Starting phenix.real_space_refine on Tue Jan 21 16:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fsm_50728/01_2025/9fsm_50728.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fsm_50728/01_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_50728/01_2025/9fsm_50728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fsm_50728/01_2025/9fsm_50728.map" model { file = "/net/cci-nas-00/data/ceres_data/9fsm_50728/01_2025/9fsm_50728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fsm_50728/01_2025/9fsm_50728.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10580 2.51 5 N 2950 2.21 5 O 3450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17060 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "B" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "C" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "D" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "E" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "F" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "G" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "H" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "I" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "J" Number of atoms: 1680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 226, 1675 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 221} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1687 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 19 Time building chain proxies: 18.38, per 1000 atoms: 1.08 Number of scatterers: 17060 At special positions: 0 Unit cell: (118.8, 114.48, 103.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3450 8.00 N 2950 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.30 Conformation dependent library (CDL) restraints added in 4.4 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 38.4% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 82 through 94 removed outlier: 3.510A pdb=" N LYS A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.485A pdb=" N GLY A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 152 through 173 Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.686A pdb=" N ALA A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.526A pdb=" N LYS B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 Processing helix chain 'B' and resid 131 through 140 removed outlier: 4.508A pdb=" N GLY B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 152 through 173 Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.672A pdb=" N ALA B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 4.179A pdb=" N LEU B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 82 through 94 removed outlier: 3.519A pdb=" N LYS C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 131 through 140 removed outlier: 4.504A pdb=" N GLY C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 152 through 173 Processing helix chain 'C' and resid 238 through 259 removed outlier: 3.642A pdb=" N ALA C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Proline residue: C 244 - end of helix removed outlier: 4.189A pdb=" N LEU C 258 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 45 Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.522A pdb=" N LYS D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.503A pdb=" N GLY D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 152 through 173 Processing helix chain 'D' and resid 238 through 259 removed outlier: 3.674A pdb=" N ALA D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Proline residue: D 244 - end of helix removed outlier: 4.195A pdb=" N LEU D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 82 through 94 removed outlier: 3.531A pdb=" N LYS E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 131 through 140 removed outlier: 4.506A pdb=" N GLY E 138 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 152 through 173 Processing helix chain 'E' and resid 238 through 259 removed outlier: 3.665A pdb=" N ALA E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) Proline residue: E 244 - end of helix removed outlier: 4.158A pdb=" N LEU E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.512A pdb=" N LYS F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 131 through 140 removed outlier: 4.494A pdb=" N GLY F 138 " --> pdb=" O GLY F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 152 through 173 Processing helix chain 'F' and resid 238 through 257 removed outlier: 3.686A pdb=" N ALA F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Proline residue: F 244 - end of helix Processing helix chain 'G' and resid 37 through 45 Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.523A pdb=" N LYS G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 131 through 140 removed outlier: 4.508A pdb=" N GLY G 138 " --> pdb=" O GLY G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 152 through 173 Processing helix chain 'G' and resid 238 through 259 removed outlier: 3.678A pdb=" N ALA G 242 " --> pdb=" O LYS G 238 " (cutoff:3.500A) Proline residue: G 244 - end of helix removed outlier: 4.177A pdb=" N LEU G 258 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 45 Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.517A pdb=" N LYS H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'H' and resid 131 through 140 removed outlier: 4.506A pdb=" N GLY H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 152 through 173 Processing helix chain 'H' and resid 238 through 259 removed outlier: 3.642A pdb=" N ALA H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Proline residue: H 244 - end of helix removed outlier: 4.188A pdb=" N LEU H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY H 259 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 45 Processing helix chain 'I' and resid 82 through 94 removed outlier: 3.523A pdb=" N LYS I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 131 through 140 removed outlier: 4.501A pdb=" N GLY I 138 " --> pdb=" O GLY I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 Processing helix chain 'I' and resid 152 through 173 Processing helix chain 'I' and resid 238 through 259 removed outlier: 3.676A pdb=" N ALA I 242 " --> pdb=" O LYS I 238 " (cutoff:3.500A) Proline residue: I 244 - end of helix removed outlier: 4.195A pdb=" N LEU I 258 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY I 259 " --> pdb=" O ALA I 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 45 Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.530A pdb=" N LYS J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 126 Processing helix chain 'J' and resid 131 through 140 removed outlier: 4.506A pdb=" N GLY J 138 " --> pdb=" O GLY J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 146 Processing helix chain 'J' and resid 152 through 173 Processing helix chain 'J' and resid 238 through 259 removed outlier: 3.664A pdb=" N ALA J 242 " --> pdb=" O LYS J 238 " (cutoff:3.500A) Proline residue: J 244 - end of helix removed outlier: 4.157A pdb=" N LEU J 258 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY J 259 " --> pdb=" O ALA J 255 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 54 removed outlier: 6.860A pdb=" N ASP A 176 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP A 120 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN A 178 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 118 " --> pdb=" O ASN A 178 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 180 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA A 116 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 182 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR A 67 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 109 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR A 69 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA A 111 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN A 71 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 113 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 73 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 205 Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 54 removed outlier: 6.810A pdb=" N ASP B 176 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP B 120 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN B 178 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 118 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 180 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 116 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 182 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 67 " --> pdb=" O TYR B 107 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B 109 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR B 69 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA B 111 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN B 71 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL B 113 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS B 73 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS B 115 " --> pdb=" O LYS B 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 54 removed outlier: 6.795A pdb=" N ASP C 176 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C 120 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C 178 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS C 118 " --> pdb=" O ASN C 178 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 180 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 116 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 182 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 67 " --> pdb=" O TYR C 107 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE C 109 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 69 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ALA C 111 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN C 71 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL C 113 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LYS C 73 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS C 115 " --> pdb=" O LYS C 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 54 removed outlier: 6.825A pdb=" N ASP D 176 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASP D 120 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN D 178 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS D 118 " --> pdb=" O ASN D 178 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 180 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 116 " --> pdb=" O THR D 180 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D 182 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR D 67 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 109 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR D 69 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA D 111 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLN D 71 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL D 113 " --> pdb=" O GLN D 71 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS D 73 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS D 115 " --> pdb=" O LYS D 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 54 removed outlier: 6.782A pdb=" N ASP E 176 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP E 120 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN E 178 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS E 118 " --> pdb=" O ASN E 178 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR E 180 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA E 116 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 182 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR E 67 " --> pdb=" O TYR E 107 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE E 109 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR E 69 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA E 111 " --> pdb=" O TYR E 69 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN E 71 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 113 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS E 73 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LYS E 115 " --> pdb=" O LYS E 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 54 removed outlier: 6.893A pdb=" N ASP F 176 " --> pdb=" O ASP F 120 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP F 120 " --> pdb=" O ASP F 176 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN F 178 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS F 118 " --> pdb=" O ASN F 178 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR F 180 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA F 116 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 182 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR F 67 " --> pdb=" O TYR F 107 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE F 109 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR F 69 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ALA F 111 " --> pdb=" O TYR F 69 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN F 71 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL F 113 " --> pdb=" O GLN F 71 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS F 73 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N LYS F 115 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 49 through 54 removed outlier: 6.834A pdb=" N ASP G 176 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G 120 " --> pdb=" O ASP G 176 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN G 178 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS G 118 " --> pdb=" O ASN G 178 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR G 180 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA G 116 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE G 182 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR G 67 " --> pdb=" O TYR G 107 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE G 109 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N TYR G 69 " --> pdb=" O ILE G 109 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ALA G 111 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN G 71 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL G 113 " --> pdb=" O GLN G 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS G 73 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS G 115 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 49 through 54 removed outlier: 6.795A pdb=" N ASP H 176 " --> pdb=" O ASP H 120 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP H 120 " --> pdb=" O ASP H 176 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN H 178 " --> pdb=" O LYS H 118 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS H 118 " --> pdb=" O ASN H 178 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR H 180 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA H 116 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE H 182 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR H 67 " --> pdb=" O TYR H 107 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE H 109 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR H 69 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ALA H 111 " --> pdb=" O TYR H 69 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN H 71 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL H 113 " --> pdb=" O GLN H 71 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS H 73 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LYS H 115 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 49 through 54 removed outlier: 6.822A pdb=" N ASP I 176 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP I 120 " --> pdb=" O ASP I 176 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN I 178 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS I 118 " --> pdb=" O ASN I 178 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR I 180 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA I 116 " --> pdb=" O THR I 180 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE I 182 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR I 67 " --> pdb=" O TYR I 107 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE I 109 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR I 69 " --> pdb=" O ILE I 109 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA I 111 " --> pdb=" O TYR I 69 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN I 71 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL I 113 " --> pdb=" O GLN I 71 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS I 73 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS I 115 " --> pdb=" O LYS I 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 49 through 54 removed outlier: 6.751A pdb=" N ASP J 176 " --> pdb=" O ASP J 120 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP J 120 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN J 178 " --> pdb=" O LYS J 118 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS J 118 " --> pdb=" O ASN J 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR J 180 " --> pdb=" O ALA J 116 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA J 116 " --> pdb=" O THR J 180 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE J 182 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR J 67 " --> pdb=" O TYR J 107 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE J 109 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR J 69 " --> pdb=" O ILE J 109 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA J 111 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN J 71 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL J 113 " --> pdb=" O GLN J 71 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS J 73 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LYS J 115 " --> pdb=" O LYS J 73 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3307 1.32 - 1.45: 3743 1.45 - 1.57: 10040 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 17240 Sorted by residual: bond pdb=" N ASN E 149 " pdb=" CA ASN E 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.68e+00 bond pdb=" N ASN J 149 " pdb=" CA ASN J 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.63e+00 bond pdb=" N ASN F 149 " pdb=" CA ASN F 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.63e+00 bond pdb=" N ASN G 149 " pdb=" CA ASN G 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.63e+00 bond pdb=" N ASN C 149 " pdb=" CA ASN C 149 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.58e+00 ... (remaining 17235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 21925 1.19 - 2.38: 1108 2.38 - 3.57: 134 3.57 - 4.75: 89 4.75 - 5.94: 34 Bond angle restraints: 23290 Sorted by residual: angle pdb=" C TYR H 148 " pdb=" N ASN H 149 " pdb=" CA ASN H 149 " ideal model delta sigma weight residual 121.19 126.83 -5.64 1.59e+00 3.96e-01 1.26e+01 angle pdb=" C TYR C 148 " pdb=" N ASN C 149 " pdb=" CA ASN C 149 " ideal model delta sigma weight residual 121.19 126.83 -5.64 1.59e+00 3.96e-01 1.26e+01 angle pdb=" C TYR I 148 " pdb=" N ASN I 149 " pdb=" CA ASN I 149 " ideal model delta sigma weight residual 121.19 126.82 -5.63 1.59e+00 3.96e-01 1.25e+01 angle pdb=" C TYR B 148 " pdb=" N ASN B 149 " pdb=" CA ASN B 149 " ideal model delta sigma weight residual 121.19 126.80 -5.61 1.59e+00 3.96e-01 1.25e+01 angle pdb=" C TYR D 148 " pdb=" N ASN D 149 " pdb=" CA ASN D 149 " ideal model delta sigma weight residual 121.19 126.80 -5.61 1.59e+00 3.96e-01 1.24e+01 ... (remaining 23285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9175 17.96 - 35.92: 1017 35.92 - 53.89: 286 53.89 - 71.85: 52 71.85 - 89.81: 60 Dihedral angle restraints: 10590 sinusoidal: 4110 harmonic: 6480 Sorted by residual: dihedral pdb=" CA GLY A 138 " pdb=" C GLY A 138 " pdb=" N ALA A 139 " pdb=" CA ALA A 139 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLY H 138 " pdb=" C GLY H 138 " pdb=" N ALA H 139 " pdb=" CA ALA H 139 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLY F 138 " pdb=" C GLY F 138 " pdb=" N ALA F 139 " pdb=" CA ALA F 139 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 10587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1499 0.027 - 0.054: 749 0.054 - 0.081: 244 0.081 - 0.107: 149 0.107 - 0.134: 99 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA GLU C 175 " pdb=" N GLU C 175 " pdb=" C GLU C 175 " pdb=" CB GLU C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA GLU H 175 " pdb=" N GLU H 175 " pdb=" C GLU H 175 " pdb=" CB GLU H 175 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA GLU B 175 " pdb=" N GLU B 175 " pdb=" C GLU B 175 " pdb=" CB GLU B 175 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 2737 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 138 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C GLY F 138 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY F 138 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA F 139 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 138 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.33e+00 pdb=" C GLY A 138 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 138 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 138 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C GLY I 138 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY I 138 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA I 139 " -0.010 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3342 2.77 - 3.31: 15181 3.31 - 3.84: 29186 3.84 - 4.37: 33772 4.37 - 4.90: 59695 Nonbonded interactions: 141176 Sorted by model distance: nonbonded pdb=" N ASP E 77 " pdb=" OD1 ASP E 77 " model vdw 2.244 3.120 nonbonded pdb=" N ASP F 77 " pdb=" OD1 ASP F 77 " model vdw 2.244 3.120 nonbonded pdb=" N ASP A 77 " pdb=" OD1 ASP A 77 " model vdw 2.244 3.120 nonbonded pdb=" N ASP J 77 " pdb=" OD1 ASP J 77 " model vdw 2.245 3.120 nonbonded pdb=" N ASP D 77 " pdb=" OD1 ASP D 77 " model vdw 2.246 3.120 ... (remaining 141171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 49.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.030 ------------------------------------------------------------------------------- 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 17240 Z= 0.423 Angle : 0.654 5.942 23290 Z= 0.367 Chirality : 0.043 0.134 2740 Planarity : 0.003 0.031 3000 Dihedral : 17.810 89.810 6450 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.39 % Allowed : 21.06 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2250 helix: 1.43 (0.20), residues: 710 sheet: -0.04 (0.18), residues: 870 loop : -1.28 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 127 HIS 0.001 0.000 HIS C 222 PHE 0.008 0.003 PHE B 239 TYR 0.007 0.001 TYR B 179 ARG 0.007 0.001 ARG F 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 581 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8092 (m) cc_final: 0.7836 (p) REVERT: A 248 ASP cc_start: 0.7238 (m-30) cc_final: 0.6874 (m-30) REVERT: B 248 ASP cc_start: 0.7387 (m-30) cc_final: 0.7121 (m-30) REVERT: B 252 LYS cc_start: 0.7506 (mttp) cc_final: 0.7255 (mmmm) REVERT: C 70 LEU cc_start: 0.7583 (mt) cc_final: 0.7294 (mm) REVERT: D 189 GLU cc_start: 0.6751 (tt0) cc_final: 0.6071 (pt0) REVERT: D 226 THR cc_start: 0.6708 (t) cc_final: 0.6411 (t) REVERT: D 248 ASP cc_start: 0.6892 (m-30) cc_final: 0.6673 (m-30) REVERT: E 57 THR cc_start: 0.7030 (m) cc_final: 0.6462 (m) REVERT: E 189 GLU cc_start: 0.7097 (tt0) cc_final: 0.6397 (tt0) REVERT: E 193 THR cc_start: 0.8205 (m) cc_final: 0.7714 (p) REVERT: F 128 LEU cc_start: 0.8264 (mt) cc_final: 0.8049 (mm) REVERT: G 55 SER cc_start: 0.7222 (OUTLIER) cc_final: 0.6918 (p) REVERT: H 217 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6307 (mp0) REVERT: I 119 MET cc_start: 0.5991 (ptp) cc_final: 0.5759 (ptp) REVERT: I 217 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6153 (mp0) REVERT: J 248 ASP cc_start: 0.6517 (m-30) cc_final: 0.6191 (m-30) outliers start: 61 outliers final: 18 residues processed: 629 average time/residue: 1.0151 time to fit residues: 728.5291 Evaluate side-chains 402 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 383 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 112 ASN Chi-restraints excluded: chain J residue 77 ASP Chi-restraints excluded: chain J residue 91 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 221 GLN B 186 GLN B 205 GLN B 221 GLN C 186 GLN D 110 GLN D 186 GLN D 221 GLN E 186 GLN E 231 ASN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN F 53 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 ASN G 110 GLN H 112 ASN H 186 GLN H 194 GLN H 225 GLN I 110 GLN ** I 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 233 ASN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 GLN J 225 GLN J 233 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.105528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.078466 restraints weight = 86053.922| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 4.58 r_work: 0.2950 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17240 Z= 0.309 Angle : 0.780 10.474 23290 Z= 0.412 Chirality : 0.048 0.203 2740 Planarity : 0.005 0.087 3000 Dihedral : 10.635 85.441 2666 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.11 % Allowed : 27.33 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2250 helix: 0.94 (0.19), residues: 740 sheet: 0.14 (0.18), residues: 830 loop : -1.12 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP H 127 HIS 0.007 0.002 HIS C 222 PHE 0.014 0.003 PHE C 239 TYR 0.018 0.002 TYR F 179 ARG 0.013 0.001 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 360 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8506 (t0) cc_final: 0.8237 (OUTLIER) REVERT: A 81 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 248 ASP cc_start: 0.8301 (m-30) cc_final: 0.8066 (m-30) REVERT: B 51 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7786 (ptpt) REVERT: B 204 ARG cc_start: 0.8459 (ttm110) cc_final: 0.7915 (ttm-80) REVERT: B 248 ASP cc_start: 0.8464 (m-30) cc_final: 0.7973 (m-30) REVERT: C 133 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6208 (pt0) REVERT: C 137 THR cc_start: 0.8074 (m) cc_final: 0.7745 (p) REVERT: C 217 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8266 (mt-10) REVERT: D 39 MET cc_start: 0.7363 (tpt) cc_final: 0.6967 (mmm) REVERT: D 49 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 133 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6215 (pt0) REVERT: D 137 THR cc_start: 0.8062 (m) cc_final: 0.7764 (p) REVERT: E 61 GLU cc_start: 0.8517 (pm20) cc_final: 0.8267 (pt0) REVERT: E 130 ARG cc_start: 0.7402 (mmt90) cc_final: 0.7166 (tpp-160) REVERT: E 175 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 204 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7995 (ttm-80) REVERT: E 241 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8478 (tt0) REVERT: F 119 MET cc_start: 0.8165 (pmm) cc_final: 0.7914 (pmm) REVERT: F 130 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6962 (mmp80) REVERT: F 171 ASP cc_start: 0.8345 (t0) cc_final: 0.8069 (t70) REVERT: G 115 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7903 (mtmm) REVERT: G 133 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6427 (pp20) REVERT: G 217 GLU cc_start: 0.8319 (tt0) cc_final: 0.7886 (mt-10) REVERT: G 241 GLU cc_start: 0.9001 (tp30) cc_final: 0.8451 (tt0) REVERT: G 248 ASP cc_start: 0.8609 (m-30) cc_final: 0.8305 (m-30) REVERT: H 49 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7938 (tm-30) REVERT: H 53 GLN cc_start: 0.8648 (mt0) cc_final: 0.8396 (mt0) REVERT: H 56 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8769 (mm-30) REVERT: H 117 ASP cc_start: 0.8472 (p0) cc_final: 0.8234 (p0) REVERT: H 171 ASP cc_start: 0.7552 (t0) cc_final: 0.7008 (t0) REVERT: H 227 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7860 (ttm170) REVERT: H 241 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8642 (tm-30) REVERT: H 248 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: I 52 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8429 (p) REVERT: I 81 SER cc_start: 0.8624 (t) cc_final: 0.8347 (p) REVERT: I 103 ASP cc_start: 0.8799 (m-30) cc_final: 0.8571 (m-30) REVERT: I 199 ASN cc_start: 0.8178 (t0) cc_final: 0.7956 (t0) REVERT: I 217 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8015 (mt-10) REVERT: I 241 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8786 (tm-30) REVERT: I 248 ASP cc_start: 0.8436 (t0) cc_final: 0.8046 (m-30) REVERT: J 49 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8098 (tm-30) REVERT: J 81 SER cc_start: 0.8706 (m) cc_final: 0.8321 (p) REVERT: J 117 ASP cc_start: 0.7783 (p0) cc_final: 0.6941 (p0) REVERT: J 119 MET cc_start: 0.7945 (ptp) cc_final: 0.7375 (ptp) REVERT: J 180 THR cc_start: 0.8382 (m) cc_final: 0.8033 (t) REVERT: J 187 ILE cc_start: 0.9017 (pt) cc_final: 0.8759 (pp) REVERT: J 248 ASP cc_start: 0.8084 (m-30) cc_final: 0.7847 (m-30) outliers start: 110 outliers final: 33 residues processed: 428 average time/residue: 1.3008 time to fit residues: 619.3021 Evaluate side-chains 328 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 287 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 241 GLU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 248 ASP Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 28 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN B 221 GLN C 53 GLN D 110 GLN F 53 GLN F 178 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN I 186 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.066081 restraints weight = 71626.515| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.97 r_work: 0.2702 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 1.0210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17240 Z= 0.346 Angle : 0.668 9.758 23290 Z= 0.347 Chirality : 0.046 0.156 2740 Planarity : 0.004 0.041 3000 Dihedral : 10.325 82.022 2644 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.33 % Allowed : 27.89 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.18), residues: 2250 helix: 1.21 (0.19), residues: 740 sheet: -0.04 (0.18), residues: 860 loop : -1.05 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 127 HIS 0.002 0.001 HIS A 222 PHE 0.023 0.003 PHE C 239 TYR 0.017 0.002 TYR G 96 ARG 0.008 0.001 ARG H 227 *********************** 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 368 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 290 time to evaluate : 1.948 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7646 (mpp) REVERT: A 148 TYR cc_start: 0.6340 (t80) cc_final: 0.5318 (t80) REVERT: A 227 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8327 (ttm-80) REVERT: A 241 GLU cc_start: 0.9179 (tt0) cc_final: 0.8969 (pt0) REVERT: B 77 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: B 79 ASP cc_start: 0.8394 (t0) cc_final: 0.8179 (t0) REVERT: B 119 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7464 (mpp) REVERT: B 148 TYR cc_start: 0.5784 (t80) cc_final: 0.4878 (t80) REVERT: D 61 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8866 (mt-10) REVERT: D 130 ARG cc_start: 0.7289 (mmt90) cc_final: 0.7018 (tpp-160) REVERT: F 120 ASP cc_start: 0.8624 (t70) cc_final: 0.7335 (t70) REVERT: F 130 ARG cc_start: 0.7836 (mmt90) cc_final: 0.7285 (mmp80) REVERT: G 129 SER cc_start: 0.6878 (OUTLIER) cc_final: 0.6516 (p) REVERT: G 217 GLU cc_start: 0.8470 (tt0) cc_final: 0.8186 (mt-10) REVERT: G 248 ASP cc_start: 0.8687 (m-30) cc_final: 0.8432 (m-30) REVERT: H 176 ASP cc_start: 0.7909 (t0) cc_final: 0.7653 (t0) REVERT: H 177 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8094 (m) REVERT: H 204 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8292 (ttm110) REVERT: H 227 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8143 (ttm170) REVERT: H 248 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: I 49 GLU cc_start: 0.8559 (tp30) cc_final: 0.8213 (tm-30) REVERT: I 103 ASP cc_start: 0.9261 (m-30) cc_final: 0.9060 (m-30) REVERT: I 127 TRP cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (p-90) REVERT: I 227 ARG cc_start: 0.8632 (ptm160) cc_final: 0.8288 (ttm170) REVERT: I 248 ASP cc_start: 0.8546 (t0) cc_final: 0.8331 (m-30) REVERT: J 119 MET cc_start: 0.8308 (ptp) cc_final: 0.7721 (ptp) outliers start: 78 outliers final: 35 residues processed: 342 average time/residue: 1.5202 time to fit residues: 571.0729 Evaluate side-chains 294 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 91 VAL 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 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 177 VAL 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 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN D 221 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 194 GLN G 225 GLN H 243 GLN I 112 ASN I 194 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.064468 restraints weight = 63945.578| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.63 r_work: 0.2646 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 1.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 17240 Z= 0.467 Angle : 0.683 9.129 23290 Z= 0.356 Chirality : 0.047 0.149 2740 Planarity : 0.004 0.032 3000 Dihedral : 10.720 78.712 2642 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.61 % Allowed : 27.00 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2250 helix: 1.05 (0.19), residues: 730 sheet: -0.17 (0.18), residues: 860 loop : -0.98 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 127 HIS 0.002 0.001 HIS H 222 PHE 0.021 0.004 PHE C 239 TYR 0.019 0.002 TYR G 96 ARG 0.006 0.001 ARG H 227 *********************** 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 363 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7526 (mpp) REVERT: A 128 LEU cc_start: 0.8456 (mt) cc_final: 0.8040 (mt) REVERT: A 184 ASP cc_start: 0.9143 (m-30) cc_final: 0.8819 (m-30) REVERT: A 227 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8264 (ttm-80) REVERT: B 77 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: B 119 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7506 (mpp) REVERT: B 148 TYR cc_start: 0.6363 (t80) cc_final: 0.5217 (t80) REVERT: C 120 ASP cc_start: 0.8571 (t70) cc_final: 0.8164 (t0) REVERT: C 130 ARG cc_start: 0.7557 (mmt90) cc_final: 0.7349 (mmt90) REVERT: D 61 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8986 (mt-10) REVERT: G 130 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7927 (mmt90) REVERT: G 132 TYR cc_start: 0.7380 (m-10) cc_final: 0.6654 (m-10) REVERT: G 217 GLU cc_start: 0.8480 (tt0) cc_final: 0.8262 (mt-10) REVERT: G 248 ASP cc_start: 0.8593 (m-30) cc_final: 0.8323 (m-30) REVERT: H 204 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8382 (ttm110) REVERT: H 227 ARG cc_start: 0.8658 (ttm-80) cc_final: 0.8392 (ttm170) REVERT: H 248 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8434 (m-30) REVERT: I 127 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.7597 (p-90) REVERT: I 227 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8417 (ttm170) REVERT: I 248 ASP cc_start: 0.8642 (t0) cc_final: 0.8356 (m-30) REVERT: J 52 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8904 (p) REVERT: J 119 MET cc_start: 0.8258 (ptp) cc_final: 0.7635 (ptp) REVERT: J 192 LYS cc_start: 0.9433 (mtmm) cc_final: 0.9092 (mtpp) outliers start: 83 outliers final: 38 residues processed: 341 average time/residue: 1.6090 time to fit residues: 600.1192 Evaluate side-chains 313 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 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 F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 177 VAL 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 H residue 248 ASP Chi-restraints excluded: chain I residue 127 TRP Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 144 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN C 194 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.065857 restraints weight = 82033.248| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.12 r_work: 0.2696 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 1.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17240 Z= 0.219 Angle : 0.552 10.654 23290 Z= 0.289 Chirality : 0.043 0.135 2740 Planarity : 0.003 0.036 3000 Dihedral : 10.136 77.553 2642 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.56 % Allowed : 27.33 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 2250 helix: 1.33 (0.20), residues: 730 sheet: -0.03 (0.19), residues: 850 loop : -0.86 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 127 HIS 0.002 0.001 HIS D 222 PHE 0.015 0.003 PHE C 239 TYR 0.009 0.001 TYR F 179 ARG 0.007 0.001 ARG A 204 *********************** 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 360 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 296 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 119 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7666 (mpp) REVERT: A 227 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8529 (ttm170) REVERT: B 77 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: B 79 ASP cc_start: 0.8517 (t0) cc_final: 0.8217 (t0) REVERT: B 119 MET cc_start: 0.8192 (mtp) cc_final: 0.7500 (mpp) REVERT: B 148 TYR cc_start: 0.6509 (t80) cc_final: 0.5397 (t80) REVERT: B 204 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8306 (ttm-80) REVERT: C 120 ASP cc_start: 0.8237 (t70) cc_final: 0.7962 (t0) REVERT: C 148 TYR cc_start: 0.6183 (t80) cc_final: 0.5302 (t80) REVERT: C 176 ASP cc_start: 0.8717 (t0) cc_final: 0.8325 (t70) REVERT: D 61 GLU cc_start: 0.9254 (mt-10) cc_final: 0.9038 (mt-10) REVERT: F 49 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: F 176 ASP cc_start: 0.8854 (t0) cc_final: 0.8591 (t70) REVERT: G 176 ASP cc_start: 0.8616 (t0) cc_final: 0.8394 (t70) REVERT: G 204 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8337 (ttm-80) REVERT: G 217 GLU cc_start: 0.8461 (tt0) cc_final: 0.8240 (mt-10) REVERT: G 248 ASP cc_start: 0.8666 (m-30) cc_final: 0.8416 (m-30) REVERT: H 204 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8316 (ttm110) REVERT: H 227 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8144 (ttm170) REVERT: I 168 MET cc_start: 0.8003 (ttm) cc_final: 0.7747 (ttp) REVERT: I 227 ARG cc_start: 0.8699 (ptm160) cc_final: 0.8322 (ttm170) REVERT: I 248 ASP cc_start: 0.8557 (t0) cc_final: 0.8329 (m-30) REVERT: J 52 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8842 (p) REVERT: J 117 ASP cc_start: 0.8267 (p0) cc_final: 0.7955 (p0) REVERT: J 119 MET cc_start: 0.8404 (ptp) cc_final: 0.7824 (ptp) REVERT: J 192 LYS cc_start: 0.9416 (mtmm) cc_final: 0.9070 (mtpp) outliers start: 64 outliers final: 41 residues processed: 340 average time/residue: 1.5658 time to fit residues: 583.1494 Evaluate side-chains 313 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 204 ARG Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 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 175 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 77 ASP Chi-restraints excluded: chain I residue 180 THR 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 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 176 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN E 194 GLN F 186 GLN F 194 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.061876 restraints weight = 73861.537| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 3.85 r_work: 0.2603 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 1.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17240 Z= 0.495 Angle : 0.669 12.483 23290 Z= 0.347 Chirality : 0.047 0.157 2740 Planarity : 0.004 0.039 3000 Dihedral : 10.627 74.328 2642 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.89 % Allowed : 26.56 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2250 helix: 1.12 (0.19), residues: 730 sheet: -0.24 (0.18), residues: 860 loop : -1.01 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 127 HIS 0.002 0.001 HIS H 222 PHE 0.020 0.004 PHE C 239 TYR 0.020 0.001 TYR G 96 ARG 0.006 0.001 ARG H 227 *********************** 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 342 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 272 time to evaluate : 1.833 Fit side-chains REVERT: A 119 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7546 (mpp) REVERT: A 148 TYR cc_start: 0.6896 (t80) cc_final: 0.6648 (t80) REVERT: A 204 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8346 (ttm-80) REVERT: B 119 MET cc_start: 0.8057 (mtp) cc_final: 0.7401 (mpp) REVERT: B 148 TYR cc_start: 0.6826 (t80) cc_final: 0.5683 (t80) REVERT: C 148 TYR cc_start: 0.6546 (t80) cc_final: 0.6092 (t80) REVERT: C 176 ASP cc_start: 0.8823 (t0) cc_final: 0.8506 (t70) REVERT: D 61 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8980 (mt-10) REVERT: D 148 TYR cc_start: 0.6735 (t80) cc_final: 0.6496 (t80) REVERT: E 49 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: E 61 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8914 (mm-30) REVERT: E 175 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: E 241 GLU cc_start: 0.9126 (tt0) cc_final: 0.8851 (tt0) REVERT: F 49 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: G 49 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: G 217 GLU cc_start: 0.8508 (tt0) cc_final: 0.8288 (mt-10) REVERT: G 225 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: G 248 ASP cc_start: 0.8580 (m-30) cc_final: 0.8318 (m-30) REVERT: H 204 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8410 (ttm110) REVERT: H 227 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8414 (ttm170) REVERT: I 49 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: I 248 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: J 117 ASP cc_start: 0.8344 (p0) cc_final: 0.8111 (p0) REVERT: J 119 MET cc_start: 0.8229 (ptp) cc_final: 0.7631 (ptp) outliers start: 70 outliers final: 49 residues processed: 321 average time/residue: 1.6673 time to fit residues: 582.2406 Evaluate side-chains 320 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 263 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 161 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 49 GLU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 248 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 69 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN G 225 GLN ** J 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.065623 restraints weight = 76749.956| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.00 r_work: 0.2694 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 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 = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 1.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17240 Z= 0.202 Angle : 0.552 16.053 23290 Z= 0.285 Chirality : 0.043 0.136 2740 Planarity : 0.003 0.042 3000 Dihedral : 10.019 73.474 2642 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.89 % Allowed : 27.11 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 2250 helix: 1.35 (0.20), residues: 730 sheet: -0.07 (0.19), residues: 850 loop : -0.89 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 127 HIS 0.002 0.001 HIS D 222 PHE 0.013 0.003 PHE C 239 TYR 0.009 0.001 TYR D 179 ARG 0.005 0.000 ARG J 190 *********************** 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 337 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 285 time to evaluate : 1.851 Fit side-chains REVERT: A 119 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7652 (mpp) REVERT: A 148 TYR cc_start: 0.6722 (t80) cc_final: 0.6433 (t80) REVERT: A 176 ASP cc_start: 0.8657 (t0) cc_final: 0.8410 (t70) REVERT: A 204 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8330 (ttm-80) REVERT: B 79 ASP cc_start: 0.8517 (t0) cc_final: 0.8259 (t0) REVERT: B 119 MET cc_start: 0.8206 (mtp) cc_final: 0.7534 (mpp) REVERT: B 148 TYR cc_start: 0.6678 (t80) cc_final: 0.5572 (t80) REVERT: B 204 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8324 (ttm-80) REVERT: C 148 TYR cc_start: 0.6360 (t80) cc_final: 0.5942 (t80) REVERT: C 176 ASP cc_start: 0.8678 (t0) cc_final: 0.8390 (t70) REVERT: D 80 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8972 (mtm) REVERT: D 148 TYR cc_start: 0.6504 (t80) cc_final: 0.6244 (t80) REVERT: E 61 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8881 (mm-30) REVERT: E 175 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8026 (mm-30) REVERT: E 241 GLU cc_start: 0.9229 (tt0) cc_final: 0.8912 (tt0) REVERT: F 176 ASP cc_start: 0.8767 (t0) cc_final: 0.8473 (t70) REVERT: G 176 ASP cc_start: 0.8726 (t0) cc_final: 0.8525 (t70) REVERT: G 217 GLU cc_start: 0.8473 (tt0) cc_final: 0.8179 (mt-10) REVERT: G 248 ASP cc_start: 0.8686 (m-30) cc_final: 0.8424 (m-30) REVERT: H 227 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8187 (ttm170) REVERT: I 248 ASP cc_start: 0.8543 (t0) cc_final: 0.8332 (m-30) REVERT: J 43 ILE cc_start: 0.8908 (tp) cc_final: 0.8504 (tp) REVERT: J 117 ASP cc_start: 0.8241 (p0) cc_final: 0.7945 (p0) REVERT: J 119 MET cc_start: 0.8424 (ptp) cc_final: 0.7887 (ptp) REVERT: J 130 ARG cc_start: 0.7994 (mmt90) cc_final: 0.7792 (mpt90) REVERT: J 248 ASP cc_start: 0.8558 (m-30) cc_final: 0.8268 (m-30) outliers start: 52 outliers final: 40 residues processed: 325 average time/residue: 1.6828 time to fit residues: 598.6784 Evaluate side-chains 313 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 85 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 225 GLN J 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.063857 restraints weight = 69624.103| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.80 r_work: 0.2657 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 1.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17240 Z= 0.312 Angle : 0.590 13.649 23290 Z= 0.303 Chirality : 0.044 0.132 2740 Planarity : 0.003 0.043 3000 Dihedral : 9.943 69.578 2642 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.06 % Allowed : 27.44 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 2250 helix: 1.32 (0.19), residues: 730 sheet: -0.10 (0.19), residues: 860 loop : -0.99 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 127 HIS 0.003 0.001 HIS G 222 PHE 0.016 0.003 PHE C 239 TYR 0.019 0.001 TYR H 179 ARG 0.005 0.001 ARG F 204 *********************** 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 324 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 269 time to evaluate : 1.883 Fit side-chains REVERT: A 119 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7542 (mpp) REVERT: A 130 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7685 (mmt180) REVERT: A 148 TYR cc_start: 0.6813 (t80) cc_final: 0.6312 (t80) REVERT: A 204 ARG cc_start: 0.8598 (ttm110) cc_final: 0.8310 (ttm-80) REVERT: B 79 ASP cc_start: 0.8459 (t0) cc_final: 0.8226 (t0) REVERT: B 119 MET cc_start: 0.8082 (mtp) cc_final: 0.7435 (mpp) REVERT: B 120 ASP cc_start: 0.8993 (t0) cc_final: 0.8755 (t0) REVERT: B 128 LEU cc_start: 0.8415 (mp) cc_final: 0.8210 (pt) REVERT: B 148 TYR cc_start: 0.6819 (t80) cc_final: 0.6284 (t80) REVERT: B 175 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 148 TYR cc_start: 0.6564 (t80) cc_final: 0.6139 (t80) REVERT: C 176 ASP cc_start: 0.8769 (t0) cc_final: 0.8500 (t70) REVERT: D 80 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8967 (mtm) REVERT: E 61 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8908 (mm-30) REVERT: E 175 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (mm-30) REVERT: E 241 GLU cc_start: 0.9203 (tt0) cc_final: 0.8904 (tt0) REVERT: G 130 ARG cc_start: 0.7801 (mmp80) cc_final: 0.7535 (mpt90) REVERT: G 217 GLU cc_start: 0.8472 (tt0) cc_final: 0.8261 (mt-10) REVERT: G 248 ASP cc_start: 0.8643 (m-30) cc_final: 0.8382 (m-30) REVERT: H 181 MET cc_start: 0.8506 (ttp) cc_final: 0.8274 (ttm) REVERT: H 227 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8144 (ttm170) REVERT: I 248 ASP cc_start: 0.8591 (t0) cc_final: 0.8340 (m-30) REVERT: J 117 ASP cc_start: 0.8277 (p0) cc_final: 0.8016 (p0) REVERT: J 119 MET cc_start: 0.8283 (ptp) cc_final: 0.7695 (ptp) outliers start: 55 outliers final: 46 residues processed: 313 average time/residue: 1.6919 time to fit residues: 578.7519 Evaluate side-chains 311 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 165 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 175 GLU 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 G residue 129 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.091347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.064786 restraints weight = 95233.959| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.31 r_work: 0.2665 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 1.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17240 Z= 0.224 Angle : 0.561 13.377 23290 Z= 0.287 Chirality : 0.043 0.144 2740 Planarity : 0.003 0.044 3000 Dihedral : 9.638 69.045 2642 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.72 % Allowed : 27.83 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 2250 helix: 1.40 (0.20), residues: 730 sheet: -0.03 (0.19), residues: 850 loop : -0.91 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 127 HIS 0.002 0.001 HIS D 222 PHE 0.014 0.003 PHE C 239 TYR 0.012 0.001 TYR H 179 ARG 0.006 0.001 ARG F 130 *********************** 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 323 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 1.878 Fit side-chains REVERT: A 119 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7674 (mpp) REVERT: A 148 TYR cc_start: 0.6793 (t80) cc_final: 0.6196 (t80) REVERT: A 204 ARG cc_start: 0.8591 (ttm110) cc_final: 0.8313 (ttm-80) REVERT: B 119 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7466 (mpp) REVERT: B 128 LEU cc_start: 0.8408 (mp) cc_final: 0.8195 (pt) REVERT: B 148 TYR cc_start: 0.6769 (t80) cc_final: 0.6247 (t80) REVERT: C 148 TYR cc_start: 0.6570 (t80) cc_final: 0.6180 (t80) REVERT: C 176 ASP cc_start: 0.8735 (t0) cc_final: 0.8509 (t70) REVERT: D 61 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9006 (mm-30) REVERT: D 80 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8978 (mtm) REVERT: E 61 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8921 (mm-30) REVERT: E 175 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8031 (mm-30) REVERT: E 241 GLU cc_start: 0.9227 (tt0) cc_final: 0.8920 (tt0) REVERT: F 176 ASP cc_start: 0.8718 (t0) cc_final: 0.8443 (t70) REVERT: G 130 ARG cc_start: 0.7809 (mmp80) cc_final: 0.7534 (mpt90) REVERT: G 217 GLU cc_start: 0.8474 (tt0) cc_final: 0.8185 (mt-10) REVERT: G 248 ASP cc_start: 0.8730 (m-30) cc_final: 0.8469 (m-30) REVERT: H 181 MET cc_start: 0.8510 (ttp) cc_final: 0.8245 (ttm) REVERT: H 227 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8323 (ttm170) REVERT: I 49 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: I 248 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: J 117 ASP cc_start: 0.8267 (p0) cc_final: 0.8003 (p0) REVERT: J 119 MET cc_start: 0.8395 (ptp) cc_final: 0.7832 (ptp) REVERT: J 248 ASP cc_start: 0.8586 (m-30) cc_final: 0.8278 (m-30) outliers start: 49 outliers final: 43 residues processed: 313 average time/residue: 1.6223 time to fit residues: 553.8679 Evaluate side-chains 316 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 1.995 ------------------------------------------------------------------------------- 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 77 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 248 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 92 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 176 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.091600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.065353 restraints weight = 79511.996| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.00 r_work: 0.2686 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 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 = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 1.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17240 Z= 0.208 Angle : 0.557 12.901 23290 Z= 0.285 Chirality : 0.043 0.147 2740 Planarity : 0.003 0.044 3000 Dihedral : 9.549 67.977 2642 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 27.94 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 2250 helix: 1.43 (0.20), residues: 730 sheet: 0.01 (0.19), residues: 850 loop : -0.90 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 127 HIS 0.002 0.001 HIS D 222 PHE 0.013 0.003 PHE C 239 TYR 0.014 0.001 TYR H 179 ARG 0.007 0.001 ARG H 130 ********************** 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 321 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 270 time to evaluate : 1.870 Fit side-chains REVERT: A 119 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7582 (mpp) REVERT: A 130 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7686 (mpt90) REVERT: A 148 TYR cc_start: 0.6773 (t80) cc_final: 0.6199 (t80) REVERT: A 204 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8256 (ttm-80) REVERT: B 119 MET cc_start: 0.8031 (mtp) cc_final: 0.7368 (mpp) REVERT: B 128 LEU cc_start: 0.8397 (mp) cc_final: 0.8169 (pt) REVERT: B 148 TYR cc_start: 0.6810 (t80) cc_final: 0.6313 (t80) REVERT: C 148 TYR cc_start: 0.6592 (t80) cc_final: 0.6242 (t80) REVERT: C 176 ASP cc_start: 0.8697 (t0) cc_final: 0.8413 (t70) REVERT: D 61 GLU cc_start: 0.9247 (mt-10) cc_final: 0.9001 (mm-30) REVERT: D 80 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8958 (mtm) REVERT: E 61 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8896 (mm-30) REVERT: E 175 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7933 (mm-30) REVERT: E 241 GLU cc_start: 0.9213 (tt0) cc_final: 0.8900 (tt0) REVERT: F 176 ASP cc_start: 0.8635 (t0) cc_final: 0.8352 (t70) REVERT: G 130 ARG cc_start: 0.7780 (mmp80) cc_final: 0.7510 (mpt90) REVERT: G 217 GLU cc_start: 0.8421 (tt0) cc_final: 0.8134 (mt-10) REVERT: G 248 ASP cc_start: 0.8664 (m-30) cc_final: 0.8396 (m-30) REVERT: H 181 MET cc_start: 0.8447 (ttp) cc_final: 0.8165 (ttm) REVERT: H 227 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8130 (ttm170) REVERT: I 49 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: I 130 ARG cc_start: 0.7861 (mpt180) cc_final: 0.7659 (mmp80) REVERT: I 227 ARG cc_start: 0.8660 (ttm170) cc_final: 0.8438 (ttm170) REVERT: I 248 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: J 117 ASP cc_start: 0.8227 (p0) cc_final: 0.7962 (p0) REVERT: J 119 MET cc_start: 0.8348 (ptp) cc_final: 0.7781 (ptp) REVERT: J 248 ASP cc_start: 0.8512 (m-30) cc_final: 0.8220 (m-30) outliers start: 51 outliers final: 44 residues processed: 308 average time/residue: 1.6113 time to fit residues: 541.4763 Evaluate side-chains 314 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 204 ARG 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 49 GLU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 183 THR Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 248 ASP Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 141 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 77 optimal weight: 0.0670 chunk 210 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 110 optimal weight: 0.0070 chunk 56 optimal weight: 5.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 GLN G 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.067751 restraints weight = 76155.148| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.01 r_work: 0.2726 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 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 = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 1.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17240 Z= 0.164 Angle : 0.539 12.790 23290 Z= 0.276 Chirality : 0.042 0.144 2740 Planarity : 0.003 0.044 3000 Dihedral : 9.296 66.696 2642 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.50 % Allowed : 28.39 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 2250 helix: 1.50 (0.20), residues: 730 sheet: 0.07 (0.19), residues: 850 loop : -0.82 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 127 HIS 0.002 0.000 HIS D 222 PHE 0.011 0.003 PHE C 239 TYR 0.010 0.001 TYR H 179 ARG 0.004 0.000 ARG F 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15097.19 seconds wall clock time: 267 minutes 21.84 seconds (16041.84 seconds total)