Starting phenix.real_space_refine on Sun Aug 24 03:54:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc3_15961/08_2025/8bc3_15961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc3_15961/08_2025/8bc3_15961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bc3_15961/08_2025/8bc3_15961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc3_15961/08_2025/8bc3_15961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bc3_15961/08_2025/8bc3_15961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc3_15961/08_2025/8bc3_15961.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10540 2.51 5 N 2700 2.21 5 O 3590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16880 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1624 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'QC9': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Time building chain proxies: 4.38, per 1000 atoms: 0.26 Number of scatterers: 16880 At special positions: 0 Unit cell: (116.1, 121.5, 81.9, 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 50 16.00 O 3590 8.00 N 2700 7.00 C 10540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 803.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4080 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 10 sheets defined 59.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 68 through 81 Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN H 123 " --> pdb=" O SER H 119 " (cutoff:3.500A) Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 136 through 142 Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 172 through 183 Processing helix chain 'H' and resid 190 through 198 Processing helix chain 'H' and resid 200 through 216 removed outlier: 3.628A pdb=" N ASP H 204 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 68 through 81 Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 216 removed outlier: 3.628A pdb=" N ASP B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 68 through 81 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 172 through 183 Processing helix chain 'C' and resid 190 through 198 Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP C 204 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY D 36 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 93 through 106 Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 172 through 183 Processing helix chain 'D' and resid 190 through 198 Processing helix chain 'D' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP D 204 " --> pdb=" O HIS D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 68 through 81 Processing helix chain 'E' and resid 93 through 106 Processing helix chain 'E' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 172 through 183 Processing helix chain 'E' and resid 190 through 198 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP E 204 " --> pdb=" O HIS E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY F 36 " --> pdb=" O ILE F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 68 through 81 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 117 through 127 removed outlier: 4.015A pdb=" N GLN F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 136 through 142 Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 190 through 198 Processing helix chain 'F' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP F 204 " --> pdb=" O HIS F 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 68 through 81 Processing helix chain 'G' and resid 93 through 106 Processing helix chain 'G' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 136 through 142 Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 172 through 183 Processing helix chain 'G' and resid 190 through 198 Processing helix chain 'G' and resid 200 through 216 removed outlier: 3.628A pdb=" N ASP G 204 " --> pdb=" O HIS G 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 50 Processing helix chain 'I' and resid 68 through 81 Processing helix chain 'I' and resid 93 through 106 Processing helix chain 'I' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN I 123 " --> pdb=" O SER I 119 " (cutoff:3.500A) Proline residue: I 124 - end of helix Processing helix chain 'I' and resid 136 through 142 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 172 through 183 Processing helix chain 'I' and resid 190 through 198 Processing helix chain 'I' and resid 200 through 216 removed outlier: 3.628A pdb=" N ASP I 204 " --> pdb=" O HIS I 200 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 28 through 36 removed outlier: 3.702A pdb=" N GLY J 36 " --> pdb=" O ILE J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 50 Processing helix chain 'J' and resid 68 through 81 Processing helix chain 'J' and resid 93 through 106 Processing helix chain 'J' and resid 117 through 127 removed outlier: 4.016A pdb=" N GLN J 123 " --> pdb=" O SER J 119 " (cutoff:3.500A) Proline residue: J 124 - end of helix Processing helix chain 'J' and resid 136 through 142 Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 190 through 198 Processing helix chain 'J' and resid 200 through 216 removed outlier: 3.627A pdb=" N ASP J 204 " --> pdb=" O HIS J 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY A 24 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 25 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A 61 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 58 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 89 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 60 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN A 111 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 88 " --> pdb=" O ASN A 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 113 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 90 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 115 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A 110 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER A 133 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 112 " --> pdb=" O SER A 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL A 132 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 165 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR A 188 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 167 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 2 through 6 removed outlier: 4.245A pdb=" N GLY H 24 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL H 25 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 61 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE H 58 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS H 89 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL H 60 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ASN H 111 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE H 88 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE H 90 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL H 115 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR H 110 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER H 133 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL H 112 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL H 132 " --> pdb=" O ILE H 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE H 165 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR H 188 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL H 167 " --> pdb=" O THR H 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY B 24 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 25 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU B 61 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 58 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS B 89 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 60 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN B 111 " --> pdb=" O PHE B 86 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 88 " --> pdb=" O ASN B 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR B 113 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 90 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL B 115 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR B 110 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER B 133 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 112 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 132 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 165 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR B 188 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 167 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY C 24 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 25 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU C 61 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE C 58 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS C 89 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL C 60 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN C 111 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE C 88 " --> pdb=" O ASN C 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR C 113 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 90 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 115 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR C 110 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 133 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL C 112 " --> pdb=" O SER C 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 132 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE C 165 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 167 " --> pdb=" O THR C 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY D 24 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 25 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU D 61 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE D 58 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS D 89 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL D 60 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN D 111 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE D 88 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR D 113 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE D 90 " --> pdb=" O THR D 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL D 115 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR D 110 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER D 133 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL D 112 " --> pdb=" O SER D 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL D 132 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE D 165 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL D 167 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY E 24 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 25 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU E 61 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 58 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS E 89 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL E 60 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN E 111 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE E 88 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR E 113 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE E 90 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL E 115 " --> pdb=" O ILE E 90 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR E 110 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER E 133 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL E 112 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 132 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE E 165 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR E 188 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 167 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY F 24 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 25 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 61 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE F 58 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS F 89 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL F 60 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN F 111 " --> pdb=" O PHE F 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE F 88 " --> pdb=" O ASN F 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR F 113 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE F 90 " --> pdb=" O THR F 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL F 115 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR F 110 " --> pdb=" O PHE F 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER F 133 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL F 112 " --> pdb=" O SER F 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 132 " --> pdb=" O ILE F 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE F 165 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR F 188 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL F 167 " --> pdb=" O THR F 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY G 24 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 25 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU G 61 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE G 58 " --> pdb=" O VAL G 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS G 89 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL G 60 " --> pdb=" O LYS G 89 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN G 111 " --> pdb=" O PHE G 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE G 88 " --> pdb=" O ASN G 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR G 113 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE G 90 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL G 115 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR G 110 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER G 133 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL G 112 " --> pdb=" O SER G 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL G 132 " --> pdb=" O ILE G 166 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE G 165 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR G 188 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL G 167 " --> pdb=" O THR G 188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 2 through 6 removed outlier: 4.245A pdb=" N GLY I 24 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL I 25 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 61 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE I 58 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS I 89 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL I 60 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN I 111 " --> pdb=" O PHE I 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE I 88 " --> pdb=" O ASN I 111 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE I 90 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL I 115 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR I 110 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER I 133 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL I 112 " --> pdb=" O SER I 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL I 132 " --> pdb=" O ILE I 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE I 165 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR I 188 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL I 167 " --> pdb=" O THR I 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 2 through 6 removed outlier: 4.244A pdb=" N GLY J 24 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL J 25 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU J 61 " --> pdb=" O VAL J 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE J 58 " --> pdb=" O VAL J 87 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS J 89 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL J 60 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN J 111 " --> pdb=" O PHE J 86 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE J 88 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE J 90 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL J 115 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR J 110 " --> pdb=" O PHE J 131 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N SER J 133 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL J 112 " --> pdb=" O SER J 133 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL J 132 " --> pdb=" O ILE J 166 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE J 165 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR J 188 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL J 167 " --> pdb=" O THR J 188 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2775 1.32 - 1.45: 4685 1.45 - 1.58: 9210 1.58 - 1.71: 30 1.71 - 1.84: 70 Bond restraints: 16770 Sorted by residual: bond pdb=" C2 QC9 E 301 " pdb=" O6 QC9 E 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C2 QC9 B 301 " pdb=" O6 QC9 B 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 I 301 " pdb=" O6 QC9 I 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 J 301 " pdb=" O6 QC9 J 301 " ideal model delta sigma weight residual 1.432 1.291 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C2 QC9 G 301 " pdb=" O6 QC9 G 301 " ideal model delta sigma weight residual 1.432 1.292 0.140 2.00e-02 2.50e+03 4.93e+01 ... (remaining 16765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.37: 22780 5.37 - 10.74: 85 10.74 - 16.11: 25 16.11 - 21.48: 10 21.48 - 26.85: 20 Bond angle restraints: 22920 Sorted by residual: angle pdb=" C3 QC9 J 301 " pdb=" C12 QC9 J 301 " pdb=" S13 QC9 J 301 " ideal model delta sigma weight residual 112.26 139.11 -26.85 3.00e+00 1.11e-01 8.01e+01 angle pdb=" C3 QC9 H 301 " pdb=" C12 QC9 H 301 " pdb=" S13 QC9 H 301 " ideal model delta sigma weight residual 112.26 139.10 -26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C3 QC9 E 301 " pdb=" C12 QC9 E 301 " pdb=" S13 QC9 E 301 " ideal model delta sigma weight residual 112.26 139.10 -26.84 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C3 QC9 D 301 " pdb=" C12 QC9 D 301 " pdb=" S13 QC9 D 301 " ideal model delta sigma weight residual 112.26 139.09 -26.83 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C3 QC9 G 301 " pdb=" C12 QC9 G 301 " pdb=" S13 QC9 G 301 " ideal model delta sigma weight residual 112.26 139.08 -26.82 3.00e+00 1.11e-01 7.99e+01 ... (remaining 22915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 8452 17.25 - 34.50: 856 34.50 - 51.76: 342 51.76 - 69.01: 90 69.01 - 86.26: 40 Dihedral angle restraints: 9780 sinusoidal: 3460 harmonic: 6320 Sorted by residual: dihedral pdb=" CD ARG B 126 " pdb=" NE ARG B 126 " pdb=" CZ ARG B 126 " pdb=" NH1 ARG B 126 " ideal model delta sinusoidal sigma weight residual 0.00 -40.64 40.64 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CD ARG H 126 " pdb=" NE ARG H 126 " pdb=" CZ ARG H 126 " pdb=" NH1 ARG H 126 " ideal model delta sinusoidal sigma weight residual 0.00 -40.59 40.59 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CD ARG J 126 " pdb=" NE ARG J 126 " pdb=" CZ ARG J 126 " pdb=" NH1 ARG J 126 " ideal model delta sinusoidal sigma weight residual 0.00 -40.58 40.58 1 1.00e+01 1.00e-02 2.31e+01 ... (remaining 9777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1546 0.092 - 0.184: 926 0.184 - 0.276: 128 0.276 - 0.369: 10 0.369 - 0.461: 20 Chirality restraints: 2630 Sorted by residual: chirality pdb=" C2 QC9 E 301 " pdb=" C1 QC9 E 301 " pdb=" C3 QC9 E 301 " pdb=" O6 QC9 E 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C2 QC9 D 301 " pdb=" C1 QC9 D 301 " pdb=" C3 QC9 D 301 " pdb=" O6 QC9 D 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C2 QC9 I 301 " pdb=" C1 QC9 I 301 " pdb=" C3 QC9 I 301 " pdb=" O6 QC9 I 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 2627 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 126 " 0.703 9.50e-02 1.11e+02 3.15e-01 6.04e+01 pdb=" NE ARG B 126 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 126 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 126 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 126 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 126 " 0.703 9.50e-02 1.11e+02 3.15e-01 6.04e+01 pdb=" NE ARG F 126 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 126 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 126 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 126 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 126 " -0.702 9.50e-02 1.11e+02 3.15e-01 6.03e+01 pdb=" NE ARG G 126 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG G 126 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 126 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 126 " -0.021 2.00e-02 2.50e+03 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4415 2.83 - 3.35: 18512 3.35 - 3.86: 32612 3.86 - 4.38: 39921 4.38 - 4.90: 60044 Nonbonded interactions: 155504 Sorted by model distance: nonbonded pdb=" O LEU J 170 " pdb=" O HOH J 401 " model vdw 2.310 3.040 nonbonded pdb=" O LEU D 170 " pdb=" O HOH D 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU C 170 " pdb=" O HOH C 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU E 170 " pdb=" O HOH E 401 " model vdw 2.311 3.040 nonbonded pdb=" O LEU G 170 " pdb=" O HOH G 401 " model vdw 2.311 3.040 ... (remaining 155499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.014 0.141 16780 Z= 1.039 Angle : 1.926 26.850 22920 Z= 1.324 Chirality : 0.104 0.461 2630 Planarity : 0.020 0.315 2950 Dihedral : 18.166 86.259 5700 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 11.95 % Allowed : 11.45 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.28 (0.13), residues: 2130 helix: -2.78 (0.10), residues: 1300 sheet: -2.96 (0.20), residues: 300 loop : -2.03 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 211 TYR 0.019 0.002 TYR F 15 PHE 0.010 0.002 PHE F 131 TRP 0.004 0.001 TRP D 214 HIS 0.004 0.001 HIS F 200 Details of bonding type rmsd covalent geometry : bond 0.01398 (16770) covalent geometry : angle 1.92608 (22920) hydrogen bonds : bond 0.24026 ( 850) hydrogen bonds : angle 8.99159 ( 2550) Misc. bond : bond 0.14054 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 463 time to evaluate : 0.614 Fit side-chains REVERT: A 150 GLN cc_start: 0.8239 (tp40) cc_final: 0.7992 (tp-100) REVERT: H 122 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8143 (tt) REVERT: B 62 ILE cc_start: 0.8411 (pt) cc_final: 0.8160 (pt) REVERT: C 122 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8128 (tt) REVERT: D 62 ILE cc_start: 0.8416 (pt) cc_final: 0.8173 (pt) REVERT: E 162 ASN cc_start: 0.7692 (m-40) cc_final: 0.7480 (m110) REVERT: F 62 ILE cc_start: 0.8495 (pt) cc_final: 0.8146 (pt) REVERT: F 122 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8347 (tt) REVERT: I 62 ILE cc_start: 0.8498 (pt) cc_final: 0.8151 (pt) REVERT: I 122 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8320 (tt) REVERT: J 150 GLN cc_start: 0.8165 (tp40) cc_final: 0.7910 (mm-40) outliers start: 190 outliers final: 9 residues processed: 530 average time/residue: 0.6539 time to fit residues: 382.4185 Evaluate side-chains 303 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 290 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain I residue 83 SER Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 83 SER Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.0870 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 111 ASN A 120 GLN A 141 ASN A 172 ASN A 175 GLN A 200 HIS H 63 ASN H 85 ASN H 111 ASN H 120 GLN H 141 ASN H 150 GLN H 172 ASN H 175 GLN H 199 GLN H 200 HIS B 111 ASN B 172 ASN B 175 GLN B 200 HIS C 63 ASN C 85 ASN C 111 ASN C 120 GLN C 141 ASN C 172 ASN C 175 GLN C 199 GLN C 200 HIS D 111 ASN D 172 ASN D 175 GLN D 200 HIS E 111 ASN E 120 GLN E 141 ASN E 150 GLN E 172 ASN E 175 GLN E 200 HIS F 111 ASN F 120 GLN F 172 ASN F 175 GLN F 200 HIS G 111 ASN G 120 GLN G 123 GLN G 141 ASN G 150 GLN G 172 ASN G 175 GLN G 200 HIS I 111 ASN I 120 GLN I 172 ASN I 175 GLN I 200 HIS ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN J 120 GLN J 141 ASN J 172 ASN J 175 GLN J 200 HIS Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.111694 restraints weight = 16666.911| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.84 r_work: 0.3206 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16780 Z= 0.135 Angle : 0.540 5.469 22920 Z= 0.293 Chirality : 0.044 0.119 2630 Planarity : 0.006 0.070 2950 Dihedral : 9.106 59.533 2473 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.45 % Allowed : 14.84 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2130 helix: 0.55 (0.13), residues: 1330 sheet: -1.38 (0.26), residues: 300 loop : -0.86 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 126 TYR 0.010 0.001 TYR B 205 PHE 0.009 0.001 PHE J 198 TRP 0.007 0.001 TRP A 214 HIS 0.006 0.002 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00287 (16770) covalent geometry : angle 0.53981 (22920) hydrogen bonds : bond 0.05374 ( 850) hydrogen bonds : angle 4.92011 ( 2550) Misc. bond : bond 0.00088 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 295 time to evaluate : 0.594 Fit side-chains REVERT: A 6 ASP cc_start: 0.8636 (t0) cc_final: 0.8330 (t0) REVERT: H 62 ILE cc_start: 0.8385 (pt) cc_final: 0.8180 (pp) REVERT: H 122 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8498 (tt) REVERT: H 171 ARG cc_start: 0.8697 (mmt-90) cc_final: 0.8389 (mpt90) REVERT: C 62 ILE cc_start: 0.8360 (pt) cc_final: 0.8157 (pp) REVERT: C 122 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8496 (tt) REVERT: C 171 ARG cc_start: 0.8700 (mmt-90) cc_final: 0.8388 (mpt90) REVERT: E 162 ASN cc_start: 0.8239 (m-40) cc_final: 0.8018 (m110) REVERT: F 12 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8620 (mt-10) REVERT: F 62 ILE cc_start: 0.8431 (pt) cc_final: 0.8036 (pt) REVERT: F 130 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8325 (tptp) REVERT: F 160 ASN cc_start: 0.8057 (m-40) cc_final: 0.7792 (t0) REVERT: I 12 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8601 (mt-10) REVERT: I 62 ILE cc_start: 0.8437 (pt) cc_final: 0.8041 (pt) REVERT: I 160 ASN cc_start: 0.8067 (m-40) cc_final: 0.7797 (t0) REVERT: J 94 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7674 (tp30) outliers start: 23 outliers final: 9 residues processed: 308 average time/residue: 0.7537 time to fit residues: 252.3419 Evaluate side-chains 285 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 130 LYS Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 26 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 165 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS A 85 ASN A 150 GLN H 150 GLN B 85 ASN B 150 GLN C 150 GLN D 85 ASN D 150 GLN E 85 ASN E 150 GLN F 85 ASN G 65 HIS G 85 ASN G 150 GLN I 85 ASN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 ASN J 150 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110180 restraints weight = 17144.962| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.85 r_work: 0.3183 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16780 Z= 0.124 Angle : 0.497 5.253 22920 Z= 0.269 Chirality : 0.045 0.123 2630 Planarity : 0.004 0.040 2950 Dihedral : 8.635 59.482 2470 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.32 % Allowed : 12.83 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2130 helix: 1.83 (0.13), residues: 1320 sheet: -0.62 (0.29), residues: 300 loop : -0.41 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.010 0.001 TYR G 205 PHE 0.008 0.001 PHE J 202 TRP 0.009 0.001 TRP J 214 HIS 0.005 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00260 (16770) covalent geometry : angle 0.49681 (22920) hydrogen bonds : bond 0.05281 ( 850) hydrogen bonds : angle 4.61390 ( 2550) Misc. bond : bond 0.00095 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 0.478 Fit side-chains REVERT: H 62 ILE cc_start: 0.8353 (pt) cc_final: 0.8118 (pp) REVERT: H 171 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8400 (mpt90) REVERT: B 122 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8579 (tt) REVERT: C 62 ILE cc_start: 0.8384 (pt) cc_final: 0.8148 (pp) REVERT: C 171 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8412 (mpt90) REVERT: D 122 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8583 (tt) REVERT: E 162 ASN cc_start: 0.8253 (m-40) cc_final: 0.8042 (m110) REVERT: F 12 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8640 (mt-10) REVERT: F 160 ASN cc_start: 0.8138 (m-40) cc_final: 0.7882 (t0) REVERT: I 12 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8680 (mt-10) REVERT: I 160 ASN cc_start: 0.8150 (m-40) cc_final: 0.7889 (t0) REVERT: J 6 ASP cc_start: 0.8678 (t0) cc_final: 0.8399 (t0) outliers start: 21 outliers final: 7 residues processed: 309 average time/residue: 0.7253 time to fit residues: 242.8552 Evaluate side-chains 278 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 269 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 63 ASN J 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108095 restraints weight = 16975.470| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.85 r_work: 0.3152 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16780 Z= 0.147 Angle : 0.528 5.190 22920 Z= 0.288 Chirality : 0.047 0.127 2630 Planarity : 0.004 0.040 2950 Dihedral : 8.269 59.463 2466 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.82 % Allowed : 12.08 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2130 helix: 2.03 (0.13), residues: 1320 sheet: -0.34 (0.29), residues: 300 loop : -0.33 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 171 TYR 0.010 0.001 TYR F 205 PHE 0.010 0.002 PHE H 202 TRP 0.009 0.001 TRP I 214 HIS 0.005 0.001 HIS J 65 Details of bonding type rmsd covalent geometry : bond 0.00315 (16770) covalent geometry : angle 0.52844 (22920) hydrogen bonds : bond 0.05834 ( 850) hydrogen bonds : angle 4.73197 ( 2550) Misc. bond : bond 0.00081 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 280 time to evaluate : 0.454 Fit side-chains REVERT: A 6 ASP cc_start: 0.8654 (t0) cc_final: 0.8383 (t0) REVERT: H 62 ILE cc_start: 0.8361 (pt) cc_final: 0.8116 (pp) REVERT: H 171 ARG cc_start: 0.8809 (mmt-90) cc_final: 0.8366 (mpt90) REVERT: H 174 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8303 (tmtp) REVERT: C 62 ILE cc_start: 0.8349 (pt) cc_final: 0.8096 (pp) REVERT: C 171 ARG cc_start: 0.8807 (mmt-90) cc_final: 0.8364 (mpt90) REVERT: C 174 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8304 (tmtp) REVERT: F 160 ASN cc_start: 0.8205 (m-40) cc_final: 0.7945 (t0) REVERT: I 160 ASN cc_start: 0.8197 (m-40) cc_final: 0.7924 (t0) outliers start: 13 outliers final: 6 residues processed: 286 average time/residue: 0.7696 time to fit residues: 237.8126 Evaluate side-chains 273 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 265 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 162 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 33 optimal weight: 0.5980 chunk 199 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 65 HIS J 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.120060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108248 restraints weight = 16907.971| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 0.84 r_work: 0.3155 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16780 Z= 0.144 Angle : 0.515 5.191 22920 Z= 0.282 Chirality : 0.046 0.126 2630 Planarity : 0.004 0.035 2950 Dihedral : 7.892 58.416 2458 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.26 % Allowed : 11.26 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.18), residues: 2130 helix: 2.13 (0.13), residues: 1320 sheet: -0.29 (0.28), residues: 300 loop : -0.29 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 211 TYR 0.010 0.001 TYR C 159 PHE 0.009 0.001 PHE B 202 TRP 0.009 0.001 TRP I 214 HIS 0.004 0.001 HIS J 65 Details of bonding type rmsd covalent geometry : bond 0.00309 (16770) covalent geometry : angle 0.51532 (22920) hydrogen bonds : bond 0.05689 ( 850) hydrogen bonds : angle 4.68762 ( 2550) Misc. bond : bond 0.00057 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 282 time to evaluate : 0.684 Fit side-chains REVERT: H 40 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7909 (mm) REVERT: H 62 ILE cc_start: 0.8348 (pt) cc_final: 0.8102 (pp) REVERT: H 94 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7306 (tp30) REVERT: H 171 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8334 (mpt90) REVERT: H 174 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8304 (tmtp) REVERT: C 62 ILE cc_start: 0.8358 (pt) cc_final: 0.8104 (pp) REVERT: C 174 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8310 (tmtp) REVERT: F 160 ASN cc_start: 0.8212 (m-40) cc_final: 0.7964 (t0) REVERT: I 160 ASN cc_start: 0.8209 (m-40) cc_final: 0.7972 (t0) REVERT: J 94 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7447 (tp30) outliers start: 20 outliers final: 8 residues processed: 287 average time/residue: 0.8659 time to fit residues: 268.7040 Evaluate side-chains 282 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 269 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain J residue 94 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 123 GLN G 150 GLN J 150 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109328 restraints weight = 16844.869| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 0.85 r_work: 0.3170 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16780 Z= 0.128 Angle : 0.492 5.188 22920 Z= 0.268 Chirality : 0.045 0.124 2630 Planarity : 0.004 0.032 2950 Dihedral : 7.647 57.509 2458 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.38 % Allowed : 11.07 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.18), residues: 2130 helix: 2.21 (0.13), residues: 1330 sheet: -0.21 (0.28), residues: 300 loop : -0.15 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 171 TYR 0.011 0.001 TYR I 205 PHE 0.006 0.001 PHE F 103 TRP 0.008 0.001 TRP I 214 HIS 0.002 0.001 HIS H 65 Details of bonding type rmsd covalent geometry : bond 0.00271 (16770) covalent geometry : angle 0.49189 (22920) hydrogen bonds : bond 0.05264 ( 850) hydrogen bonds : angle 4.57490 ( 2550) Misc. bond : bond 0.00051 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 0.833 Fit side-chains REVERT: H 62 ILE cc_start: 0.8366 (pt) cc_final: 0.8117 (pp) REVERT: H 171 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8330 (mpt90) REVERT: H 174 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8298 (tmtp) REVERT: B 108 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7993 (mp) REVERT: C 62 ILE cc_start: 0.8341 (pt) cc_final: 0.8092 (pp) REVERT: C 94 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: C 174 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8295 (tmtp) REVERT: D 108 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8000 (mp) REVERT: F 160 ASN cc_start: 0.8210 (m-40) cc_final: 0.7970 (t0) REVERT: I 157 LYS cc_start: 0.8577 (mttm) cc_final: 0.8329 (mttt) REVERT: I 160 ASN cc_start: 0.8201 (m-40) cc_final: 0.7970 (t0) outliers start: 22 outliers final: 6 residues processed: 293 average time/residue: 0.8857 time to fit residues: 280.5728 Evaluate side-chains 288 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 277 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 162 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 34 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN E 150 GLN G 150 GLN J 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107938 restraints weight = 16852.679| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.84 r_work: 0.3150 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16780 Z= 0.151 Angle : 0.527 5.184 22920 Z= 0.288 Chirality : 0.047 0.132 2630 Planarity : 0.004 0.034 2950 Dihedral : 7.903 57.702 2458 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.75 % Allowed : 11.82 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.18), residues: 2130 helix: 2.20 (0.13), residues: 1320 sheet: -0.19 (0.28), residues: 300 loop : -0.23 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.012 0.001 TYR I 205 PHE 0.009 0.001 PHE B 202 TRP 0.009 0.001 TRP I 214 HIS 0.003 0.001 HIS G 185 Details of bonding type rmsd covalent geometry : bond 0.00326 (16770) covalent geometry : angle 0.52695 (22920) hydrogen bonds : bond 0.05867 ( 850) hydrogen bonds : angle 4.74034 ( 2550) Misc. bond : bond 0.00055 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 0.492 Fit side-chains REVERT: H 62 ILE cc_start: 0.8332 (pt) cc_final: 0.8087 (pp) REVERT: H 171 ARG cc_start: 0.8803 (mmt-90) cc_final: 0.8319 (mpt90) REVERT: H 174 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8310 (tmtp) REVERT: B 196 GLU cc_start: 0.8082 (mp0) cc_final: 0.7830 (mm-30) REVERT: C 62 ILE cc_start: 0.8337 (pt) cc_final: 0.8085 (pp) REVERT: C 174 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8313 (tmtp) REVERT: D 14 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7628 (mtm180) REVERT: D 196 GLU cc_start: 0.8083 (mp0) cc_final: 0.7833 (mm-30) REVERT: F 160 ASN cc_start: 0.8217 (m-40) cc_final: 0.7988 (t0) REVERT: I 160 ASN cc_start: 0.8218 (m-40) cc_final: 0.7993 (t0) outliers start: 12 outliers final: 5 residues processed: 292 average time/residue: 0.8631 time to fit residues: 272.0981 Evaluate side-chains 286 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 278 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 57 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 98 optimal weight: 0.1980 chunk 94 optimal weight: 5.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110095 restraints weight = 17029.647| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 0.86 r_work: 0.3182 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16780 Z= 0.119 Angle : 0.477 5.229 22920 Z= 0.261 Chirality : 0.044 0.124 2630 Planarity : 0.004 0.035 2950 Dihedral : 7.510 56.834 2458 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.94 % Allowed : 11.64 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.18), residues: 2130 helix: 2.32 (0.13), residues: 1330 sheet: -0.10 (0.29), residues: 300 loop : -0.07 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 171 TYR 0.013 0.001 TYR I 205 PHE 0.007 0.001 PHE I 131 TRP 0.008 0.001 TRP I 214 HIS 0.002 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00251 (16770) covalent geometry : angle 0.47705 (22920) hydrogen bonds : bond 0.04991 ( 850) hydrogen bonds : angle 4.50479 ( 2550) Misc. bond : bond 0.00044 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 288 time to evaluate : 0.638 Fit side-chains REVERT: A 6 ASP cc_start: 0.8533 (t0) cc_final: 0.8313 (t0) REVERT: H 62 ILE cc_start: 0.8343 (pt) cc_final: 0.8096 (pp) REVERT: H 171 ARG cc_start: 0.8789 (mmt-90) cc_final: 0.8342 (mpt90) REVERT: B 108 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8008 (mp) REVERT: C 62 ILE cc_start: 0.8346 (pt) cc_final: 0.8098 (pp) REVERT: D 108 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8011 (mp) REVERT: F 160 ASN cc_start: 0.8193 (m-40) cc_final: 0.7960 (t0) REVERT: I 157 LYS cc_start: 0.8573 (mttm) cc_final: 0.8331 (mttt) REVERT: I 160 ASN cc_start: 0.8194 (m-40) cc_final: 0.7961 (t0) outliers start: 15 outliers final: 5 residues processed: 295 average time/residue: 0.8966 time to fit residues: 285.4714 Evaluate side-chains 283 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 276 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 134 optimal weight: 0.2980 chunk 170 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108471 restraints weight = 16945.919| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.85 r_work: 0.3159 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16780 Z= 0.143 Angle : 0.516 5.171 22920 Z= 0.283 Chirality : 0.046 0.136 2630 Planarity : 0.004 0.035 2950 Dihedral : 7.788 57.199 2458 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 0.50 % Allowed : 12.14 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.18), residues: 2130 helix: 2.31 (0.13), residues: 1320 sheet: -0.12 (0.28), residues: 300 loop : -0.21 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 211 TYR 0.013 0.001 TYR F 205 PHE 0.007 0.001 PHE H 202 TRP 0.008 0.001 TRP I 214 HIS 0.003 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00307 (16770) covalent geometry : angle 0.51642 (22920) hydrogen bonds : bond 0.05636 ( 850) hydrogen bonds : angle 4.68079 ( 2550) Misc. bond : bond 0.00048 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 278 time to evaluate : 0.710 Fit side-chains REVERT: A 6 ASP cc_start: 0.8578 (t0) cc_final: 0.8349 (t0) REVERT: H 62 ILE cc_start: 0.8332 (pt) cc_final: 0.8083 (pp) REVERT: H 171 ARG cc_start: 0.8798 (mmt-90) cc_final: 0.8316 (mpt90) REVERT: B 108 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8003 (mp) REVERT: B 196 GLU cc_start: 0.8059 (mp0) cc_final: 0.7835 (mm-30) REVERT: C 62 ILE cc_start: 0.8343 (pt) cc_final: 0.8091 (pp) REVERT: D 108 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8006 (mp) REVERT: D 196 GLU cc_start: 0.8080 (mp0) cc_final: 0.7854 (mm-30) REVERT: F 160 ASN cc_start: 0.8216 (m-40) cc_final: 0.7984 (t0) REVERT: I 157 LYS cc_start: 0.8561 (mttm) cc_final: 0.8321 (mttt) REVERT: I 160 ASN cc_start: 0.8206 (m-40) cc_final: 0.7982 (t0) outliers start: 8 outliers final: 5 residues processed: 285 average time/residue: 0.9262 time to fit residues: 285.0184 Evaluate side-chains 283 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 276 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 50 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 207 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 152 optimal weight: 0.0770 chunk 123 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109384 restraints weight = 16821.703| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.85 r_work: 0.3172 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16780 Z= 0.132 Angle : 0.500 5.188 22920 Z= 0.273 Chirality : 0.045 0.134 2630 Planarity : 0.004 0.035 2950 Dihedral : 7.732 56.603 2458 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.82 % Allowed : 11.76 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.18), residues: 2130 helix: 2.28 (0.13), residues: 1330 sheet: -0.11 (0.28), residues: 300 loop : -0.12 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 211 TYR 0.013 0.001 TYR F 205 PHE 0.007 0.001 PHE E 131 TRP 0.008 0.001 TRP I 214 HIS 0.003 0.001 HIS C 65 Details of bonding type rmsd covalent geometry : bond 0.00283 (16770) covalent geometry : angle 0.49978 (22920) hydrogen bonds : bond 0.05300 ( 850) hydrogen bonds : angle 4.60918 ( 2550) Misc. bond : bond 0.00043 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 278 time to evaluate : 0.620 Fit side-chains REVERT: A 6 ASP cc_start: 0.8563 (t0) cc_final: 0.8345 (t0) REVERT: H 62 ILE cc_start: 0.8332 (pt) cc_final: 0.8083 (pp) REVERT: H 171 ARG cc_start: 0.8794 (mmt-90) cc_final: 0.8302 (mpt90) REVERT: B 108 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8020 (mp) REVERT: C 62 ILE cc_start: 0.8335 (pt) cc_final: 0.8083 (pp) REVERT: C 174 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8397 (tmtp) REVERT: D 108 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8013 (mp) REVERT: D 196 GLU cc_start: 0.8038 (mp0) cc_final: 0.7835 (mm-30) REVERT: F 160 ASN cc_start: 0.8224 (m-40) cc_final: 0.7977 (t0) REVERT: I 157 LYS cc_start: 0.8565 (mttm) cc_final: 0.8324 (mttt) REVERT: I 160 ASN cc_start: 0.8196 (m-40) cc_final: 0.7971 (t0) outliers start: 13 outliers final: 5 residues processed: 285 average time/residue: 0.8624 time to fit residues: 265.7090 Evaluate side-chains 284 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 277 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 120 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN H 150 GLN B 150 GLN C 150 GLN D 150 GLN ** E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106460 restraints weight = 16806.784| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.84 r_work: 0.3128 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16780 Z= 0.210 Angle : 0.605 5.228 22920 Z= 0.332 Chirality : 0.051 0.186 2630 Planarity : 0.005 0.040 2950 Dihedral : 8.558 58.183 2458 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.31 % Allowed : 11.95 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.17), residues: 2130 helix: 2.07 (0.13), residues: 1320 sheet: -0.17 (0.28), residues: 300 loop : -0.44 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 211 TYR 0.014 0.002 TYR H 159 PHE 0.013 0.002 PHE B 202 TRP 0.008 0.002 TRP F 214 HIS 0.006 0.002 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00468 (16770) covalent geometry : angle 0.60452 (22920) hydrogen bonds : bond 0.06847 ( 850) hydrogen bonds : angle 4.96482 ( 2550) Misc. bond : bond 0.00052 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.83 seconds wall clock time: 112 minutes 46.75 seconds (6766.75 seconds total)