Starting phenix.real_space_refine on Sun Jun 15 07:46:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fsm_50728/06_2025/9fsm_50728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fsm_50728/06_2025/9fsm_50728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fsm_50728/06_2025/9fsm_50728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fsm_50728/06_2025/9fsm_50728.map" model { file = "/net/cci-nas-00/data/ceres_data/9fsm_50728/06_2025/9fsm_50728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fsm_50728/06_2025/9fsm_50728.cif" } resolution = 2.47 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10580 2.51 5 N 2950 2.21 5 O 3450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17060 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "B" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "C" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "D" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "E" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "F" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "G" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "H" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "I" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "J" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 19.66, per 1000 atoms: 1.15 Number of scatterers: 17060 At special positions: 0 Unit cell: (118.8, 114.48, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3450 8.00 N 2950 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 4.3 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 38.4% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.510A pdb=" N LYS A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.485A pdb=" N GLY A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 152 through 173 Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.686A pdb=" N ALA A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.526A pdb=" N LYS B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 131 through 140 removed outlier: 4.508A pdb=" N GLY B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 152 through 173 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.672A pdb=" N ALA B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 4.179A pdb=" N LEU B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.519A pdb=" N LYS C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 131 through 140 removed outlier: 4.504A pdb=" N GLY C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 152 through 173 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.642A pdb=" N ALA C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Proline residue: C 244 - end of helix removed outlier: 4.189A pdb=" N LEU C 258 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 45 Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.522A pdb=" N LYS D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.503A pdb=" N GLY D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 152 through 173 Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.674A pdb=" N ALA D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Proline residue: D 244 - end of helix removed outlier: 4.195A pdb=" N LEU D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.531A pdb=" N LYS E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 131 through 140 removed outlier: 4.506A pdb=" N GLY E 138 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 152 through 173 Processing helix chain 'E' and resid 238 through 259 removed outlier: 3.665A pdb=" N ALA E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Proline residue: E 244 - end of helix removed outlier: 4.158A pdb=" N LEU E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.512A pdb=" N LYS F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 131 through 140 removed outlier: 4.494A pdb=" N GLY F 138 " --> pdb=" O GLY F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 152 through 173 Processing helix chain 'F' and resid 238 through 257 removed outlier: 3.686A pdb=" N ALA F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Proline residue: F 244 - end of helix Processing helix chain 'G' and resid 37 through 45 Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.523A pdb=" N LYS G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 131 through 140 removed outlier: 4.508A pdb=" N GLY G 138 " --> pdb=" O GLY G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 152 through 173 Processing helix chain 'G' and resid 238 through 259 removed outlier: 3.678A pdb=" N ALA G 242 " --> pdb=" O LYS G 238 " (cutoff:3.500A) Proline residue: G 244 - end of helix removed outlier: 4.177A pdb=" N LEU G 258 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 45 Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.517A pdb=" N LYS H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'H' and resid 131 through 140 removed outlier: 4.506A pdb=" N GLY H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 152 through 173 Processing helix chain 'H' and resid 238 through 259 removed outlier: 3.642A pdb=" N ALA H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Proline residue: H 244 - end of helix removed outlier: 4.188A pdb=" N LEU H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY H 259 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 45 Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.523A pdb=" N LYS I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 131 through 140 removed outlier: 4.501A pdb=" N GLY I 138 " --> pdb=" O GLY I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 Processing helix chain 'I' and resid 152 through 173 Processing helix chain 'I' and resid 238 through 259 removed outlier: 3.676A pdb=" N ALA I 242 " --> pdb=" O LYS I 238 " (cutoff:3.500A) Proline residue: I 244 - end of helix removed outlier: 4.195A pdb=" N LEU I 258 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY I 259 " --> pdb=" O ALA I 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 45 Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.530A pdb=" N LYS J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 131 through 140 removed outlier: 4.506A pdb=" N GLY J 138 " --> pdb=" O GLY J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 152 through 173 Processing helix chain 'J' and resid 238 through 259 removed outlier: 3.664A pdb=" N ALA J 242 " --> pdb=" O LYS J 238 " (cutoff:3.500A) Proline residue: J 244 - end of helix removed outlier: 4.157A pdb=" N LEU J 258 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY J 259 " --> pdb=" O ALA J 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 54 removed outlier: 6.860A pdb=" N ASP A 176 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP A 120 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 178 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 118 " --> pdb=" O ASN A 178 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 180 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA A 116 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 182 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 67 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 109 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR A 69 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA A 111 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A 71 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 113 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 73 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 205 Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 54 removed outlier: 6.810A pdb=" N ASP B 176 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP B 120 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN B 178 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 118 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 180 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 116 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 182 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 67 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B 109 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA B 111 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 71 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL B 113 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS B 73 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS B 115 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 54 removed outlier: 6.795A pdb=" N ASP C 176 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C 120 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C 178 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS C 118 " --> pdb=" O ASN C 178 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 180 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 116 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 182 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 67 " --> pdb=" O TYR C 107 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 109 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 69 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA C 111 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN C 71 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL C 113 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS C 73 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS C 115 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 54 removed outlier: 6.825A pdb=" N ASP D 176 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP D 120 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN D 178 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS D 118 " --> pdb=" O ASN D 178 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 180 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 116 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D 182 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR D 67 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 109 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR D 69 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA D 111 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN D 71 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL D 113 " --> pdb=" O GLN D 71 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS D 73 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS D 115 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 54 removed outlier: 6.782A pdb=" N ASP E 176 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP E 120 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN E 178 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS E 118 " --> pdb=" O ASN E 178 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR E 180 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA E 116 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 182 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR E 67 " --> pdb=" O TYR E 107 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE E 109 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR E 69 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA E 111 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN E 71 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 113 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS E 73 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LYS E 115 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 54 removed outlier: 6.893A pdb=" N ASP F 176 " --> pdb=" O ASP F 120 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP F 120 " --> pdb=" O ASP F 176 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN F 178 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS F 118 " --> pdb=" O ASN F 178 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR F 180 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA F 116 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 182 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR F 67 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE F 109 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR F 69 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA F 111 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN F 71 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL F 113 " --> pdb=" O GLN F 71 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS F 73 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS F 115 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 49 through 54 removed outlier: 6.834A pdb=" N ASP G 176 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G 120 " --> pdb=" O ASP G 176 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN G 178 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS G 118 " --> pdb=" O ASN G 178 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR G 180 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA G 116 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE G 182 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR G 67 " --> pdb=" O TYR G 107 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE G 109 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR G 69 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA G 111 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN G 71 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL G 113 " --> pdb=" O GLN G 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS G 73 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS G 115 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 49 through 54 removed outlier: 6.795A pdb=" N ASP H 176 " --> pdb=" O ASP H 120 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP H 120 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN H 178 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS H 118 " --> pdb=" O ASN H 178 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR H 180 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 116 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE H 182 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR H 67 " --> pdb=" O TYR H 107 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE H 109 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR H 69 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA H 111 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN H 71 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL H 113 " --> pdb=" O GLN H 71 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS H 73 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS H 115 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 49 through 54 removed outlier: 6.822A pdb=" N ASP I 176 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP I 120 " --> pdb=" O ASP I 176 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN I 178 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS I 118 " --> pdb=" O ASN I 178 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR I 180 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA I 116 " --> pdb=" O THR I 180 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE I 182 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR I 67 " --> pdb=" O TYR I 107 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE I 109 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR I 69 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA I 111 " --> pdb=" O TYR I 69 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN I 71 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL I 113 " --> pdb=" O GLN I 71 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS I 73 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS I 115 " --> pdb=" O LYS I 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 49 through 54 removed outlier: 6.751A pdb=" N ASP J 176 " --> pdb=" O ASP J 120 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP J 120 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN J 178 " --> pdb=" O LYS J 118 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS J 118 " --> pdb=" O ASN J 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR J 180 " --> pdb=" O ALA J 116 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA J 116 " --> pdb=" O THR J 180 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE J 182 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR J 67 " --> pdb=" O TYR J 107 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE J 109 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR J 69 " --> pdb=" O ILE J 109 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA J 111 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN J 71 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL J 113 " --> pdb=" O GLN J 71 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS J 73 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LYS J 115 " --> pdb=" O LYS J 73 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2703 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: 5.64 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3307 1.32 - 1.45: 3743 1.45 - 1.57: 10040 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 17240 Sorted by residual: bond pdb=" N ASN E 149 " pdb=" CA ASN E 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.68e+00 bond pdb=" N ASN J 149 " pdb=" CA ASN J 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.63e+00 bond pdb=" N ASN F 149 " pdb=" CA ASN F 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.63e+00 bond pdb=" N ASN G 149 " pdb=" CA ASN G 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.63e+00 bond pdb=" N ASN C 149 " pdb=" CA ASN C 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.58e+00 ... (remaining 17235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 21925 1.19 - 2.38: 1108 2.38 - 3.57: 134 3.57 - 4.75: 89 4.75 - 5.94: 34 Bond angle restraints: 23290 Sorted by residual: angle pdb=" C TYR H 148 " pdb=" N ASN H 149 " pdb=" CA ASN H 149 " ideal model delta sigma weight residual 121.19 126.83 -5.64 1.59e+00 3.96e-01 1.26e+01 angle pdb=" C TYR C 148 " pdb=" N ASN C 149 " pdb=" CA ASN C 149 " ideal model delta sigma weight residual 121.19 126.83 -5.64 1.59e+00 3.96e-01 1.26e+01 angle pdb=" C TYR I 148 " pdb=" N ASN I 149 " pdb=" CA ASN I 149 " ideal model delta sigma weight residual 121.19 126.82 -5.63 1.59e+00 3.96e-01 1.25e+01 angle pdb=" C TYR B 148 " pdb=" N ASN B 149 " pdb=" CA ASN B 149 " ideal model delta sigma weight residual 121.19 126.80 -5.61 1.59e+00 3.96e-01 1.25e+01 angle pdb=" C TYR D 148 " pdb=" N ASN D 149 " pdb=" CA ASN D 149 " ideal model delta sigma weight residual 121.19 126.80 -5.61 1.59e+00 3.96e-01 1.24e+01 ... (remaining 23285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9175 17.96 - 35.92: 1017 35.92 - 53.89: 286 53.89 - 71.85: 52 71.85 - 89.81: 60 Dihedral angle restraints: 10590 sinusoidal: 4110 harmonic: 6480 Sorted by residual: dihedral pdb=" CA GLY A 138 " pdb=" C GLY A 138 " pdb=" N ALA A 139 " pdb=" CA ALA A 139 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLY H 138 " pdb=" C GLY H 138 " pdb=" N ALA H 139 " pdb=" CA ALA H 139 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLY F 138 " pdb=" C GLY F 138 " pdb=" N ALA F 139 " pdb=" CA ALA F 139 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 10587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1499 0.027 - 0.054: 749 0.054 - 0.081: 244 0.081 - 0.107: 149 0.107 - 0.134: 99 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA GLU C 175 " pdb=" N GLU C 175 " pdb=" C GLU C 175 " pdb=" CB GLU C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA GLU H 175 " pdb=" N GLU H 175 " pdb=" C GLU H 175 " pdb=" CB GLU H 175 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA GLU B 175 " pdb=" N GLU B 175 " pdb=" C GLU B 175 " pdb=" CB GLU B 175 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2737 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 138 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C GLY F 138 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY F 138 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA F 139 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 138 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C GLY A 138 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 138 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 138 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C GLY I 138 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY I 138 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA I 139 " -0.010 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3342 2.77 - 3.31: 15181 3.31 - 3.84: 29186 3.84 - 4.37: 33772 4.37 - 4.90: 59695 Nonbonded interactions: 141176 Sorted by model distance: nonbonded pdb=" N ASP E 77 " pdb=" OD1 ASP E 77 " model vdw 2.244 3.120 nonbonded pdb=" N ASP F 77 " pdb=" OD1 ASP F 77 " model vdw 2.244 3.120 nonbonded pdb=" N ASP A 77 " pdb=" OD1 ASP A 77 " model vdw 2.244 3.120 nonbonded pdb=" N ASP J 77 " pdb=" OD1 ASP J 77 " model vdw 2.245 3.120 nonbonded pdb=" N ASP D 77 " pdb=" OD1 ASP D 77 " model vdw 2.246 3.120 ... (remaining 141171 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 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: 11.770 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 53.050 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.130 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 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 : 0.006 0.043 17250 Z= 0.290 Angle : 0.654 5.942 23290 Z= 0.367 Chirality : 0.043 0.134 2740 Planarity : 0.003 0.031 3000 Dihedral : 17.810 89.810 6450 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.39 % Allowed : 21.06 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.04 (0.19), residues: 2250 helix: 1.43 (0.20), residues: 710 sheet: -0.04 (0.18), residues: 870 loop : -1.28 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 127 HIS 0.001 0.000 HIS C 222 PHE 0.008 0.003 PHE B 239 TYR 0.007 0.001 TYR B 179 ARG 0.007 0.001 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.10352 ( 991) hydrogen bonds : angle 6.11739 ( 2703) covalent geometry : bond 0.00638 (17240) covalent geometry : angle 0.65356 (23290) Misc. bond : bond 0.00105 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 581 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8092 (m) cc_final: 0.7836 (p) REVERT: A 248 ASP cc_start: 0.7238 (m-30) cc_final: 0.6874 (m-30) REVERT: B 248 ASP cc_start: 0.7387 (m-30) cc_final: 0.7121 (m-30) REVERT: B 252 LYS cc_start: 0.7506 (mttp) cc_final: 0.7255 (mmmm) REVERT: C 70 LEU cc_start: 0.7583 (mt) cc_final: 0.7294 (mm) REVERT: D 189 GLU cc_start: 0.6751 (tt0) cc_final: 0.6071 (pt0) REVERT: D 226 THR cc_start: 0.6708 (t) cc_final: 0.6411 (t) REVERT: D 248 ASP cc_start: 0.6892 (m-30) cc_final: 0.6673 (m-30) REVERT: E 57 THR cc_start: 0.7030 (m) cc_final: 0.6462 (m) REVERT: E 189 GLU cc_start: 0.7097 (tt0) cc_final: 0.6397 (tt0) REVERT: E 193 THR cc_start: 0.8205 (m) cc_final: 0.7714 (p) REVERT: F 128 LEU cc_start: 0.8264 (mt) cc_final: 0.8049 (mm) REVERT: G 55 SER cc_start: 0.7222 (OUTLIER) cc_final: 0.6918 (p) REVERT: H 217 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6307 (mp0) REVERT: I 119 MET cc_start: 0.5991 (ptp) cc_final: 0.5759 (ptp) REVERT: I 217 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6153 (mp0) REVERT: J 248 ASP cc_start: 0.6517 (m-30) cc_final: 0.6191 (m-30) outliers start: 61 outliers final: 18 residues processed: 629 average time/residue: 1.0703 time to fit residues: 767.8015 Evaluate side-chains 402 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 383 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 112 ASN Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 91 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 221 GLN B 186 GLN B 205 GLN B 221 GLN C 186 GLN D 110 GLN D 186 GLN D 221 GLN E 186 GLN E 231 ASN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN F 53 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 ASN G 110 GLN H 112 ASN H 186 GLN H 194 GLN H 225 GLN I 110 GLN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 233 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN J 225 GLN J 233 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.105700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079061 restraints weight = 86009.754| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.55 r_work: 0.2951 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17250 Z= 0.210 Angle : 0.780 10.474 23290 Z= 0.412 Chirality : 0.048 0.203 2740 Planarity : 0.005 0.087 3000 Dihedral : 10.635 85.441 2666 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.11 % Allowed : 27.33 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.18), residues: 2250 helix: 0.94 (0.19), residues: 740 sheet: 0.14 (0.18), residues: 830 loop : -1.12 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP H 127 HIS 0.007 0.002 HIS C 222 PHE 0.014 0.003 PHE C 239 TYR 0.018 0.002 TYR F 179 ARG 0.013 0.001 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 991) hydrogen bonds : angle 5.71148 ( 2703) covalent geometry : bond 0.00464 (17240) covalent geometry : angle 0.77972 (23290) Misc. bond : bond 0.00048 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 360 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8504 (t0) cc_final: 0.8234 (OUTLIER) REVERT: A 81 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8453 (m) REVERT: A 248 ASP cc_start: 0.8289 (m-30) cc_final: 0.8054 (m-30) REVERT: B 51 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7770 (ptpt) REVERT: B 204 ARG cc_start: 0.8451 (ttm110) cc_final: 0.7907 (ttm-80) REVERT: B 248 ASP cc_start: 0.8451 (m-30) cc_final: 0.7959 (m-30) REVERT: C 133 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6210 (pt0) REVERT: C 137 THR cc_start: 0.8068 (m) cc_final: 0.7743 (p) REVERT: C 217 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8251 (mt-10) REVERT: D 39 MET cc_start: 0.7359 (tpt) cc_final: 0.6964 (mmm) REVERT: D 49 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 133 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6218 (pt0) REVERT: D 137 THR cc_start: 0.8059 (m) cc_final: 0.7764 (p) REVERT: E 61 GLU cc_start: 0.8513 (pm20) cc_final: 0.8261 (pt0) REVERT: E 130 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7166 (tpp-160) REVERT: E 175 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8257 (mm-30) REVERT: E 204 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7989 (ttm-80) REVERT: E 241 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: F 119 MET cc_start: 0.8163 (pmm) cc_final: 0.7911 (pmm) REVERT: F 130 ARG cc_start: 0.7374 (mmt90) cc_final: 0.6960 (mmp80) REVERT: F 171 ASP cc_start: 0.8351 (t0) cc_final: 0.8075 (t70) REVERT: G 115 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7884 (mtmm) REVERT: G 217 GLU cc_start: 0.8309 (tt0) cc_final: 0.7877 (mt-10) REVERT: G 241 GLU cc_start: 0.8995 (tp30) cc_final: 0.8442 (tt0) REVERT: G 248 ASP cc_start: 0.8594 (m-30) cc_final: 0.8290 (m-30) REVERT: H 49 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7929 (tm-30) REVERT: H 53 GLN cc_start: 0.8638 (mt0) cc_final: 0.8385 (mt0) REVERT: H 56 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8765 (mm-30) REVERT: H 117 ASP cc_start: 0.8462 (p0) cc_final: 0.8221 (p0) REVERT: H 171 ASP cc_start: 0.7552 (t0) cc_final: 0.7014 (t0) REVERT: H 227 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7852 (ttm170) REVERT: H 241 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8636 (tm-30) REVERT: H 248 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8374 (m-30) REVERT: I 52 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8420 (p) REVERT: I 81 SER cc_start: 0.8624 (t) cc_final: 0.8345 (p) REVERT: I 103 ASP cc_start: 0.8796 (m-30) cc_final: 0.8568 (m-30) REVERT: I 199 ASN cc_start: 0.8165 (t0) cc_final: 0.7940 (t0) REVERT: I 217 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8010 (mt-10) REVERT: I 241 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8782 (tm-30) REVERT: I 248 ASP cc_start: 0.8428 (t0) cc_final: 0.8038 (m-30) REVERT: J 49 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8091 (tm-30) REVERT: J 81 SER cc_start: 0.8704 (m) cc_final: 0.8319 (p) REVERT: J 117 ASP cc_start: 0.7776 (p0) cc_final: 0.6935 (p0) REVERT: J 119 MET cc_start: 0.7936 (ptp) cc_final: 0.7367 (ptp) REVERT: J 180 THR cc_start: 0.8366 (m) cc_final: 0.8026 (t) REVERT: J 187 ILE cc_start: 0.9009 (pt) cc_final: 0.8750 (pp) REVERT: J 248 ASP cc_start: 0.8070 (m-30) cc_final: 0.7833 (m-30) outliers start: 110 outliers final: 33 residues processed: 428 average time/residue: 1.2383 time to fit residues: 590.0779 Evaluate side-chains 327 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 287 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 28 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 171 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 53 GLN D 110 GLN F 53 GLN F 178 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN I 186 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.068662 restraints weight = 71585.017| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.04 r_work: 0.2752 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.9804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17250 Z= 0.180 Angle : 0.628 10.062 23290 Z= 0.326 Chirality : 0.045 0.141 2740 Planarity : 0.004 0.032 3000 Dihedral : 10.086 82.872 2644 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.22 % Allowed : 28.33 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2250 helix: 1.36 (0.19), residues: 740 sheet: 0.12 (0.18), residues: 850 loop : -0.93 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 127 HIS 0.002 0.000 HIS A 222 PHE 0.023 0.003 PHE C 239 TYR 0.012 0.001 TYR G 96 ARG 0.007 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 991) hydrogen bonds : angle 5.10193 ( 2703) covalent geometry : bond 0.00407 (17240) covalent geometry : angle 0.62799 (23290) Misc. bond : bond 0.00027 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 298 time to evaluate : 1.768 Fit side-chains REVERT: A 119 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7730 (mtm) REVERT: A 148 TYR cc_start: 0.6188 (t80) cc_final: 0.5151 (t80) REVERT: A 227 ARG cc_start: 0.8618 (ttm-80) cc_final: 0.8395 (ttm-80) REVERT: B 79 ASP cc_start: 0.8400 (t0) cc_final: 0.8198 (t0) REVERT: B 119 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: B 248 ASP cc_start: 0.8489 (m-30) cc_final: 0.8253 (m-30) REVERT: D 61 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8786 (mt-10) REVERT: D 119 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7986 (pmm) REVERT: D 130 ARG cc_start: 0.7214 (mmt90) cc_final: 0.7004 (tpp-160) REVERT: E 175 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8043 (mm-30) REVERT: F 61 GLU cc_start: 0.9106 (tt0) cc_final: 0.8891 (mm-30) REVERT: F 130 ARG cc_start: 0.7703 (mmt90) cc_final: 0.7197 (mmp80) REVERT: G 49 GLU cc_start: 0.8334 (tp30) cc_final: 0.8112 (tm-30) REVERT: G 204 ARG cc_start: 0.8530 (ptp-110) cc_final: 0.8258 (ttm-80) REVERT: G 217 GLU cc_start: 0.8382 (tt0) cc_final: 0.8062 (mt-10) REVERT: G 248 ASP cc_start: 0.8647 (m-30) cc_final: 0.8401 (m-30) REVERT: H 173 MET cc_start: 0.8123 (tpp) cc_final: 0.7887 (mtt) REVERT: H 176 ASP cc_start: 0.7685 (t0) cc_final: 0.7441 (t0) REVERT: H 177 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7642 (m) REVERT: H 204 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8326 (ttm110) REVERT: H 227 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.8271 (ttm170) REVERT: H 248 ASP cc_start: 0.8664 (t0) cc_final: 0.8436 (m-30) REVERT: I 49 GLU cc_start: 0.8500 (tp30) cc_final: 0.8169 (tm-30) REVERT: I 52 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8862 (p) REVERT: I 103 ASP cc_start: 0.9172 (m-30) cc_final: 0.8949 (m-30) REVERT: I 127 TRP cc_start: 0.8297 (OUTLIER) cc_final: 0.8017 (p-90) REVERT: I 227 ARG cc_start: 0.8586 (ptm160) cc_final: 0.8277 (ttm170) REVERT: J 49 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8299 (tm-30) REVERT: J 119 MET cc_start: 0.8228 (ptp) cc_final: 0.7644 (ptp) REVERT: J 157 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6642 (tm) REVERT: J 248 ASP cc_start: 0.8386 (m-30) cc_final: 0.8107 (m-30) outliers start: 76 outliers final: 38 residues processed: 347 average time/residue: 1.4699 time to fit residues: 563.6052 Evaluate side-chains 307 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 127 TRP Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN G 110 GLN G 194 GLN G 225 GLN H 243 GLN I 112 ASN I 194 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.063622 restraints weight = 64367.294| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.67 r_work: 0.2651 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 1.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 17250 Z= 0.292 Angle : 0.684 9.002 23290 Z= 0.357 Chirality : 0.047 0.156 2740 Planarity : 0.004 0.033 3000 Dihedral : 10.583 78.879 2642 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.50 % Allowed : 27.72 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2250 helix: 1.13 (0.19), residues: 730 sheet: -0.13 (0.18), residues: 860 loop : -0.96 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 127 HIS 0.002 0.001 HIS H 222 PHE 0.023 0.004 PHE C 239 TYR 0.025 0.002 TYR H 179 ARG 0.007 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 991) hydrogen bonds : angle 5.49096 ( 2703) covalent geometry : bond 0.00664 (17240) covalent geometry : angle 0.68397 (23290) Misc. bond : bond 0.00025 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 285 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7499 (mpp) REVERT: A 128 LEU cc_start: 0.8489 (mt) cc_final: 0.8122 (mt) REVERT: A 148 TYR cc_start: 0.6692 (t80) cc_final: 0.5493 (t80) REVERT: A 184 ASP cc_start: 0.9142 (m-30) cc_final: 0.8802 (m-30) REVERT: A 227 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8230 (ttm-80) REVERT: B 119 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7482 (mpp) REVERT: B 184 ASP cc_start: 0.9168 (m-30) cc_final: 0.8894 (m-30) REVERT: C 120 ASP cc_start: 0.8476 (t70) cc_final: 0.8035 (t0) REVERT: C 130 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7243 (mmt90) REVERT: D 61 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8975 (mt-10) REVERT: E 241 GLU cc_start: 0.9105 (tt0) cc_final: 0.8809 (tt0) REVERT: F 120 ASP cc_start: 0.9021 (t0) cc_final: 0.8119 (t70) REVERT: G 132 TYR cc_start: 0.7479 (m-10) cc_final: 0.6894 (m-10) REVERT: G 173 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8338 (mtt) REVERT: G 217 GLU cc_start: 0.8512 (tt0) cc_final: 0.8234 (mt-10) REVERT: G 248 ASP cc_start: 0.8586 (m-30) cc_final: 0.8318 (m-30) REVERT: H 176 ASP cc_start: 0.8299 (t0) cc_final: 0.8071 (t0) REVERT: H 177 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8187 (m) REVERT: H 204 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8334 (ttm110) REVERT: H 227 ARG cc_start: 0.8672 (ttm-80) cc_final: 0.8463 (ttm170) REVERT: H 248 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: I 127 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.7634 (p-90) REVERT: J 52 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8932 (p) REVERT: J 119 MET cc_start: 0.8243 (ptp) cc_final: 0.7613 (ptp) REVERT: J 192 LYS cc_start: 0.9427 (mtmm) cc_final: 0.8985 (mmtm) outliers start: 81 outliers final: 42 residues processed: 341 average time/residue: 1.5754 time to fit residues: 587.3682 Evaluate side-chains 312 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain I residue 127 TRP Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 144 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN C 194 GLN G 225 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.065320 restraints weight = 81900.666| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.14 r_work: 0.2686 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 1.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17250 Z= 0.159 Angle : 0.561 10.587 23290 Z= 0.292 Chirality : 0.043 0.132 2740 Planarity : 0.003 0.033 3000 Dihedral : 10.176 78.969 2642 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.39 % Allowed : 27.83 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2250 helix: 1.37 (0.19), residues: 730 sheet: -0.05 (0.19), residues: 850 loop : -0.88 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 127 HIS 0.001 0.001 HIS D 222 PHE 0.016 0.003 PHE C 239 TYR 0.015 0.001 TYR H 179 ARG 0.008 0.001 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 991) hydrogen bonds : angle 5.08378 ( 2703) covalent geometry : bond 0.00356 (17240) covalent geometry : angle 0.56061 (23290) Misc. bond : bond 0.00020 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 285 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7654 (mpp) REVERT: A 148 TYR cc_start: 0.6828 (t80) cc_final: 0.5582 (t80) REVERT: A 227 ARG cc_start: 0.8738 (ttm-80) cc_final: 0.8451 (ttm170) REVERT: B 119 MET cc_start: 0.8193 (mtp) cc_final: 0.7511 (mpp) REVERT: B 148 TYR cc_start: 0.6385 (t80) cc_final: 0.5298 (t80) REVERT: B 184 ASP cc_start: 0.9136 (m-30) cc_final: 0.8864 (m-30) REVERT: B 204 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8282 (ttm-80) REVERT: C 120 ASP cc_start: 0.8150 (t70) cc_final: 0.7730 (t0) REVERT: C 148 TYR cc_start: 0.6031 (t80) cc_final: 0.5146 (t80) REVERT: C 175 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7657 (mm-30) REVERT: C 176 ASP cc_start: 0.8782 (t0) cc_final: 0.8421 (t70) REVERT: D 61 GLU cc_start: 0.9251 (mt-10) cc_final: 0.9033 (mt-10) REVERT: F 120 ASP cc_start: 0.8714 (t0) cc_final: 0.8350 (t70) REVERT: F 175 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7795 (mm-30) REVERT: G 173 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8363 (mtt) REVERT: G 204 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7898 (ttm170) REVERT: G 217 GLU cc_start: 0.8444 (tt0) cc_final: 0.8223 (mt-10) REVERT: G 248 ASP cc_start: 0.8658 (m-30) cc_final: 0.8413 (m-30) REVERT: H 177 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8168 (m) REVERT: H 181 MET cc_start: 0.8485 (ttp) cc_final: 0.8109 (ttm) REVERT: H 227 ARG cc_start: 0.8664 (ttm-80) cc_final: 0.8301 (ttm170) REVERT: I 227 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8383 (ttm170) REVERT: J 117 ASP cc_start: 0.8278 (p0) cc_final: 0.8009 (p0) REVERT: J 119 MET cc_start: 0.8365 (ptp) cc_final: 0.7771 (ptp) REVERT: J 192 LYS cc_start: 0.9436 (mtmm) cc_final: 0.8981 (mmtm) REVERT: J 248 ASP cc_start: 0.8438 (m-30) cc_final: 0.8095 (m-30) outliers start: 61 outliers final: 36 residues processed: 328 average time/residue: 1.4886 time to fit residues: 534.8869 Evaluate side-chains 307 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 176 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 210 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 203 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 221 GLN F 194 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.063231 restraints weight = 73731.522| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.88 r_work: 0.2636 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 1.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17250 Z= 0.243 Angle : 0.616 10.053 23290 Z= 0.319 Chirality : 0.045 0.140 2740 Planarity : 0.003 0.036 3000 Dihedral : 10.409 75.172 2642 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.44 % Allowed : 27.39 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2250 helix: 1.28 (0.19), residues: 730 sheet: -0.19 (0.18), residues: 860 loop : -0.99 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 127 HIS 0.002 0.001 HIS H 222 PHE 0.018 0.003 PHE C 239 TYR 0.024 0.001 TYR H 179 ARG 0.005 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.03348 ( 991) hydrogen bonds : angle 5.24260 ( 2703) covalent geometry : bond 0.00552 (17240) covalent geometry : angle 0.61559 (23290) Misc. bond : bond 0.00023 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 1.848 Fit side-chains REVERT: A 119 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7571 (mpp) REVERT: A 204 ARG cc_start: 0.8584 (ttm110) cc_final: 0.8297 (ttm-80) REVERT: B 119 MET cc_start: 0.8108 (mtp) cc_final: 0.7453 (mpp) REVERT: B 148 TYR cc_start: 0.6614 (t80) cc_final: 0.5478 (t80) REVERT: B 184 ASP cc_start: 0.9171 (m-30) cc_final: 0.8914 (m-30) REVERT: C 148 TYR cc_start: 0.6347 (t80) cc_final: 0.5416 (t80) REVERT: C 176 ASP cc_start: 0.8756 (t0) cc_final: 0.8550 (t70) REVERT: D 61 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8987 (mt-10) REVERT: D 120 ASP cc_start: 0.8902 (t0) cc_final: 0.8645 (t70) REVERT: D 175 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7237 (mm-30) REVERT: E 61 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8890 (mm-30) REVERT: E 175 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: E 241 GLU cc_start: 0.9217 (tt0) cc_final: 0.8947 (tt0) REVERT: F 120 ASP cc_start: 0.8757 (t0) cc_final: 0.8539 (t70) REVERT: F 123 GLU cc_start: 0.7920 (mp0) cc_final: 0.7648 (mp0) REVERT: G 173 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (mtt) REVERT: G 204 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8414 (ttm-80) REVERT: G 217 GLU cc_start: 0.8480 (tt0) cc_final: 0.8245 (mt-10) REVERT: G 248 ASP cc_start: 0.8601 (m-30) cc_final: 0.8341 (m-30) REVERT: H 49 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: H 177 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8100 (m) REVERT: H 227 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8376 (ttm170) REVERT: J 117 ASP cc_start: 0.8275 (p0) cc_final: 0.8025 (p0) REVERT: J 119 MET cc_start: 0.8273 (ptp) cc_final: 0.7677 (ptp) REVERT: J 248 ASP cc_start: 0.8419 (m-30) cc_final: 0.8127 (m-30) outliers start: 62 outliers final: 43 residues processed: 320 average time/residue: 1.7005 time to fit residues: 593.2983 Evaluate side-chains 312 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN G 225 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.065161 restraints weight = 76549.319| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.05 r_work: 0.2682 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 1.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17250 Z= 0.146 Angle : 0.549 13.612 23290 Z= 0.282 Chirality : 0.043 0.130 2740 Planarity : 0.003 0.039 3000 Dihedral : 9.950 74.101 2642 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.00 % Allowed : 27.72 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.19), residues: 2250 helix: 1.46 (0.20), residues: 730 sheet: -0.06 (0.19), residues: 850 loop : -0.89 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 127 HIS 0.002 0.001 HIS D 222 PHE 0.014 0.003 PHE C 239 TYR 0.016 0.001 TYR H 179 ARG 0.004 0.000 ARG J 190 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 991) hydrogen bonds : angle 4.98074 ( 2703) covalent geometry : bond 0.00326 (17240) covalent geometry : angle 0.54908 (23290) Misc. bond : bond 0.00022 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 274 time to evaluate : 1.916 Fit side-chains REVERT: A 119 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7641 (mpp) REVERT: A 204 ARG cc_start: 0.8577 (ttm110) cc_final: 0.8300 (ttm-80) REVERT: B 119 MET cc_start: 0.8154 (mtp) cc_final: 0.7485 (mpp) REVERT: B 148 TYR cc_start: 0.6599 (t80) cc_final: 0.5485 (t80) REVERT: B 184 ASP cc_start: 0.9150 (m-30) cc_final: 0.8911 (m-30) REVERT: C 148 TYR cc_start: 0.6274 (t80) cc_final: 0.5384 (t80) REVERT: D 80 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8981 (mtm) REVERT: E 61 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8880 (mm-30) REVERT: E 80 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8968 (mtm) REVERT: E 241 GLU cc_start: 0.9234 (tt0) cc_final: 0.8951 (tt0) REVERT: F 120 ASP cc_start: 0.8630 (t0) cc_final: 0.8107 (t70) REVERT: F 123 GLU cc_start: 0.8019 (mp0) cc_final: 0.7606 (mp0) REVERT: F 175 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7825 (mm-30) REVERT: F 176 ASP cc_start: 0.8743 (t0) cc_final: 0.8504 (t70) REVERT: G 130 ARG cc_start: 0.7834 (mmp80) cc_final: 0.7528 (mpt90) REVERT: G 173 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8424 (mtt) REVERT: G 204 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8323 (ttm-80) REVERT: G 217 GLU cc_start: 0.8444 (tt0) cc_final: 0.8146 (mt-10) REVERT: G 248 ASP cc_start: 0.8695 (m-30) cc_final: 0.8443 (m-30) REVERT: H 177 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8049 (m) REVERT: H 181 MET cc_start: 0.8348 (ttp) cc_final: 0.8057 (ttm) REVERT: H 227 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8249 (ttm170) REVERT: J 117 ASP cc_start: 0.8201 (p0) cc_final: 0.7931 (p0) REVERT: J 119 MET cc_start: 0.8436 (ptp) cc_final: 0.7875 (ptp) REVERT: J 248 ASP cc_start: 0.8495 (m-30) cc_final: 0.8149 (m-30) outliers start: 54 outliers final: 39 residues processed: 313 average time/residue: 1.6337 time to fit residues: 557.0049 Evaluate side-chains 309 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 119 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 85 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 0.0020 chunk 82 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 194 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.090319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.063867 restraints weight = 69409.962| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.83 r_work: 0.2659 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 1.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17250 Z= 0.189 Angle : 0.579 16.274 23290 Z= 0.297 Chirality : 0.043 0.131 2740 Planarity : 0.003 0.039 3000 Dihedral : 9.879 69.851 2642 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.00 % Allowed : 27.83 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 2250 helix: 1.44 (0.20), residues: 730 sheet: -0.10 (0.19), residues: 860 loop : -1.00 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 127 HIS 0.002 0.001 HIS G 222 PHE 0.016 0.003 PHE C 239 TYR 0.019 0.001 TYR H 179 ARG 0.004 0.001 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 991) hydrogen bonds : angle 5.04413 ( 2703) covalent geometry : bond 0.00429 (17240) covalent geometry : angle 0.57933 (23290) Misc. bond : bond 0.00025 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 2.074 Fit side-chains REVERT: A 119 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7565 (mpp) REVERT: A 204 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8342 (ttm-80) REVERT: B 119 MET cc_start: 0.8084 (mtp) cc_final: 0.7440 (mpp) REVERT: B 128 LEU cc_start: 0.8271 (mt) cc_final: 0.8065 (pt) REVERT: B 148 TYR cc_start: 0.6714 (t80) cc_final: 0.5589 (t80) REVERT: B 184 ASP cc_start: 0.9151 (m-30) cc_final: 0.8899 (m-30) REVERT: C 148 TYR cc_start: 0.6475 (t80) cc_final: 0.6054 (t80) REVERT: D 80 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8974 (mtm) REVERT: D 123 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8072 (mp0) REVERT: D 148 TYR cc_start: 0.6623 (t80) cc_final: 0.6414 (t80) REVERT: E 61 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8892 (mm-30) REVERT: E 80 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8959 (mtm) REVERT: E 241 GLU cc_start: 0.9205 (tt0) cc_final: 0.8921 (tt0) REVERT: F 49 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: F 120 ASP cc_start: 0.8638 (t0) cc_final: 0.8372 (t70) REVERT: F 123 GLU cc_start: 0.8173 (mp0) cc_final: 0.7900 (mp0) REVERT: F 175 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7728 (mm-30) REVERT: G 173 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8420 (mtt) REVERT: G 204 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8352 (ttm-80) REVERT: G 217 GLU cc_start: 0.8451 (tt0) cc_final: 0.8247 (mt-10) REVERT: G 248 ASP cc_start: 0.8668 (m-30) cc_final: 0.8400 (m-30) REVERT: H 177 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8014 (m) REVERT: H 181 MET cc_start: 0.8424 (ttp) cc_final: 0.8086 (ttm) REVERT: H 227 ARG cc_start: 0.8720 (ttm-80) cc_final: 0.8263 (ttm170) REVERT: J 117 ASP cc_start: 0.8263 (p0) cc_final: 0.7998 (p0) REVERT: J 119 MET cc_start: 0.8356 (ptp) cc_final: 0.7782 (ptp) REVERT: J 130 ARG cc_start: 0.8044 (mmt90) cc_final: 0.7782 (mpt90) REVERT: J 248 ASP cc_start: 0.8472 (m-30) cc_final: 0.8145 (m-30) outliers start: 54 outliers final: 42 residues processed: 308 average time/residue: 1.7814 time to fit residues: 598.2657 Evaluate side-chains 314 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 173 MET Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 217 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 178 ASN F 231 ASN G 110 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066839 restraints weight = 94505.926| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.37 r_work: 0.2695 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 1.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17250 Z= 0.126 Angle : 0.531 14.673 23290 Z= 0.273 Chirality : 0.042 0.132 2740 Planarity : 0.003 0.040 3000 Dihedral : 9.545 67.988 2642 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.67 % Allowed : 27.89 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2250 helix: 1.54 (0.20), residues: 730 sheet: 0.18 (0.19), residues: 830 loop : -0.84 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 127 HIS 0.002 0.001 HIS B 222 PHE 0.013 0.003 PHE C 239 TYR 0.013 0.001 TYR H 179 ARG 0.005 0.000 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.02651 ( 991) hydrogen bonds : angle 4.86333 ( 2703) covalent geometry : bond 0.00279 (17240) covalent geometry : angle 0.53143 (23290) Misc. bond : bond 0.00023 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 1.883 Fit side-chains REVERT: A 119 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7682 (mpp) REVERT: A 204 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8281 (ttm-80) REVERT: B 119 MET cc_start: 0.8119 (mtp) cc_final: 0.7471 (mpp) REVERT: B 148 TYR cc_start: 0.6636 (t80) cc_final: 0.5496 (t80) REVERT: B 184 ASP cc_start: 0.9127 (m-30) cc_final: 0.8867 (m-30) REVERT: B 204 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8289 (ttm-80) REVERT: C 148 TYR cc_start: 0.6442 (t80) cc_final: 0.6014 (t80) REVERT: D 61 GLU cc_start: 0.9239 (mt-10) cc_final: 0.9001 (mm-30) REVERT: D 80 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8941 (mtm) REVERT: D 176 ASP cc_start: 0.8633 (t0) cc_final: 0.8308 (t70) REVERT: D 181 MET cc_start: 0.8627 (ttm) cc_final: 0.8365 (ttm) REVERT: E 61 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8904 (mm-30) REVERT: E 241 GLU cc_start: 0.9261 (tt0) cc_final: 0.8981 (tt0) REVERT: F 123 GLU cc_start: 0.8144 (mp0) cc_final: 0.7943 (mp0) REVERT: F 176 ASP cc_start: 0.8712 (t0) cc_final: 0.8474 (t70) REVERT: G 130 ARG cc_start: 0.7814 (mmp80) cc_final: 0.7403 (mmt180) REVERT: G 204 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8380 (ttm-80) REVERT: G 217 GLU cc_start: 0.8496 (tt0) cc_final: 0.8235 (mt-10) REVERT: G 248 ASP cc_start: 0.8694 (m-30) cc_final: 0.8447 (m-30) REVERT: H 130 ARG cc_start: 0.8245 (mpt180) cc_final: 0.7990 (mmp80) REVERT: H 177 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7949 (m) REVERT: H 227 ARG cc_start: 0.8670 (ttm-80) cc_final: 0.8287 (ttm170) REVERT: J 117 ASP cc_start: 0.8231 (p0) cc_final: 0.7956 (p0) REVERT: J 119 MET cc_start: 0.8454 (ptp) cc_final: 0.7889 (ptp) REVERT: J 130 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7802 (mpt90) REVERT: J 248 ASP cc_start: 0.8520 (m-30) cc_final: 0.8144 (m-30) outliers start: 48 outliers final: 39 residues processed: 315 average time/residue: 1.6009 time to fit residues: 554.2193 Evaluate side-chains 306 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 92 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 221 GLN G 110 GLN I 231 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.064834 restraints weight = 79275.434| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.05 r_work: 0.2668 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 1.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17250 Z= 0.181 Angle : 0.569 14.111 23290 Z= 0.292 Chirality : 0.043 0.188 2740 Planarity : 0.003 0.041 3000 Dihedral : 9.531 66.588 2641 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.39 % Allowed : 28.50 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 2250 helix: 1.51 (0.20), residues: 730 sheet: -0.01 (0.19), residues: 860 loop : -0.94 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 127 HIS 0.002 0.001 HIS B 222 PHE 0.016 0.003 PHE C 239 TYR 0.017 0.001 TYR H 179 ARG 0.008 0.001 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 991) hydrogen bonds : angle 4.90296 ( 2703) covalent geometry : bond 0.00411 (17240) covalent geometry : angle 0.56925 (23290) Misc. bond : bond 0.00026 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 267 time to evaluate : 2.042 Fit side-chains REVERT: A 119 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7585 (mpp) REVERT: A 204 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8333 (ttm-80) REVERT: B 119 MET cc_start: 0.8073 (mtp) cc_final: 0.7444 (mpp) REVERT: B 148 TYR cc_start: 0.6709 (t80) cc_final: 0.5567 (t80) REVERT: B 184 ASP cc_start: 0.9130 (m-30) cc_final: 0.8856 (m-30) REVERT: C 148 TYR cc_start: 0.6522 (t80) cc_final: 0.6162 (t80) REVERT: D 61 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9016 (mm-30) REVERT: D 80 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8982 (mtm) REVERT: D 176 ASP cc_start: 0.8643 (t0) cc_final: 0.8263 (t70) REVERT: E 61 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8914 (mm-30) REVERT: E 241 GLU cc_start: 0.9234 (tt0) cc_final: 0.8944 (tt0) REVERT: F 120 ASP cc_start: 0.8293 (t70) cc_final: 0.8084 (t70) REVERT: F 123 GLU cc_start: 0.8278 (mp0) cc_final: 0.8040 (mp0) REVERT: F 130 ARG cc_start: 0.7130 (mmp80) cc_final: 0.6840 (mpt90) REVERT: F 175 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7883 (mm-30) REVERT: F 176 ASP cc_start: 0.8615 (t0) cc_final: 0.8355 (OUTLIER) REVERT: G 130 ARG cc_start: 0.7815 (mmp80) cc_final: 0.7562 (mpt90) REVERT: G 204 ARG cc_start: 0.8672 (ttm110) cc_final: 0.8383 (ttm-80) REVERT: G 217 GLU cc_start: 0.8498 (tt0) cc_final: 0.8287 (mt-10) REVERT: G 248 ASP cc_start: 0.8708 (m-30) cc_final: 0.8439 (m-30) REVERT: H 177 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7980 (m) REVERT: H 227 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8340 (ttm170) REVERT: J 117 ASP cc_start: 0.8323 (p0) cc_final: 0.8090 (p0) REVERT: J 119 MET cc_start: 0.8428 (ptp) cc_final: 0.7585 (pmm) REVERT: J 248 ASP cc_start: 0.8538 (m-30) cc_final: 0.8202 (m-30) outliers start: 43 outliers final: 39 residues processed: 301 average time/residue: 1.6097 time to fit residues: 528.2269 Evaluate side-chains 304 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 77 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.064943 restraints weight = 76222.646| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.99 r_work: 0.2676 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 1.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17250 Z= 0.164 Angle : 0.566 13.512 23290 Z= 0.288 Chirality : 0.043 0.151 2740 Planarity : 0.003 0.041 3000 Dihedral : 9.485 65.743 2641 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 28.44 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.19), residues: 2250 helix: 1.51 (0.20), residues: 730 sheet: 0.03 (0.19), residues: 850 loop : -0.84 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 127 HIS 0.002 0.001 HIS D 222 PHE 0.015 0.003 PHE C 239 TYR 0.017 0.001 TYR H 179 ARG 0.006 0.001 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 991) hydrogen bonds : angle 4.90712 ( 2703) covalent geometry : bond 0.00373 (17240) covalent geometry : angle 0.56559 (23290) Misc. bond : bond 0.00022 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16473.30 seconds wall clock time: 282 minutes 56.78 seconds (16976.78 seconds total)