Starting phenix.real_space_refine on Sun Jun 15 02:16:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bc3_15961/06_2025/8bc3_15961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bc3_15961/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bc3_15961/06_2025/8bc3_15961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bc3_15961/06_2025/8bc3_15961.map" model { file = "/net/cci-nas-00/data/ceres_data/8bc3_15961/06_2025/8bc3_15961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bc3_15961/06_2025/8bc3_15961.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: 10.63, per 1000 atoms: 0.63 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: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.97 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: 5.60 Time building geometry restraints manager: 4.67 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.260 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: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 38.620 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.450 ------------------------------------------------------------------------------- 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 : 1.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP D 214 HIS 0.004 0.001 HIS F 200 PHE 0.010 0.002 PHE F 131 TYR 0.019 0.002 TYR F 15 ARG 0.003 0.001 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.24026 ( 850) hydrogen bonds : angle 8.99159 ( 2550) covalent geometry : bond 0.01398 (16770) covalent geometry : angle 1.92608 (22920) 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 : 1.791 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: 1.3780 time to fit residues: 805.8236 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 : 1.884 ------------------------------------------------------------------------------- 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 177 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 190 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 120 GLN A 141 ASN A 172 ASN A 175 GLN A 200 HIS H 63 ASN H 120 GLN H 141 ASN H 150 GLN H 172 ASN H 175 GLN H 199 GLN H 200 HIS B 172 ASN B 175 GLN B 200 HIS C 63 ASN C 120 GLN C 141 ASN C 172 ASN C 175 GLN C 199 GLN C 200 HIS 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 31 HIS G 111 ASN G 120 GLN G 141 ASN G 150 GLN G 172 ASN G 175 GLN G 200 HIS I 120 GLN I 172 ASN I 175 GLN I 200 HIS J 63 ASN J 120 GLN J 141 ASN J 172 ASN J 175 GLN J 200 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110601 restraints weight = 16730.553| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.84 r_work: 0.3189 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2521 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= 0.141 Angle : 0.552 5.413 22920 Z= 0.300 Chirality : 0.045 0.123 2630 Planarity : 0.006 0.072 2950 Dihedral : 9.213 59.957 2473 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.51 % Allowed : 14.84 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2130 helix: 0.58 (0.13), residues: 1320 sheet: -1.28 (0.26), residues: 300 loop : -0.90 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 214 HIS 0.008 0.002 HIS G 200 PHE 0.010 0.002 PHE C 198 TYR 0.010 0.001 TYR B 205 ARG 0.003 0.001 ARG I 211 Details of bonding type rmsd hydrogen bonds : bond 0.05697 ( 850) hydrogen bonds : angle 4.96699 ( 2550) covalent geometry : bond 0.00299 (16770) covalent geometry : angle 0.55218 (22920) Misc. bond : bond 0.00086 ( 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: 24 poor density : 294 time to evaluate : 2.008 Fit side-chains REVERT: A 6 ASP cc_start: 0.8644 (t0) cc_final: 0.8341 (t0) REVERT: H 62 ILE cc_start: 0.8385 (pt) cc_final: 0.8177 (pp) REVERT: H 122 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8541 (tt) REVERT: H 171 ARG cc_start: 0.8722 (mmt-90) cc_final: 0.8349 (mpt90) REVERT: C 62 ILE cc_start: 0.8364 (pt) cc_final: 0.8159 (pp) REVERT: C 122 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8533 (tt) REVERT: C 171 ARG cc_start: 0.8728 (mmt-90) cc_final: 0.8358 (mpt90) REVERT: E 162 ASN cc_start: 0.8240 (m-40) cc_final: 0.8023 (m110) REVERT: F 62 ILE cc_start: 0.8422 (pt) cc_final: 0.8031 (pt) REVERT: F 130 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8377 (tttp) REVERT: F 160 ASN cc_start: 0.8072 (m-40) cc_final: 0.7801 (t0) REVERT: I 12 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8593 (mt-10) REVERT: I 62 ILE cc_start: 0.8426 (pt) cc_final: 0.8035 (pt) REVERT: I 160 ASN cc_start: 0.8085 (m-40) cc_final: 0.7806 (t0) REVERT: J 6 ASP cc_start: 0.8632 (t0) cc_final: 0.8349 (t0) REVERT: J 94 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7630 (tp30) outliers start: 24 outliers final: 7 residues processed: 307 average time/residue: 1.6667 time to fit residues: 557.3108 Evaluate side-chains 282 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 271 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 130 LYS Chi-restraints excluded: chain G residue 48 SER Chi-restraints excluded: chain G 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 36 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 186 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 85 ASN H 150 GLN B 85 ASN B 150 GLN C 85 ASN 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 85 ASN J 150 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108894 restraints weight = 16814.532| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.84 r_work: 0.3163 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.25 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2903 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= 0.138 Angle : 0.518 5.231 22920 Z= 0.283 Chirality : 0.046 0.124 2630 Planarity : 0.005 0.044 2950 Dihedral : 8.627 59.553 2466 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.26 % Allowed : 12.64 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 2130 helix: 1.73 (0.13), residues: 1320 sheet: -0.57 (0.29), residues: 300 loop : -0.50 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 214 HIS 0.006 0.001 HIS G 65 PHE 0.009 0.001 PHE C 202 TYR 0.010 0.001 TYR G 205 ARG 0.002 0.000 ARG I 211 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 850) hydrogen bonds : angle 4.72874 ( 2550) covalent geometry : bond 0.00291 (16770) covalent geometry : angle 0.51849 (22920) Misc. bond : bond 0.00093 ( 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 306 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 286 time to evaluate : 1.760 Fit side-chains REVERT: H 62 ILE cc_start: 0.8395 (pt) cc_final: 0.8153 (pp) REVERT: H 171 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8410 (mpt90) REVERT: B 122 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8583 (tt) REVERT: C 62 ILE cc_start: 0.8353 (pt) cc_final: 0.8108 (pp) REVERT: C 171 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8411 (mpt90) REVERT: D 122 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8589 (tt) REVERT: E 162 ASN cc_start: 0.8269 (m-40) cc_final: 0.8061 (m110) REVERT: F 160 ASN cc_start: 0.8173 (m-40) cc_final: 0.7898 (t0) REVERT: I 160 ASN cc_start: 0.8140 (m-40) cc_final: 0.7856 (t0) REVERT: I 171 ARG cc_start: 0.8723 (mmt-90) cc_final: 0.8515 (mmt-90) REVERT: J 6 ASP cc_start: 0.8643 (t0) cc_final: 0.8351 (t0) outliers start: 20 outliers final: 7 residues processed: 296 average time/residue: 1.6963 time to fit residues: 545.2056 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 : 1.857 ------------------------------------------------------------------------------- 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 203 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 206 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.121952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110150 restraints weight = 16784.276| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 0.85 r_work: 0.3182 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: 0.8609 moved from start: 0.3045 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= 0.120 Angle : 0.487 5.200 22920 Z= 0.263 Chirality : 0.045 0.122 2630 Planarity : 0.004 0.034 2950 Dihedral : 7.985 58.888 2466 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.82 % Allowed : 12.64 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.18), residues: 2130 helix: 2.08 (0.14), residues: 1330 sheet: -0.30 (0.29), residues: 300 loop : -0.21 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 214 HIS 0.003 0.001 HIS J 65 PHE 0.007 0.001 PHE A 202 TYR 0.010 0.001 TYR I 205 ARG 0.003 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.05051 ( 850) hydrogen bonds : angle 4.53761 ( 2550) covalent geometry : bond 0.00252 (16770) covalent geometry : angle 0.48698 (22920) Misc. bond : bond 0.00069 ( 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 305 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 292 time to evaluate : 1.897 Fit side-chains REVERT: A 6 ASP cc_start: 0.8625 (t0) cc_final: 0.8325 (t0) REVERT: H 62 ILE cc_start: 0.8347 (pt) cc_final: 0.8111 (pp) REVERT: H 171 ARG cc_start: 0.8782 (mmt-90) cc_final: 0.8327 (mpt90) REVERT: H 174 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8188 (tmmt) REVERT: B 122 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8580 (tt) REVERT: C 62 ILE cc_start: 0.8307 (pt) cc_final: 0.8069 (pp) REVERT: C 171 ARG cc_start: 0.8779 (mmt-90) cc_final: 0.8330 (mpt90) REVERT: C 174 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8183 (tmmt) REVERT: D 122 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8581 (tt) REVERT: E 30 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8212 (ttp-170) REVERT: E 162 ASN cc_start: 0.8248 (m-40) cc_final: 0.8048 (m110) REVERT: F 160 ASN cc_start: 0.8153 (m-40) cc_final: 0.7897 (t0) REVERT: I 160 ASN cc_start: 0.8154 (m-40) cc_final: 0.7910 (t0) REVERT: J 6 ASP cc_start: 0.8594 (t0) cc_final: 0.8333 (t0) outliers start: 13 outliers final: 6 residues processed: 300 average time/residue: 1.7274 time to fit residues: 561.8019 Evaluate side-chains 284 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 274 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 174 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 80 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 56 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108435 restraints weight = 17005.106| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.85 r_work: 0.3158 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3089 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= 0.140 Angle : 0.511 5.194 22920 Z= 0.280 Chirality : 0.046 0.125 2630 Planarity : 0.004 0.034 2950 Dihedral : 8.028 58.270 2464 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.19 % Allowed : 11.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2130 helix: 2.20 (0.13), residues: 1320 sheet: -0.24 (0.29), residues: 300 loop : -0.25 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS E 185 PHE 0.009 0.001 PHE C 202 TYR 0.011 0.001 TYR F 205 ARG 0.002 0.000 ARG D 171 Details of bonding type rmsd hydrogen bonds : bond 0.05641 ( 850) hydrogen bonds : angle 4.67436 ( 2550) covalent geometry : bond 0.00300 (16770) covalent geometry : angle 0.51122 (22920) Misc. bond : bond 0.00069 ( 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 303 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 284 time to evaluate : 1.997 Fit side-chains REVERT: A 6 ASP cc_start: 0.8651 (t0) cc_final: 0.8408 (t0) REVERT: H 62 ILE cc_start: 0.8379 (pt) cc_final: 0.8120 (pp) REVERT: H 171 ARG cc_start: 0.8798 (mmt-90) cc_final: 0.8348 (mpt90) REVERT: H 174 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8303 (tmtp) REVERT: B 94 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: C 62 ILE cc_start: 0.8314 (pt) cc_final: 0.8060 (pp) REVERT: C 94 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: C 171 ARG cc_start: 0.8799 (mmt-90) cc_final: 0.8343 (mpt90) REVERT: C 174 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8304 (tmtp) REVERT: D 94 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: F 160 ASN cc_start: 0.8204 (m-40) cc_final: 0.7959 (t0) REVERT: I 160 ASN cc_start: 0.8208 (m-40) cc_final: 0.7964 (t0) REVERT: J 6 ASP cc_start: 0.8615 (t0) cc_final: 0.8350 (t0) outliers start: 19 outliers final: 5 residues processed: 290 average time/residue: 1.7500 time to fit residues: 550.7382 Evaluate side-chains 283 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 273 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain B residue 94 GLU 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 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 170 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 I 111 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 = 0.3383 r_free = 0.3383 target = 0.119202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107312 restraints weight = 17022.364| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 0.85 r_work: 0.3141 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16780 Z= 0.163 Angle : 0.541 5.217 22920 Z= 0.297 Chirality : 0.047 0.131 2630 Planarity : 0.004 0.039 2950 Dihedral : 8.126 58.047 2458 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.19 % Allowed : 11.51 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2130 helix: 2.15 (0.13), residues: 1320 sheet: -0.26 (0.28), residues: 300 loop : -0.34 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 214 HIS 0.004 0.001 HIS G 185 PHE 0.010 0.002 PHE B 202 TYR 0.011 0.002 TYR C 159 ARG 0.002 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.06138 ( 850) hydrogen bonds : angle 4.79634 ( 2550) covalent geometry : bond 0.00355 (16770) covalent geometry : angle 0.54078 (22920) Misc. bond : bond 0.00053 ( 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 303 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 284 time to evaluate : 1.921 Fit side-chains REVERT: H 62 ILE cc_start: 0.8366 (pt) cc_final: 0.8128 (pp) REVERT: H 171 ARG cc_start: 0.8809 (mmt-90) cc_final: 0.8352 (mpt90) REVERT: H 174 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8276 (tmtp) REVERT: B 94 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: C 62 ILE cc_start: 0.8306 (pt) cc_final: 0.8059 (pp) REVERT: C 94 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: C 171 ARG cc_start: 0.8809 (mmt-90) cc_final: 0.8354 (mpt90) REVERT: C 174 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8286 (tmtp) REVERT: D 94 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: F 130 LYS cc_start: 0.8592 (tttm) cc_final: 0.8318 (tttp) REVERT: F 160 ASN cc_start: 0.8245 (m-40) cc_final: 0.7990 (t0) REVERT: I 160 ASN cc_start: 0.8225 (m-40) cc_final: 0.7986 (t0) outliers start: 19 outliers final: 6 residues processed: 289 average time/residue: 1.7561 time to fit residues: 549.1399 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 : 1.703 ------------------------------------------------------------------------------- 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 94 GLU 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 94 GLU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 130 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 5 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 135 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 1.0580 ------------------------------------------------------------------------------- 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 = 0.3395 r_free = 0.3395 target = 0.120169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108258 restraints weight = 16903.271| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 0.85 r_work: 0.3155 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3163 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= 0.147 Angle : 0.521 5.208 22920 Z= 0.285 Chirality : 0.047 0.128 2630 Planarity : 0.004 0.034 2950 Dihedral : 7.981 57.665 2458 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.13 % Allowed : 11.64 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2130 helix: 2.23 (0.13), residues: 1320 sheet: -0.20 (0.28), residues: 300 loop : -0.27 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 214 HIS 0.003 0.001 HIS E 185 PHE 0.008 0.001 PHE B 202 TYR 0.010 0.001 TYR H 159 ARG 0.002 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 850) hydrogen bonds : angle 4.69745 ( 2550) covalent geometry : bond 0.00317 (16770) covalent geometry : angle 0.52129 (22920) Misc. bond : bond 0.00041 ( 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 303 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 2.033 Fit side-chains REVERT: H 62 ILE cc_start: 0.8353 (pt) cc_final: 0.8107 (pp) REVERT: H 171 ARG cc_start: 0.8796 (mmt-90) cc_final: 0.8321 (mpt90) REVERT: H 174 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8272 (tmtp) REVERT: B 94 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: B 108 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8010 (mp) REVERT: C 62 ILE cc_start: 0.8305 (pt) cc_final: 0.8058 (pp) REVERT: C 94 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: C 171 ARG cc_start: 0.8792 (mmt-90) cc_final: 0.8319 (mpt90) REVERT: C 174 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8276 (tmtp) REVERT: D 94 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: D 108 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8017 (mp) REVERT: F 160 ASN cc_start: 0.8219 (m-40) cc_final: 0.7988 (t0) REVERT: I 157 LYS cc_start: 0.8571 (mttm) cc_final: 0.8328 (mttt) REVERT: I 160 ASN cc_start: 0.8222 (m-40) cc_final: 0.7986 (t0) REVERT: J 6 ASP cc_start: 0.8596 (t0) cc_final: 0.8384 (t0) outliers start: 18 outliers final: 6 residues processed: 292 average time/residue: 1.8178 time to fit residues: 575.4350 Evaluate side-chains 288 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 275 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 94 GLU 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 94 GLU 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 130 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.120735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.108894 restraints weight = 16880.104| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.85 r_work: 0.3164 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3174 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= 0.135 Angle : 0.503 5.195 22920 Z= 0.276 Chirality : 0.046 0.126 2630 Planarity : 0.004 0.034 2950 Dihedral : 7.824 57.396 2458 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.13 % Allowed : 11.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.18), residues: 2130 helix: 2.30 (0.13), residues: 1320 sheet: -0.15 (0.28), residues: 300 loop : -0.22 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 214 HIS 0.003 0.001 HIS B 65 PHE 0.007 0.001 PHE B 202 TYR 0.011 0.001 TYR I 205 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.05456 ( 850) hydrogen bonds : angle 4.63882 ( 2550) covalent geometry : bond 0.00289 (16770) covalent geometry : angle 0.50338 (22920) Misc. bond : bond 0.00040 ( 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 301 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 2.070 Fit side-chains REVERT: H 62 ILE cc_start: 0.8349 (pt) cc_final: 0.8101 (pp) REVERT: H 171 ARG cc_start: 0.8788 (mmt-90) cc_final: 0.8310 (mpt90) REVERT: H 174 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8311 (tmtp) REVERT: B 108 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8006 (mp) REVERT: C 62 ILE cc_start: 0.8308 (pt) cc_final: 0.8061 (pp) REVERT: C 171 ARG cc_start: 0.8786 (mmt-90) cc_final: 0.8313 (mpt90) REVERT: C 174 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8308 (tmtp) REVERT: D 108 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8012 (mp) REVERT: F 160 ASN cc_start: 0.8213 (m-40) cc_final: 0.7991 (t0) REVERT: I 157 LYS cc_start: 0.8569 (mttm) cc_final: 0.8326 (mttt) REVERT: I 160 ASN cc_start: 0.8209 (m-40) cc_final: 0.7984 (t0) outliers start: 18 outliers final: 5 residues processed: 290 average time/residue: 2.0589 time to fit residues: 647.9443 Evaluate side-chains 283 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 274 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 42 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.120583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.108692 restraints weight = 17010.846| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 0.85 r_work: 0.3161 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3177 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= 0.137 Angle : 0.508 5.198 22920 Z= 0.278 Chirality : 0.046 0.125 2630 Planarity : 0.004 0.035 2950 Dihedral : 7.843 57.384 2458 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.18), residues: 2130 helix: 2.30 (0.13), residues: 1320 sheet: -0.14 (0.28), residues: 300 loop : -0.24 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 214 HIS 0.003 0.001 HIS B 65 PHE 0.007 0.001 PHE B 202 TYR 0.012 0.001 TYR I 205 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.05512 ( 850) hydrogen bonds : angle 4.65235 ( 2550) covalent geometry : bond 0.00295 (16770) covalent geometry : angle 0.50821 (22920) Misc. bond : bond 0.00043 ( 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 288 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 276 time to evaluate : 1.754 Fit side-chains REVERT: H 62 ILE cc_start: 0.8361 (pt) cc_final: 0.8108 (pp) REVERT: H 171 ARG cc_start: 0.8800 (mmt-90) cc_final: 0.8315 (mpt90) REVERT: H 174 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8282 (tmtm) REVERT: B 108 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7987 (mp) REVERT: C 62 ILE cc_start: 0.8306 (pt) cc_final: 0.8057 (pp) REVERT: C 171 ARG cc_start: 0.8795 (mmt-90) cc_final: 0.8311 (mpt90) REVERT: C 174 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8301 (tmtp) REVERT: D 108 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7990 (mp) REVERT: F 160 ASN cc_start: 0.8212 (m-40) cc_final: 0.7986 (t0) REVERT: I 157 LYS cc_start: 0.8558 (mttm) cc_final: 0.8314 (mttt) REVERT: I 160 ASN cc_start: 0.8207 (m-40) cc_final: 0.7991 (t0) REVERT: J 6 ASP cc_start: 0.8586 (t0) cc_final: 0.8365 (t0) outliers start: 12 outliers final: 5 residues processed: 283 average time/residue: 1.8079 time to fit residues: 553.0283 Evaluate side-chains 285 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 276 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 56 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 207 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 186 optimal weight: 0.0270 chunk 25 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.122439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110620 restraints weight = 16911.606| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 0.85 r_work: 0.3189 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16780 Z= 0.116 Angle : 0.479 5.208 22920 Z= 0.261 Chirality : 0.044 0.146 2630 Planarity : 0.004 0.035 2950 Dihedral : 7.460 56.685 2458 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.88 % Allowed : 11.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.18), residues: 2130 helix: 2.33 (0.13), residues: 1330 sheet: -0.04 (0.29), residues: 300 loop : -0.08 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 214 HIS 0.002 0.001 HIS G 185 PHE 0.007 0.001 PHE I 131 TYR 0.013 0.001 TYR I 205 ARG 0.001 0.000 ARG B 171 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 850) hydrogen bonds : angle 4.47530 ( 2550) covalent geometry : bond 0.00245 (16770) covalent geometry : angle 0.47932 (22920) Misc. bond : bond 0.00040 ( 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 301 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 287 time to evaluate : 2.209 Fit side-chains REVERT: H 62 ILE cc_start: 0.8363 (pt) cc_final: 0.8120 (pp) REVERT: H 171 ARG cc_start: 0.8780 (mmt-90) cc_final: 0.8245 (mpt90) REVERT: B 108 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 62 ILE cc_start: 0.8302 (pt) cc_final: 0.8059 (pp) REVERT: C 171 ARG cc_start: 0.8778 (mmt-90) cc_final: 0.8246 (mpt90) REVERT: D 108 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8028 (mp) REVERT: F 160 ASN cc_start: 0.8202 (m-40) cc_final: 0.7971 (t0) REVERT: I 157 LYS cc_start: 0.8563 (mttm) cc_final: 0.8319 (mttt) REVERT: I 160 ASN cc_start: 0.8182 (m-40) cc_final: 0.7960 (t0) REVERT: J 6 ASP cc_start: 0.8536 (t0) cc_final: 0.8328 (t0) outliers start: 14 outliers final: 5 residues processed: 295 average time/residue: 2.0393 time to fit residues: 653.0969 Evaluate side-chains 285 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 278 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 147 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.121070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109255 restraints weight = 16861.329| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.85 r_work: 0.3171 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3216 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= 0.133 Angle : 0.506 5.199 22920 Z= 0.276 Chirality : 0.045 0.131 2630 Planarity : 0.004 0.036 2950 Dihedral : 7.652 56.706 2458 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.57 % Allowed : 12.39 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.18), residues: 2130 helix: 2.31 (0.13), residues: 1330 sheet: -0.08 (0.28), residues: 300 loop : -0.13 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 214 HIS 0.002 0.001 HIS C 65 PHE 0.006 0.001 PHE I 50 TYR 0.014 0.001 TYR I 205 ARG 0.002 0.000 ARG I 14 Details of bonding type rmsd hydrogen bonds : bond 0.05345 ( 850) hydrogen bonds : angle 4.60834 ( 2550) covalent geometry : bond 0.00284 (16770) covalent geometry : angle 0.50562 (22920) Misc. bond : bond 0.00047 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14282.00 seconds wall clock time: 246 minutes 42.58 seconds (14802.58 seconds total)