb=" CA VAL B 71 " pdb=" C VAL B 71 " ideal model delta sigma weight residual 108.81 101.87 6.94 1.62e+00 3.81e-01 1.84e+01 angle pdb=" CB TPO G 363 " pdb=" OG1 TPO G 363 " pdb=" P TPO G 363 " ideal model delta sigma weight residual 119.31 106.51 12.80 3.00e+00 1.11e-01 1.82e+01 ... (remaining 18681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7347 17.79 - 35.58: 638 35.58 - 53.37: 197 53.37 - 71.16: 22 71.16 - 88.95: 23 Dihedral angle restraints: 8227 sinusoidal: 3187 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 59.96 33.04 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 99 " pdb=" CB CYS M 99 " ideal model delta sinusoidal sigma weight residual 93.00 64.38 28.62 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP B 79 " pdb=" CB ASP B 79 " pdb=" CG ASP B 79 " pdb=" OD1 ASP B 79 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 8224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1808 0.058 - 0.116: 266 0.116 - 0.174: 33 0.174 - 0.232: 1 0.232 - 0.291: 1 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB TPO V 352 " pdb=" CA TPO V 352 " pdb=" OG1 TPO V 352 " pdb=" CG2 TPO V 352 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA CYS B 69 " pdb=" N CYS B 69 " pdb=" C CYS B 69 " pdb=" CB CYS B 69 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2106 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 96 " -0.051 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO C 97 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 84 " 0.011 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE E 84 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 84 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 84 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 84 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 84 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 84 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO C 92 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.028 5.00e-02 4.00e+02 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 923 2.74 - 3.28: 12445 3.28 - 3.82: 21241 3.82 - 4.36: 25148 4.36 - 4.90: 46054 Nonbonded interactions: 105811 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OH TYR B 209 " model vdw 2.199 3.040 nonbonded pdb=" N GLU C 177 " pdb=" OE1 GLU C 177 " model vdw 2.216 3.120 nonbonded pdb=" N ASN C 93 " pdb=" OD1 ASN C 93 " model vdw 2.250 3.120 nonbonded pdb=" OD2 ASP A 136 " pdb=" NH1 ARG A 286 " model vdw 2.253 3.120 nonbonded pdb=" O THR C 222 " pdb=" OG1 THR C 222 " model vdw 2.262 3.040 ... (remaining 105806 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 7 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 160 or \ (resid 161 through 162 and (name N or name CA or name C or name O or name CB )) \ or resid 163 through 191 or (resid 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 307 or (resid 308 and (name N or name CA o \ r name C or name O or name CB )) or resid 309 through 311 or (resid 312 through \ 314 and (name N or name CA or name C or name O or name CB )) or resid 315 throug \ h 350)) selection = (chain 'B' and (resid 7 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 75 or (resid 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 110 or (r \ esid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 t \ hrough 157 or (resid 158 and (name N or name CA or name C or name O or name CB ) \ ) or resid 159 through 160 or (resid 161 through 162 and (name N or name CA or n \ ame C or name O or name CB )) or resid 163 through 307 or (resid 308 and (name N \ or name CA or name C or name O or name CB )) or resid 309 through 350)) selection = (chain 'C' and (resid 7 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or \ resid 77 through 110 or (resid 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 311 or (resid 312 through 314 and (name N or na \ me CA or name C or name O or name CB )) or resid 315 through 350)) } ncs_group { reference = (chain 'D' and (resid 5 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 106 or (resid 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) selection = (chain 'H' and (resid 5 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 122)) selection = (chain 'M' and (resid 5 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 122)) } ncs_group { reference = (chain 'E' and (resid 1 through 30 or resid 33 through 107)) selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.970 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.004 0.110 13735 Z= 0.302 Angle : 0.636 12.797 18686 Z= 0.307 Chirality : 0.044 0.291 2109 Planarity : 0.004 0.074 2391 Dihedral : 15.504 88.948 4971 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 18.24 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.22), residues: 1687 helix: 1.80 (0.82), residues: 36 sheet: 1.51 (0.20), residues: 790 loop : -0.24 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 106 HIS 0.006 0.001 HIS B 160 PHE 0.039 0.001 PHE E 84 TYR 0.026 0.001 TYR C 48 ARG 0.009 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 1.712 Fit side-chains outliers start: 33 outliers final: 33 residues processed: 224 average time/residue: 0.9454 time to fit residues: 238.3604 Evaluate side-chains 218 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 131 GLN B 218 ASN B 220 HIS B 281 ASN C 262 GLN D 6 GLN H 80 ASN L 7 GLN M 38 HIS U 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13735 Z= 0.163 Angle : 0.551 9.048 18686 Z= 0.285 Chirality : 0.044 0.172 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.789 58.761 1946 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.16 % Allowed : 17.01 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1687 helix: 2.09 (0.85), residues: 36 sheet: 1.55 (0.19), residues: 784 loop : -0.34 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.005 0.001 HIS B 160 PHE 0.028 0.001 PHE E 84 TYR 0.012 0.001 TYR H 107 ARG 0.006 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 1.493 Fit side-chains REVERT: B 316 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7921 (mp) REVERT: C 30 ASP cc_start: 0.8285 (t0) cc_final: 0.8054 (t0) REVERT: C 163 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.6921 (p0) REVERT: D 92 GLU cc_start: 0.7337 (pm20) cc_final: 0.7052 (pm20) outliers start: 46 outliers final: 26 residues processed: 231 average time/residue: 0.9848 time to fit residues: 254.8771 Evaluate side-chains 210 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS H 80 ASN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13735 Z= 0.269 Angle : 0.589 7.446 18686 Z= 0.306 Chirality : 0.045 0.163 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.520 54.933 1922 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.73 % Allowed : 17.01 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1687 helix: 2.13 (0.85), residues: 36 sheet: 1.36 (0.19), residues: 789 loop : -0.41 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 106 HIS 0.006 0.001 HIS B 112 PHE 0.032 0.002 PHE M 105 TYR 0.017 0.001 TYR C 48 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 190 time to evaluate : 1.423 Fit side-chains REVERT: C 30 ASP cc_start: 0.8289 (t0) cc_final: 0.7982 (t0) REVERT: C 163 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7096 (p0) REVERT: D 49 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: D 92 GLU cc_start: 0.7562 (pm20) cc_final: 0.7268 (pm20) REVERT: E 89 CYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7589 (p) REVERT: H 92 GLU cc_start: 0.7679 (pm20) cc_final: 0.7423 (pm20) REVERT: L 93 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8844 (tmtm) outliers start: 69 outliers final: 46 residues processed: 240 average time/residue: 1.0631 time to fit residues: 286.3294 Evaluate side-chains 232 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13735 Z= 0.209 Angle : 0.558 7.999 18686 Z= 0.288 Chirality : 0.044 0.154 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.317 49.342 1920 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.14 % Allowed : 17.83 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1687 helix: 2.16 (0.86), residues: 36 sheet: 1.29 (0.19), residues: 789 loop : -0.40 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 50 HIS 0.004 0.001 HIS B 112 PHE 0.039 0.002 PHE E 84 TYR 0.015 0.001 TYR H 107 ARG 0.006 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 192 time to evaluate : 1.481 Fit side-chains REVERT: B 222 THR cc_start: 0.7747 (m) cc_final: 0.7365 (p) REVERT: C 30 ASP cc_start: 0.8236 (t0) cc_final: 0.7943 (t0) REVERT: C 163 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7038 (p0) REVERT: D 92 GLU cc_start: 0.7554 (pm20) cc_final: 0.7170 (pm20) REVERT: E 89 CYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7651 (p) REVERT: H 31 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8326 (m110) REVERT: H 49 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: H 86 MET cc_start: 0.7778 (mtp) cc_final: 0.6600 (mtp) REVERT: H 92 GLU cc_start: 0.7670 (pm20) cc_final: 0.7449 (pm20) REVERT: L 89 CYS cc_start: 0.7280 (OUTLIER) cc_final: 0.7040 (p) outliers start: 75 outliers final: 45 residues processed: 252 average time/residue: 0.9682 time to fit residues: 273.8981 Evaluate side-chains 234 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 40 optimal weight: 0.0170 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 220 HIS B 262 GLN H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13735 Z= 0.336 Angle : 0.621 7.997 18686 Z= 0.323 Chirality : 0.046 0.169 2109 Planarity : 0.005 0.052 2391 Dihedral : 5.480 46.838 1920 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.42 % Allowed : 18.66 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1687 helix: 2.11 (0.85), residues: 36 sheet: 1.18 (0.19), residues: 786 loop : -0.48 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 106 HIS 0.008 0.001 HIS B 160 PHE 0.039 0.002 PHE M 105 TYR 0.015 0.001 TYR H 107 ARG 0.008 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 188 time to evaluate : 1.701 Fit side-chains REVERT: C 30 ASP cc_start: 0.8438 (t0) cc_final: 0.8082 (t0) REVERT: C 163 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7065 (p0) REVERT: C 195 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: D 49 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: D 92 GLU cc_start: 0.7582 (pm20) cc_final: 0.7209 (pm20) REVERT: E 89 CYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7747 (p) REVERT: H 31 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8354 (m110) REVERT: H 49 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: H 86 MET cc_start: 0.7991 (mtp) cc_final: 0.6755 (mtp) REVERT: H 92 GLU cc_start: 0.7682 (pm20) cc_final: 0.7455 (pm20) REVERT: L 89 CYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7249 (p) REVERT: L 93 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8860 (tmtm) outliers start: 79 outliers final: 54 residues processed: 250 average time/residue: 0.9565 time to fit residues: 268.3168 Evaluate side-chains 243 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 181 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 86 GLN B 160 HIS B 218 ASN B 220 HIS B 262 GLN H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13735 Z= 0.216 Angle : 0.569 10.050 18686 Z= 0.291 Chirality : 0.044 0.148 2109 Planarity : 0.004 0.051 2391 Dihedral : 5.240 41.579 1920 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.76 % Allowed : 19.14 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1687 helix: 2.15 (0.86), residues: 36 sheet: 1.18 (0.19), residues: 786 loop : -0.47 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 106 HIS 0.009 0.001 HIS B 160 PHE 0.027 0.002 PHE M 105 TYR 0.016 0.001 TYR H 107 ARG 0.007 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 182 time to evaluate : 1.590 Fit side-chains REVERT: C 30 ASP cc_start: 0.8365 (t0) cc_final: 0.8032 (t0) REVERT: C 163 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7169 (p0) REVERT: C 195 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: D 49 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: D 92 GLU cc_start: 0.7505 (pm20) cc_final: 0.7127 (pm20) REVERT: E 89 CYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7687 (p) REVERT: H 49 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: H 86 MET cc_start: 0.7773 (mtp) cc_final: 0.6582 (mtp) REVERT: H 92 GLU cc_start: 0.7665 (pm20) cc_final: 0.7390 (pm20) REVERT: L 89 CYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7196 (p) outliers start: 84 outliers final: 50 residues processed: 249 average time/residue: 0.9358 time to fit residues: 261.8817 Evaluate side-chains 237 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS B 262 GLN H 80 ASN L 39 GLN N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13735 Z= 0.258 Angle : 0.589 8.470 18686 Z= 0.303 Chirality : 0.045 0.158 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.129 38.095 1918 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.28 % Allowed : 19.75 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1687 helix: 2.11 (0.85), residues: 36 sheet: 1.13 (0.19), residues: 786 loop : -0.50 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.040 0.002 PHE E 84 TYR 0.015 0.001 TYR H 107 ARG 0.007 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 185 time to evaluate : 1.456 Fit side-chains REVERT: B 207 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: C 30 ASP cc_start: 0.8209 (t0) cc_final: 0.7914 (t0) REVERT: C 163 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7282 (p0) REVERT: C 195 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: D 49 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: D 92 GLU cc_start: 0.7501 (pm20) cc_final: 0.7101 (pm20) REVERT: E 89 CYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7719 (p) REVERT: H 49 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: H 86 MET cc_start: 0.7814 (mtp) cc_final: 0.6597 (mtp) REVERT: H 92 GLU cc_start: 0.7663 (pm20) cc_final: 0.7455 (pm20) REVERT: L 89 CYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7212 (p) outliers start: 77 outliers final: 54 residues processed: 245 average time/residue: 0.9767 time to fit residues: 268.7676 Evaluate side-chains 240 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 chunk 101 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 79 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 218 ASN B 220 HIS B 262 GLN H 80 ASN L 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13735 Z= 0.156 Angle : 0.547 12.547 18686 Z= 0.276 Chirality : 0.043 0.151 2109 Planarity : 0.004 0.051 2391 Dihedral : 4.779 39.063 1917 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.32 % Allowed : 20.92 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.21), residues: 1687 helix: 2.21 (0.86), residues: 36 sheet: 1.21 (0.19), residues: 786 loop : -0.45 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 106 HIS 0.003 0.001 HIS B 112 PHE 0.024 0.001 PHE B 269 TYR 0.013 0.001 TYR H 107 ARG 0.009 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 1.567 Fit side-chains REVERT: B 222 THR cc_start: 0.7630 (m) cc_final: 0.7351 (p) REVERT: C 163 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7349 (p0) REVERT: C 195 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6574 (m-30) REVERT: D 92 GLU cc_start: 0.7470 (pm20) cc_final: 0.7228 (pm20) REVERT: E 89 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7620 (p) REVERT: H 86 MET cc_start: 0.7894 (mtp) cc_final: 0.6726 (mtp) REVERT: H 92 GLU cc_start: 0.7654 (pm20) cc_final: 0.7450 (pm20) REVERT: L 89 CYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7075 (p) outliers start: 63 outliers final: 48 residues processed: 246 average time/residue: 0.9369 time to fit residues: 260.2163 Evaluate side-chains 235 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 148 optimal weight: 0.0470 chunk 97 optimal weight: 0.0770 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS B 262 GLN C 131 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13735 Z= 0.178 Angle : 0.565 12.679 18686 Z= 0.285 Chirality : 0.044 0.150 2109 Planarity : 0.004 0.051 2391 Dihedral : 4.720 38.565 1917 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.05 % Allowed : 22.29 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1687 helix: 2.22 (0.87), residues: 36 sheet: 1.27 (0.19), residues: 780 loop : -0.39 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 50 HIS 0.003 0.001 HIS B 112 PHE 0.044 0.002 PHE E 84 TYR 0.013 0.001 TYR H 107 ARG 0.009 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 1.682 Fit side-chains revert: symmetry clash REVERT: B 222 THR cc_start: 0.7627 (m) cc_final: 0.7377 (p) REVERT: C 163 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7319 (p0) REVERT: C 195 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6577 (m-30) REVERT: C 258 GLU cc_start: 0.6044 (tm-30) cc_final: 0.5817 (tm-30) REVERT: D 92 GLU cc_start: 0.7457 (pm20) cc_final: 0.7218 (pm20) REVERT: E 89 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7660 (p) REVERT: H 86 MET cc_start: 0.7960 (mtp) cc_final: 0.6828 (mtp) REVERT: H 92 GLU cc_start: 0.7651 (pm20) cc_final: 0.7444 (pm20) REVERT: L 89 CYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7141 (p) outliers start: 59 outliers final: 50 residues processed: 237 average time/residue: 0.9919 time to fit residues: 264.9192 Evaluate side-chains 240 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 165 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 190 HIS B 262 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13735 Z= 0.183 Angle : 0.566 12.042 18686 Z= 0.287 Chirality : 0.044 0.150 2109 Planarity : 0.004 0.051 2391 Dihedral : 4.705 38.508 1917 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.05 % Allowed : 22.43 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1687 helix: 2.27 (0.87), residues: 36 sheet: 1.28 (0.19), residues: 780 loop : -0.38 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 50 HIS 0.003 0.001 HIS B 112 PHE 0.063 0.002 PHE E 84 TYR 0.013 0.001 TYR H 107 ARG 0.009 0.000 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: B 222 THR cc_start: 0.7633 (m) cc_final: 0.7376 (p) REVERT: C 163 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7322 (p0) REVERT: C 195 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6591 (m-30) REVERT: D 92 GLU cc_start: 0.7355 (pm20) cc_final: 0.7109 (pm20) REVERT: E 89 CYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7665 (p) REVERT: H 49 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: H 86 MET cc_start: 0.7968 (mtp) cc_final: 0.6827 (mtp) REVERT: H 92 GLU cc_start: 0.7647 (pm20) cc_final: 0.7444 (pm20) REVERT: L 89 CYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7142 (p) outliers start: 59 outliers final: 51 residues processed: 237 average time/residue: 0.9935 time to fit residues: 268.7047 Evaluate side-chains 245 residues out of total 1507 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 189 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 89 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 121 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 131 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN L 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112333 restraints weight = 19301.524| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.75 r_work: 0.3240 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13735 Z= 0.170 Angle : 0.560 13.732 18686 Z= 0.282 Chirality : 0.044 0.150 2109 Planarity : 0.004 0.051 2391 Dihedral : 4.602 38.131 1917 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.05 % Allowed : 22.22 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1687 helix: 2.29 (0.88), residues: 36 sheet: 1.31 (0.19), residues: 780 loop : -0.37 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 106 HIS 0.003 0.001 HIS B 112 PHE 0.021 0.001 PHE M 105 TYR 0.013 0.001 TYR H 107 ARG 0.004 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4801.81 seconds wall clock time: 87 minutes 20.42 seconds (5240.42 seconds total)