Starting phenix.real_space_refine on Sun Aug 24 04:46:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fsm_50728/08_2025/9fsm_50728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fsm_50728/08_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_50728/08_2025/9fsm_50728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fsm_50728/08_2025/9fsm_50728.map" model { file = "/net/cci-nas-00/data/ceres_data/9fsm_50728/08_2025/9fsm_50728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fsm_50728/08_2025/9fsm_50728.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.16, per 1000 atoms: 0.42 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: 1.44 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.60 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: 3.12 Time building geometry restraints manager: 1.90 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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: 8.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.630 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG F 204 TYR 0.007 0.001 TYR B 179 PHE 0.008 0.003 PHE B 239 TRP 0.014 0.001 TRP G 127 HIS 0.001 0.000 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00638 (17240) covalent geometry : angle 0.65356 (23290) hydrogen bonds : bond 0.10352 ( 991) hydrogen bonds : angle 6.11739 ( 2703) 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 : 0.739 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: 0.4796 time to fit residues: 344.2872 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 : 0.563 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 231 ASN 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 110 GLN ** 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080617 restraints weight = 77326.678| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 4.35 r_work: 0.3006 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.7519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17250 Z= 0.185 Angle : 0.736 10.411 23290 Z= 0.391 Chirality : 0.047 0.188 2740 Planarity : 0.005 0.055 3000 Dihedral : 10.355 85.262 2666 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.56 % Allowed : 27.61 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.18), residues: 2250 helix: 1.20 (0.20), residues: 720 sheet: 0.22 (0.18), residues: 830 loop : -1.05 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 190 TYR 0.021 0.002 TYR F 179 PHE 0.010 0.003 PHE I 239 TRP 0.067 0.003 TRP G 127 HIS 0.008 0.001 HIS C 222 Details of bonding type rmsd covalent geometry : bond 0.00403 (17240) covalent geometry : angle 0.73553 (23290) hydrogen bonds : bond 0.03619 ( 991) hydrogen bonds : angle 5.57562 ( 2703) Misc. bond : bond 0.00031 ( 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 464 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 364 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7968 (tt0) REVERT: A 137 THR cc_start: 0.7787 (m) cc_final: 0.7373 (p) REVERT: A 184 ASP cc_start: 0.8154 (m-30) cc_final: 0.7626 (m-30) REVERT: A 227 ARG cc_start: 0.8427 (mtm180) cc_final: 0.8058 (ttm-80) REVERT: A 248 ASP cc_start: 0.8220 (m-30) cc_final: 0.7804 (m-30) REVERT: B 51 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7544 (ptpt) REVERT: B 248 ASP cc_start: 0.8363 (m-30) cc_final: 0.8011 (m-30) REVERT: C 39 MET cc_start: 0.6910 (tpt) cc_final: 0.6682 (tpt) REVERT: C 53 GLN cc_start: 0.8647 (pt0) cc_final: 0.8383 (mt0) REVERT: C 133 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6203 (pt0) REVERT: C 217 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8224 (mt-10) REVERT: D 39 MET cc_start: 0.7005 (tpt) cc_final: 0.6590 (mmm) REVERT: D 49 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 173 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7212 (mmt) REVERT: D 175 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7860 (mm-30) REVERT: D 216 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8769 (m) REVERT: E 93 SER cc_start: 0.8801 (m) cc_final: 0.8556 (p) REVERT: E 128 LEU cc_start: 0.8033 (mt) cc_final: 0.7783 (pp) REVERT: E 130 ARG cc_start: 0.7225 (mmt90) cc_final: 0.6896 (mmp80) REVERT: F 93 SER cc_start: 0.8906 (m) cc_final: 0.8667 (p) REVERT: F 119 MET cc_start: 0.7932 (pmm) cc_final: 0.7726 (pmm) REVERT: F 130 ARG cc_start: 0.7118 (mmt90) cc_final: 0.6716 (mmp80) REVERT: F 171 ASP cc_start: 0.8194 (t0) cc_final: 0.7872 (t70) REVERT: F 182 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8525 (mp) REVERT: G 53 GLN cc_start: 0.8327 (mt0) cc_final: 0.8021 (mt0) REVERT: G 182 ILE cc_start: 0.8866 (mm) cc_final: 0.8642 (mp) REVERT: G 241 GLU cc_start: 0.8872 (tp30) cc_final: 0.8624 (tm-30) REVERT: G 248 ASP cc_start: 0.8513 (m-30) cc_final: 0.8255 (m-30) REVERT: H 49 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7618 (tm-30) REVERT: H 52 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8297 (p) REVERT: H 53 GLN cc_start: 0.8410 (mt0) cc_final: 0.8023 (mt0) REVERT: H 117 ASP cc_start: 0.8348 (p0) cc_final: 0.7978 (p0) REVERT: H 171 ASP cc_start: 0.7181 (t0) cc_final: 0.6903 (t0) REVERT: H 227 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7648 (ttm170) REVERT: H 241 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8490 (tm-30) REVERT: H 248 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: I 81 SER cc_start: 0.8371 (t) cc_final: 0.8060 (p) REVERT: I 103 ASP cc_start: 0.8527 (m-30) cc_final: 0.8308 (m-30) REVERT: I 117 ASP cc_start: 0.8562 (p0) cc_final: 0.8305 (p0) REVERT: I 248 ASP cc_start: 0.8333 (t0) cc_final: 0.7895 (m-30) REVERT: J 49 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7795 (tm-30) REVERT: J 119 MET cc_start: 0.7649 (ptp) cc_final: 0.7038 (ptp) REVERT: J 248 ASP cc_start: 0.7858 (m-30) cc_final: 0.7652 (m-30) outliers start: 100 outliers final: 33 residues processed: 428 average time/residue: 0.6569 time to fit residues: 311.2520 Evaluate side-chains 344 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 133 GLU 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 174 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 216 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 F residue 177 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL 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 141 LEU 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 178 ASN 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 194 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 152 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 186 GLN B 221 GLN D 53 GLN D 110 GLN F 53 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN I 186 GLN J 110 GLN J 199 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.070764 restraints weight = 85348.552| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.44 r_work: 0.2806 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.9063 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= 0.163 Angle : 0.627 10.628 23290 Z= 0.323 Chirality : 0.044 0.184 2740 Planarity : 0.004 0.035 3000 Dihedral : 9.948 83.391 2643 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.61 % Allowed : 28.22 % Favored : 67.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 2250 helix: 1.45 (0.19), residues: 740 sheet: 0.19 (0.18), residues: 850 loop : -0.95 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 227 TYR 0.016 0.001 TYR I 179 PHE 0.018 0.003 PHE C 239 TRP 0.053 0.002 TRP G 127 HIS 0.002 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00368 (17240) covalent geometry : angle 0.62671 (23290) hydrogen bonds : bond 0.03224 ( 991) hydrogen bonds : angle 5.05956 ( 2703) Misc. bond : bond 0.00024 ( 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 386 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 303 time to evaluate : 0.696 Fit side-chains REVERT: A 119 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7729 (mtm) REVERT: A 148 TYR cc_start: 0.5930 (t80) cc_final: 0.4931 (t80) REVERT: B 119 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7415 (mpp) REVERT: B 248 ASP cc_start: 0.8571 (m-30) cc_final: 0.8189 (m-30) REVERT: C 53 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8520 (mt0) REVERT: D 61 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8843 (mt-10) REVERT: D 119 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8156 (pmm) REVERT: D 130 ARG cc_start: 0.6966 (mmt90) cc_final: 0.6643 (tpp-160) REVERT: F 130 ARG cc_start: 0.7543 (mmt90) cc_final: 0.7045 (mmp80) REVERT: F 171 ASP cc_start: 0.8523 (t0) cc_final: 0.8196 (t0) REVERT: F 173 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8311 (mtt) REVERT: F 182 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8684 (mp) REVERT: G 49 GLU cc_start: 0.8109 (tp30) cc_final: 0.7829 (tm-30) REVERT: G 217 GLU cc_start: 0.8423 (tt0) cc_final: 0.8055 (mt-10) REVERT: G 248 ASP cc_start: 0.8663 (m-30) cc_final: 0.8400 (m-30) REVERT: H 227 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8124 (ttm170) REVERT: H 238 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8161 (mmtm) REVERT: H 248 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: I 49 GLU cc_start: 0.8398 (tp30) cc_final: 0.8146 (tp30) REVERT: I 52 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8703 (p) REVERT: I 84 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: I 103 ASP cc_start: 0.9082 (m-30) cc_final: 0.8842 (m-30) REVERT: I 248 ASP cc_start: 0.8486 (t0) cc_final: 0.8219 (m-30) REVERT: J 49 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8275 (tm-30) REVERT: J 119 MET cc_start: 0.8163 (ptp) cc_final: 0.7617 (ptp) outliers start: 83 outliers final: 43 residues processed: 359 average time/residue: 0.6544 time to fit residues: 258.5953 Evaluate side-chains 316 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 241 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 176 ASP 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 53 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 180 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 C residue 245 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 173 MET Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 77 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 H residue 238 LYS Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 177 VAL 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 39 MET Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 79 ASP 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 103 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN C 221 GLN D 221 GLN F 53 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN I 112 ASN J 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.065552 restraints weight = 90656.510| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.42 r_work: 0.2689 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 1.0579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17250 Z= 0.210 Angle : 0.637 9.773 23290 Z= 0.331 Chirality : 0.045 0.146 2740 Planarity : 0.004 0.050 3000 Dihedral : 10.016 78.352 2643 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.17 % Allowed : 28.17 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.18), residues: 2250 helix: 1.39 (0.19), residues: 730 sheet: 0.08 (0.18), residues: 860 loop : -0.93 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 227 TYR 0.017 0.001 TYR A 179 PHE 0.021 0.004 PHE A 239 TRP 0.053 0.002 TRP G 127 HIS 0.002 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00471 (17240) covalent geometry : angle 0.63680 (23290) hydrogen bonds : bond 0.03247 ( 991) hydrogen bonds : angle 5.19803 ( 2703) Misc. bond : bond 0.00018 ( 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 360 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 285 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7586 (mpp) REVERT: A 184 ASP cc_start: 0.8893 (m-30) cc_final: 0.8584 (m-30) REVERT: B 119 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7489 (mpp) REVERT: B 184 ASP cc_start: 0.9255 (m-30) cc_final: 0.9040 (m-30) REVERT: D 61 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9039 (mt-10) REVERT: D 120 ASP cc_start: 0.8137 (t70) cc_final: 0.7003 (t0) REVERT: D 181 MET cc_start: 0.8690 (ttm) cc_final: 0.8477 (ttm) REVERT: G 49 GLU cc_start: 0.8238 (tp30) cc_final: 0.7868 (tm-30) REVERT: G 217 GLU cc_start: 0.8422 (tt0) cc_final: 0.8075 (mt-10) REVERT: G 248 ASP cc_start: 0.8663 (m-30) cc_final: 0.8398 (m-30) REVERT: H 227 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8316 (ttm170) REVERT: H 248 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: I 49 GLU cc_start: 0.8402 (tp30) cc_final: 0.8050 (tm-30) REVERT: I 103 ASP cc_start: 0.9285 (m-30) cc_final: 0.9078 (m-30) REVERT: I 127 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.7840 (p-90) REVERT: I 182 ILE cc_start: 0.8848 (mt) cc_final: 0.8623 (mp) REVERT: I 227 ARG cc_start: 0.8650 (ttm170) cc_final: 0.8419 (ttm170) REVERT: I 248 ASP cc_start: 0.8520 (t0) cc_final: 0.8288 (m-30) REVERT: J 52 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8785 (p) REVERT: J 119 MET cc_start: 0.8265 (ptp) cc_final: 0.7673 (ptp) outliers start: 75 outliers final: 42 residues processed: 335 average time/residue: 0.5933 time to fit residues: 219.2750 Evaluate side-chains 310 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 174 VAL 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 77 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 174 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 B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 180 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 C residue 203 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 168 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 E residue 180 THR Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR 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 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 79 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 201 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 191 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 GLN F 53 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.066243 restraints weight = 94458.890| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.37 r_work: 0.2702 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 1.0795 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= 0.166 Angle : 0.580 9.744 23290 Z= 0.299 Chirality : 0.043 0.127 2740 Planarity : 0.003 0.045 3000 Dihedral : 9.940 77.486 2643 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.44 % Allowed : 29.00 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.19), residues: 2250 helix: 1.51 (0.19), residues: 730 sheet: 0.13 (0.19), residues: 850 loop : -0.84 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 204 TYR 0.011 0.001 TYR A 179 PHE 0.016 0.003 PHE C 239 TRP 0.056 0.002 TRP G 127 HIS 0.002 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00375 (17240) covalent geometry : angle 0.57957 (23290) hydrogen bonds : bond 0.02908 ( 991) hydrogen bonds : angle 4.96829 ( 2703) Misc. bond : bond 0.00011 ( 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: 62 poor density : 284 time to evaluate : 0.686 Fit side-chains REVERT: A 119 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7675 (mpp) REVERT: A 148 TYR cc_start: 0.6501 (t80) cc_final: 0.5276 (t80) REVERT: A 184 ASP cc_start: 0.8853 (m-30) cc_final: 0.8379 (m-30) REVERT: B 119 MET cc_start: 0.8151 (mtp) cc_final: 0.7463 (mpp) REVERT: B 148 TYR cc_start: 0.6097 (t80) cc_final: 0.5039 (t80) REVERT: C 130 ARG cc_start: 0.7451 (mmt90) cc_final: 0.7250 (mmt90) REVERT: D 61 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9044 (mt-10) REVERT: D 119 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7855 (pmm) REVERT: D 181 MET cc_start: 0.8684 (ttm) cc_final: 0.8446 (ttm) REVERT: E 175 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7872 (mm-30) REVERT: F 120 ASP cc_start: 0.8527 (t70) cc_final: 0.7429 (t70) REVERT: G 49 GLU cc_start: 0.8198 (tp30) cc_final: 0.7824 (tm-30) REVERT: G 173 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8389 (mtt) REVERT: G 204 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8144 (ttm-80) REVERT: G 217 GLU cc_start: 0.8393 (tt0) cc_final: 0.8074 (mt-10) REVERT: G 248 ASP cc_start: 0.8643 (m-30) cc_final: 0.8390 (m-30) REVERT: H 227 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.8164 (ttm170) REVERT: I 49 GLU cc_start: 0.8334 (tp30) cc_final: 0.7994 (tm-30) REVERT: I 227 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8427 (ttm170) REVERT: J 52 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8767 (p) REVERT: J 117 ASP cc_start: 0.8317 (p0) cc_final: 0.8028 (p0) REVERT: J 119 MET cc_start: 0.8325 (ptp) cc_final: 0.7740 (ptp) REVERT: J 192 LYS cc_start: 0.9411 (mtmm) cc_final: 0.9045 (mmpt) outliers start: 62 outliers final: 38 residues processed: 327 average time/residue: 0.6596 time to fit residues: 236.5264 Evaluate side-chains 306 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 B residue 77 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 174 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 B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 180 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 91 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 200 VAL 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 204 ARG Chi-restraints excluded: chain H residue 79 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 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 191 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 216 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 218 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.093791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.066830 restraints weight = 78514.937| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 4.17 r_work: 0.2725 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 1.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17250 Z= 0.144 Angle : 0.551 10.961 23290 Z= 0.285 Chirality : 0.043 0.127 2740 Planarity : 0.003 0.048 3000 Dihedral : 9.715 74.886 2643 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.33 % Allowed : 28.50 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 2250 helix: 1.57 (0.19), residues: 730 sheet: 0.15 (0.19), residues: 850 loop : -0.79 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 122 TYR 0.011 0.001 TYR A 179 PHE 0.015 0.003 PHE C 239 TRP 0.053 0.002 TRP G 127 HIS 0.002 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00319 (17240) covalent geometry : angle 0.55100 (23290) hydrogen bonds : bond 0.02743 ( 991) hydrogen bonds : angle 4.86023 ( 2703) Misc. bond : bond 0.00016 ( 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 337 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 0.603 Fit side-chains REVERT: A 119 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7642 (mpp) REVERT: A 148 TYR cc_start: 0.6490 (t80) cc_final: 0.5252 (t80) REVERT: A 184 ASP cc_start: 0.8809 (m-30) cc_final: 0.8469 (m-30) REVERT: B 119 MET cc_start: 0.8179 (mtp) cc_final: 0.7529 (mpp) REVERT: C 130 ARG cc_start: 0.7494 (mmt90) cc_final: 0.7291 (mmt90) REVERT: D 61 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9058 (mt-10) REVERT: D 119 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7966 (pmm) REVERT: D 181 MET cc_start: 0.8667 (ttm) cc_final: 0.8437 (ttm) REVERT: F 176 ASP cc_start: 0.8727 (t0) cc_final: 0.8460 (t70) REVERT: G 49 GLU cc_start: 0.8193 (tp30) cc_final: 0.7800 (tm-30) REVERT: G 173 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: G 204 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8255 (ttm-80) REVERT: G 217 GLU cc_start: 0.8410 (tt0) cc_final: 0.8138 (mt-10) REVERT: G 248 ASP cc_start: 0.8659 (m-30) cc_final: 0.8415 (m-30) REVERT: H 227 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8207 (ttm170) REVERT: I 49 GLU cc_start: 0.8340 (tp30) cc_final: 0.8002 (tm-30) REVERT: I 227 ARG cc_start: 0.8742 (ttm170) cc_final: 0.8417 (ttm170) REVERT: J 52 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (p) REVERT: J 119 MET cc_start: 0.8328 (ptp) cc_final: 0.7769 (ptp) outliers start: 60 outliers final: 38 residues processed: 319 average time/residue: 0.6554 time to fit residues: 228.6904 Evaluate side-chains 304 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 174 VAL 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 77 ASP 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 200 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 180 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 77 ASP Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 121 LEU 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 200 VAL Chi-restraints excluded: chain F residue 55 SER 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 180 THR Chi-restraints excluded: chain H residue 183 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 189 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 186 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.091275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.064590 restraints weight = 70210.131| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.85 r_work: 0.2674 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 1.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17250 Z= 0.203 Angle : 0.588 10.736 23290 Z= 0.305 Chirality : 0.044 0.133 2740 Planarity : 0.003 0.049 3000 Dihedral : 9.799 73.105 2642 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.33 % Allowed : 28.22 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 2250 helix: 1.52 (0.19), residues: 730 sheet: 0.03 (0.19), residues: 860 loop : -0.88 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 227 TYR 0.014 0.001 TYR A 179 PHE 0.017 0.003 PHE C 239 TRP 0.055 0.002 TRP G 127 HIS 0.002 0.001 HIS G 222 Details of bonding type rmsd covalent geometry : bond 0.00463 (17240) covalent geometry : angle 0.58798 (23290) hydrogen bonds : bond 0.03101 ( 991) hydrogen bonds : angle 5.00394 ( 2703) Misc. bond : bond 0.00023 ( 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 335 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 275 time to evaluate : 0.552 Fit side-chains REVERT: A 119 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7607 (mpp) REVERT: A 148 TYR cc_start: 0.6690 (t80) cc_final: 0.5448 (t80) REVERT: A 184 ASP cc_start: 0.8918 (m-30) cc_final: 0.8584 (m-30) REVERT: B 119 MET cc_start: 0.8163 (mtp) cc_final: 0.7472 (mpp) REVERT: B 148 TYR cc_start: 0.6443 (t80) cc_final: 0.5356 (t80) REVERT: C 130 ARG cc_start: 0.7594 (mmt90) cc_final: 0.7379 (mmt90) REVERT: D 61 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9086 (mt-10) REVERT: D 130 ARG cc_start: 0.7382 (tpp-160) cc_final: 0.7079 (mmt90) REVERT: D 181 MET cc_start: 0.8684 (ttm) cc_final: 0.8442 (ttm) REVERT: E 61 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8931 (mm-30) REVERT: G 49 GLU cc_start: 0.8214 (tp30) cc_final: 0.7853 (tm-30) REVERT: G 173 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: G 204 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8320 (ttm-80) REVERT: G 217 GLU cc_start: 0.8422 (tt0) cc_final: 0.8150 (mt-10) REVERT: G 248 ASP cc_start: 0.8632 (m-30) cc_final: 0.8365 (m-30) REVERT: H 49 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: H 227 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8283 (ttm170) REVERT: I 49 GLU cc_start: 0.8343 (tp30) cc_final: 0.8018 (tm-30) REVERT: I 130 ARG cc_start: 0.7541 (mmp80) cc_final: 0.7284 (mmt180) REVERT: J 117 ASP cc_start: 0.8343 (p0) cc_final: 0.8109 (p0) REVERT: J 119 MET cc_start: 0.8313 (ptp) cc_final: 0.7731 (ptp) outliers start: 60 outliers final: 44 residues processed: 318 average time/residue: 0.7565 time to fit residues: 262.4875 Evaluate side-chains 308 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 57 THR Chi-restraints excluded: chain B residue 77 ASP 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 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 180 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 119 MET Chi-restraints excluded: chain D residue 121 LEU 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 200 VAL Chi-restraints excluded: chain F residue 55 SER 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 141 LEU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR 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 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 109 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 208 optimal weight: 0.0060 chunk 71 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.066877 restraints weight = 76775.711| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.11 r_work: 0.2721 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 1.1191 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= 0.132 Angle : 0.536 10.079 23290 Z= 0.278 Chirality : 0.042 0.125 2740 Planarity : 0.003 0.049 3000 Dihedral : 9.460 69.872 2642 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.78 % Allowed : 29.17 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.19), residues: 2250 helix: 1.66 (0.20), residues: 730 sheet: 0.12 (0.19), residues: 850 loop : -0.77 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 204 TYR 0.009 0.001 TYR A 179 PHE 0.014 0.003 PHE C 239 TRP 0.055 0.002 TRP G 127 HIS 0.002 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00298 (17240) covalent geometry : angle 0.53573 (23290) hydrogen bonds : bond 0.02670 ( 991) hydrogen bonds : angle 4.80407 ( 2703) Misc. bond : bond 0.00018 ( 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 316 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 0.655 Fit side-chains REVERT: A 119 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7665 (mpp) REVERT: A 148 TYR cc_start: 0.6566 (t80) cc_final: 0.5290 (t80) REVERT: A 176 ASP cc_start: 0.8673 (t0) cc_final: 0.8453 (t70) REVERT: A 184 ASP cc_start: 0.8782 (m-30) cc_final: 0.8522 (m-30) REVERT: B 119 MET cc_start: 0.8201 (mtp) cc_final: 0.7503 (mpp) REVERT: C 130 ARG cc_start: 0.7647 (mmt90) cc_final: 0.7441 (mmt90) REVERT: D 61 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9080 (mt-10) REVERT: D 119 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8006 (pmm) REVERT: D 130 ARG cc_start: 0.7260 (tpp-160) cc_final: 0.7044 (mmt90) REVERT: D 181 MET cc_start: 0.8673 (ttm) cc_final: 0.8453 (ttm) REVERT: E 61 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8877 (mm-30) REVERT: F 176 ASP cc_start: 0.8667 (t0) cc_final: 0.8355 (t70) REVERT: G 49 GLU cc_start: 0.8171 (tp30) cc_final: 0.7814 (tm-30) REVERT: G 173 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8306 (mtt) REVERT: G 204 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8295 (ttm-80) REVERT: G 217 GLU cc_start: 0.8442 (tt0) cc_final: 0.8178 (mt-10) REVERT: G 248 ASP cc_start: 0.8653 (m-30) cc_final: 0.8412 (m-30) REVERT: H 130 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7763 (mpt90) REVERT: H 227 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8158 (ttm170) REVERT: I 49 GLU cc_start: 0.8336 (tp30) cc_final: 0.7983 (tm-30) REVERT: I 168 MET cc_start: 0.7968 (ttm) cc_final: 0.7760 (ttp) REVERT: I 227 ARG cc_start: 0.8781 (ttm170) cc_final: 0.8437 (ttm170) REVERT: I 241 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8936 (pt0) REVERT: J 80 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: J 117 ASP cc_start: 0.8396 (p0) cc_final: 0.8059 (p0) REVERT: J 119 MET cc_start: 0.8362 (ptp) cc_final: 0.7611 (pmm) REVERT: J 192 LYS cc_start: 0.9428 (mtmm) cc_final: 0.9065 (mmmt) outliers start: 50 outliers final: 38 residues processed: 305 average time/residue: 0.6973 time to fit residues: 231.6611 Evaluate side-chains 295 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 41 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASP 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 200 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 79 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 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 91 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 93 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 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 80 MET 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 257 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** 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 = 0.3355 r_free = 0.3355 target = 0.091677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.064789 restraints weight = 75361.744| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.99 r_work: 0.2679 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 1.1287 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= 0.190 Angle : 0.585 9.831 23290 Z= 0.302 Chirality : 0.043 0.140 2740 Planarity : 0.003 0.050 3000 Dihedral : 9.506 67.869 2641 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.67 % Allowed : 29.50 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 2250 helix: 1.58 (0.19), residues: 730 sheet: 0.03 (0.19), residues: 860 loop : -0.85 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 204 TYR 0.013 0.001 TYR A 179 PHE 0.015 0.003 PHE C 239 TRP 0.056 0.002 TRP G 127 HIS 0.002 0.001 HIS G 222 Details of bonding type rmsd covalent geometry : bond 0.00433 (17240) covalent geometry : angle 0.58543 (23290) hydrogen bonds : bond 0.03018 ( 991) hydrogen bonds : angle 4.93605 ( 2703) Misc. bond : bond 0.00024 ( 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 312 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 264 time to evaluate : 0.665 Fit side-chains REVERT: A 119 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7582 (mpp) REVERT: A 130 ARG cc_start: 0.7865 (mpt180) cc_final: 0.7583 (mpt90) REVERT: A 184 ASP cc_start: 0.8916 (m-30) cc_final: 0.8634 (m-30) REVERT: B 119 MET cc_start: 0.8124 (mtp) cc_final: 0.7435 (mpp) REVERT: B 128 LEU cc_start: 0.8358 (mt) cc_final: 0.8147 (pt) REVERT: B 148 TYR cc_start: 0.6644 (t80) cc_final: 0.5534 (t80) REVERT: C 130 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7449 (mmt90) REVERT: C 148 TYR cc_start: 0.6366 (t80) cc_final: 0.5424 (t80) REVERT: C 181 MET cc_start: 0.8265 (ttp) cc_final: 0.8021 (ttm) REVERT: D 61 GLU cc_start: 0.9301 (mt-10) cc_final: 0.9088 (mt-10) REVERT: D 119 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7950 (pmm) REVERT: D 130 ARG cc_start: 0.7265 (tpp-160) cc_final: 0.7031 (mmt90) REVERT: E 61 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8934 (mm-30) REVERT: E 123 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8202 (mp0) REVERT: F 241 GLU cc_start: 0.9228 (tm-30) cc_final: 0.9006 (tt0) REVERT: G 49 GLU cc_start: 0.8189 (tp30) cc_final: 0.7846 (tm-30) REVERT: G 173 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8350 (mtt) REVERT: G 204 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8310 (ttm-80) REVERT: G 217 GLU cc_start: 0.8439 (tt0) cc_final: 0.8181 (mt-10) REVERT: G 248 ASP cc_start: 0.8659 (m-30) cc_final: 0.8387 (m-30) REVERT: H 227 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8261 (ttm170) REVERT: I 49 GLU cc_start: 0.8353 (tp30) cc_final: 0.8012 (tm-30) REVERT: I 130 ARG cc_start: 0.7698 (mmp80) cc_final: 0.7443 (mmt180) REVERT: I 168 MET cc_start: 0.8012 (ttm) cc_final: 0.7807 (ttp) REVERT: I 241 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8909 (pt0) REVERT: J 80 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8210 (mtt) REVERT: J 117 ASP cc_start: 0.8366 (p0) cc_final: 0.8053 (p0) REVERT: J 119 MET cc_start: 0.8355 (ptp) cc_final: 0.7540 (pmm) REVERT: J 130 ARG cc_start: 0.8028 (mpt180) cc_final: 0.7685 (mmp80) outliers start: 48 outliers final: 40 residues processed: 301 average time/residue: 0.6610 time to fit residues: 216.9637 Evaluate side-chains 302 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 B residue 41 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASP 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 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 245 VAL 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 D residue 75 THR 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 91 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 93 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 43 ILE 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 80 MET 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 75 optimal weight: 10.0000 chunk 202 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 209 optimal weight: 0.0470 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 225 GLN ** 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 = 0.3387 r_free = 0.3387 target = 0.092937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.066653 restraints weight = 77059.805| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.02 r_work: 0.2714 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 1.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17250 Z= 0.145 Angle : 0.552 9.842 23290 Z= 0.285 Chirality : 0.043 0.127 2740 Planarity : 0.003 0.050 3000 Dihedral : 9.338 66.871 2641 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.50 % Allowed : 29.61 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.19), residues: 2250 helix: 1.61 (0.20), residues: 730 sheet: 0.04 (0.19), residues: 850 loop : -0.76 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 204 TYR 0.010 0.001 TYR H 179 PHE 0.014 0.003 PHE C 239 TRP 0.056 0.002 TRP G 127 HIS 0.002 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00325 (17240) covalent geometry : angle 0.55191 (23290) hydrogen bonds : bond 0.02774 ( 991) hydrogen bonds : angle 4.86844 ( 2703) Misc. bond : bond 0.00022 ( 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 308 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 263 time to evaluate : 0.608 Fit side-chains REVERT: A 119 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7590 (mpp) REVERT: A 130 ARG cc_start: 0.7892 (mpt180) cc_final: 0.7591 (mpt90) REVERT: A 184 ASP cc_start: 0.8825 (m-30) cc_final: 0.8562 (m-30) REVERT: B 119 MET cc_start: 0.8143 (mtp) cc_final: 0.7449 (mpp) REVERT: B 130 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7712 (mmt180) REVERT: B 148 TYR cc_start: 0.6584 (t80) cc_final: 0.5470 (t80) REVERT: C 119 MET cc_start: 0.8877 (ptp) cc_final: 0.8415 (pmm) REVERT: C 181 MET cc_start: 0.8220 (ttp) cc_final: 0.7921 (ttm) REVERT: D 61 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9081 (mt-10) REVERT: D 119 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8023 (pmm) REVERT: D 130 ARG cc_start: 0.7284 (tpp-160) cc_final: 0.7072 (mmt90) REVERT: E 61 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8920 (mm-30) REVERT: E 123 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8196 (mp0) REVERT: F 176 ASP cc_start: 0.8603 (t0) cc_final: 0.8386 (OUTLIER) REVERT: F 241 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8980 (tt0) REVERT: G 49 GLU cc_start: 0.8157 (tp30) cc_final: 0.7854 (tt0) REVERT: G 173 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (mtt) REVERT: G 204 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (ttm-80) REVERT: G 217 GLU cc_start: 0.8406 (tt0) cc_final: 0.8168 (mt-10) REVERT: G 248 ASP cc_start: 0.8645 (m-30) cc_final: 0.8397 (m-30) REVERT: H 130 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7802 (mmt180) REVERT: H 227 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8097 (ttm170) REVERT: I 49 GLU cc_start: 0.8319 (tp30) cc_final: 0.7971 (tm-30) REVERT: I 130 ARG cc_start: 0.7734 (mmp80) cc_final: 0.7507 (mmt180) REVERT: I 241 GLU cc_start: 0.9160 (tt0) cc_final: 0.8919 (pt0) REVERT: J 80 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8331 (mtt) REVERT: J 117 ASP cc_start: 0.8363 (p0) cc_final: 0.8049 (p0) REVERT: J 119 MET cc_start: 0.8376 (ptp) cc_final: 0.7539 (pmm) REVERT: J 130 ARG cc_start: 0.8050 (mpt180) cc_final: 0.7761 (mmp80) REVERT: J 192 LYS cc_start: 0.9441 (mtmm) cc_final: 0.9121 (mmpt) outliers start: 45 outliers final: 39 residues processed: 299 average time/residue: 0.6736 time to fit residues: 219.6860 Evaluate side-chains 299 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 256 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 B residue 41 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASP 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 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 245 VAL 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 D residue 75 THR 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 200 VAL Chi-restraints excluded: chain G residue 93 SER 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 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 80 MET 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 54 optimal weight: 9.9990 chunk 141 optimal weight: 0.0980 chunk 206 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 143 optimal weight: 0.0670 chunk 131 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 174 optimal weight: 0.4980 chunk 152 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 225 GLN ** 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 = 0.3395 r_free = 0.3395 target = 0.093154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.066628 restraints weight = 85140.156| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.20 r_work: 0.2699 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2726 r_free = 0.2726 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 1.1372 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= 0.151 Angle : 0.564 12.681 23290 Z= 0.287 Chirality : 0.043 0.127 2740 Planarity : 0.003 0.051 3000 Dihedral : 9.213 65.879 2641 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.56 % Allowed : 29.94 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.19), residues: 2250 helix: 1.62 (0.20), residues: 730 sheet: 0.04 (0.19), residues: 850 loop : -0.74 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 204 TYR 0.011 0.001 TYR H 179 PHE 0.014 0.003 PHE C 239 TRP 0.057 0.002 TRP G 127 HIS 0.002 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00341 (17240) covalent geometry : angle 0.56362 (23290) hydrogen bonds : bond 0.02761 ( 991) hydrogen bonds : angle 4.84985 ( 2703) Misc. bond : bond 0.00015 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7160.69 seconds wall clock time: 122 minutes 42.51 seconds (7362.51 seconds total)