Starting phenix.real_space_refine on Wed Nov 15 22:12:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/11_2023/7ojg_12950_updated.pdb" } resolution = 3.4 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= 0.002 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: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 33 5.16 5 C 8492 2.51 5 N 2013 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 22": "OD1" <-> "OD2" Residue "A ASP 27": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ASP 27": "OD1" <-> "OD2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D ASP 27": "OD1" <-> "OD2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E ASP 27": "OD1" <-> "OD2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F ASP 27": "OD1" <-> "OD2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "G ASP 22": "OD1" <-> "OD2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "H ASP 22": "OD1" <-> "OD2" Residue "H ASP 27": "OD1" <-> "OD2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "I ASP 22": "OD1" <-> "OD2" Residue "I ASP 27": "OD1" <-> "OD2" Residue "I GLU 115": "OE1" <-> "OE2" Residue "J ASP 22": "OD1" <-> "OD2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13255 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "F" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "J" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 967 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 238 Unusual residues: {'GOL': 1, 'L8Z': 1, 'LPP': 1, 'PLM': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PLM:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 7.36, per 1000 atoms: 0.56 Number of scatterers: 13255 At special positions: 0 Unit cell: (118.384, 119.952, 95.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 33 15.00 O 2684 8.00 N 2013 7.00 C 8492 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 - 3.50 Amino acid : False - 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.2 seconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 22 sheets defined 25.4% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 62 through 72 Processing helix chain 'B' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 83 through 103 removed outlier: 3.777A pdb=" N ALA C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 62 through 72 Processing helix chain 'D' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 62 through 72 Processing helix chain 'E' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 62 through 72 Processing helix chain 'F' and resid 83 through 103 removed outlier: 3.777A pdb=" N ALA F 87 " --> pdb=" O GLY F 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 62 through 72 Processing helix chain 'G' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA G 87 " --> pdb=" O GLY G 83 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN G 100 " --> pdb=" O GLY G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 62 through 72 Processing helix chain 'H' and resid 83 through 103 removed outlier: 3.777A pdb=" N ALA H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN H 100 " --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 33 No H-bonds generated for 'chain 'I' and resid 31 through 33' Processing helix chain 'I' and resid 62 through 72 Processing helix chain 'I' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA I 87 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN I 100 " --> pdb=" O GLY I 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 33 No H-bonds generated for 'chain 'J' and resid 31 through 33' Processing helix chain 'J' and resid 62 through 72 Processing helix chain 'J' and resid 83 through 103 removed outlier: 3.778A pdb=" N ALA J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN J 100 " --> pdb=" O GLY J 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 33 No H-bonds generated for 'chain 'K' and resid 31 through 33' Processing helix chain 'K' and resid 62 through 72 Processing helix chain 'K' and resid 83 through 103 removed outlier: 3.777A pdb=" N ALA K 87 " --> pdb=" O GLY K 83 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN K 100 " --> pdb=" O GLY K 96 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL A 141 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 142 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 153 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 49 through 54 Processing sheet with id= C, first strand: chain 'B' and resid 123 through 129 removed outlier: 3.648A pdb=" N VAL B 141 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 142 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 153 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 149 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 49 through 54 Processing sheet with id= E, first strand: chain 'C' and resid 123 through 129 removed outlier: 3.648A pdb=" N VAL C 141 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 142 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 153 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 149 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 49 through 54 Processing sheet with id= G, first strand: chain 'D' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL D 141 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 142 " --> pdb=" O SER D 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 153 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D 149 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 49 through 54 Processing sheet with id= I, first strand: chain 'E' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL E 141 " --> pdb=" O GLY E 43 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 142 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER E 153 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN E 149 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 49 through 54 Processing sheet with id= K, first strand: chain 'F' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL F 141 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 142 " --> pdb=" O SER F 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER F 153 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN F 149 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 49 through 54 Processing sheet with id= M, first strand: chain 'G' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL G 141 " --> pdb=" O GLY G 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL G 142 " --> pdb=" O SER G 153 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER G 153 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN G 149 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 49 through 54 Processing sheet with id= O, first strand: chain 'H' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL H 141 " --> pdb=" O GLY H 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 142 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER H 153 " --> pdb=" O VAL H 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H 149 " --> pdb=" O ASN H 146 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 49 through 54 Processing sheet with id= Q, first strand: chain 'I' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL I 141 " --> pdb=" O GLY I 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 142 " --> pdb=" O SER I 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER I 153 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN I 149 " --> pdb=" O ASN I 146 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 49 through 54 Processing sheet with id= S, first strand: chain 'J' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL J 141 " --> pdb=" O GLY J 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL J 142 " --> pdb=" O SER J 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER J 153 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN J 149 " --> pdb=" O ASN J 146 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 49 through 54 Processing sheet with id= U, first strand: chain 'K' and resid 123 through 129 removed outlier: 3.647A pdb=" N VAL K 141 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 142 " --> pdb=" O SER K 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER K 153 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN K 149 " --> pdb=" O ASN K 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 49 through 54 484 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2035 1.32 - 1.45: 3231 1.45 - 1.59: 7901 1.59 - 1.73: 55 1.73 - 1.87: 66 Bond restraints: 13288 Sorted by residual: bond pdb=" C11 L8Z D 205 " pdb=" C12 L8Z D 205 " ideal model delta sigma weight residual 1.338 1.562 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C11 L8Z H 205 " pdb=" C12 L8Z H 205 " ideal model delta sigma weight residual 1.338 1.562 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C11 L8Z B 205 " pdb=" C12 L8Z B 205 " ideal model delta sigma weight residual 1.338 1.562 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C11 L8Z C 205 " pdb=" C12 L8Z C 205 " ideal model delta sigma weight residual 1.338 1.562 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C11 L8Z E 205 " pdb=" C12 L8Z E 205 " ideal model delta sigma weight residual 1.338 1.562 -0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 99.62 - 105.51: 169 105.51 - 111.39: 5464 111.39 - 117.27: 4929 117.27 - 123.16: 6208 123.16 - 129.04: 720 Bond angle restraints: 17490 Sorted by residual: angle pdb=" C11 L8Z A 203 " pdb=" C12 L8Z A 203 " pdb=" C13 L8Z A 203 " ideal model delta sigma weight residual 152.65 116.44 36.21 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C11 L8Z C 205 " pdb=" C12 L8Z C 205 " pdb=" C13 L8Z C 205 " ideal model delta sigma weight residual 152.65 116.44 36.21 3.00e+00 1.11e-01 1.46e+02 angle pdb=" C11 L8Z H 205 " pdb=" C12 L8Z H 205 " pdb=" C13 L8Z H 205 " ideal model delta sigma weight residual 152.65 116.47 36.18 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C11 L8Z J 205 " pdb=" C12 L8Z J 205 " pdb=" C13 L8Z J 205 " ideal model delta sigma weight residual 152.65 116.47 36.18 3.00e+00 1.11e-01 1.45e+02 angle pdb=" C11 L8Z I 205 " pdb=" C12 L8Z I 205 " pdb=" C13 L8Z I 205 " ideal model delta sigma weight residual 152.65 116.50 36.15 3.00e+00 1.11e-01 1.45e+02 ... (remaining 17485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.58: 7238 30.58 - 61.16: 660 61.16 - 91.74: 187 91.74 - 122.32: 22 122.32 - 152.90: 33 Dihedral angle restraints: 8140 sinusoidal: 4103 harmonic: 4037 Sorted by residual: dihedral pdb=" C16 L8Z D 205 " pdb=" C17 L8Z D 205 " pdb=" C18 L8Z D 205 " pdb=" C19 L8Z D 205 " ideal model delta sinusoidal sigma weight residual 168.68 -38.42 -152.90 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C16 L8Z J 205 " pdb=" C17 L8Z J 205 " pdb=" C18 L8Z J 205 " pdb=" C19 L8Z J 205 " ideal model delta sinusoidal sigma weight residual 168.68 -38.43 -152.89 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C16 L8Z G 205 " pdb=" C17 L8Z G 205 " pdb=" C18 L8Z G 205 " pdb=" C19 L8Z G 205 " ideal model delta sinusoidal sigma weight residual 168.68 -38.43 -152.89 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 8137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1588 0.077 - 0.153: 316 0.153 - 0.230: 10 0.230 - 0.307: 11 0.307 - 0.384: 11 Chirality restraints: 1936 Sorted by residual: chirality pdb=" C4A L8Z K 205 " pdb=" C3B L8Z K 205 " pdb=" C56 L8Z K 205 " pdb=" O4 L8Z K 205 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C4A L8Z D 205 " pdb=" C3B L8Z D 205 " pdb=" C56 L8Z D 205 " pdb=" O4 L8Z D 205 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C4A L8Z H 205 " pdb=" C3B L8Z H 205 " pdb=" C56 L8Z H 205 " pdb=" O4 L8Z H 205 " both_signs ideal model delta sigma weight residual False -2.49 -2.88 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1933 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 L8Z K 205 " -0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C11 L8Z K 205 " 0.111 2.00e-02 2.50e+03 pdb=" C12 L8Z K 205 " 0.112 2.00e-02 2.50e+03 pdb=" C13 L8Z K 205 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 L8Z D 205 " -0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C11 L8Z D 205 " 0.111 2.00e-02 2.50e+03 pdb=" C12 L8Z D 205 " 0.112 2.00e-02 2.50e+03 pdb=" C13 L8Z D 205 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 L8Z E 205 " -0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C11 L8Z E 205 " 0.111 2.00e-02 2.50e+03 pdb=" C12 L8Z E 205 " 0.112 2.00e-02 2.50e+03 pdb=" C13 L8Z E 205 " -0.112 2.00e-02 2.50e+03 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 33 2.05 - 2.76: 2073 2.76 - 3.48: 14416 3.48 - 4.19: 23838 4.19 - 4.90: 43536 Nonbonded interactions: 83896 Sorted by model distance: nonbonded pdb=" O2 GOL E 203 " pdb=" C1 PLM E 204 " model vdw 1.340 3.270 nonbonded pdb=" O2 GOL D 203 " pdb=" C1 PLM D 204 " model vdw 1.341 3.270 nonbonded pdb=" O2 GOL I 203 " pdb=" C1 PLM I 204 " model vdw 1.341 3.270 nonbonded pdb=" O2 GOL G 203 " pdb=" C1 PLM G 204 " model vdw 1.341 3.270 nonbonded pdb=" O2 GOL K 203 " pdb=" C1 PLM K 204 " model vdw 1.341 3.270 ... (remaining 83891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 155 or resid 201)) selection = (chain 'B' and (resid 18 through 155 or resid 201)) selection = (chain 'C' and (resid 18 through 155 or resid 201)) selection = (chain 'D' and (resid 18 through 155 or resid 201)) selection = (chain 'E' and (resid 18 through 155 or resid 201)) selection = (chain 'F' and (resid 18 through 155 or resid 201)) selection = (chain 'G' and (resid 18 through 155 or resid 201)) selection = (chain 'H' and (resid 18 through 155 or resid 201)) selection = (chain 'I' and (resid 18 through 155 or resid 201)) selection = (chain 'J' and (resid 18 through 155 or resid 201)) selection = (chain 'K' and (resid 18 through 155 or resid 201)) } 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: 1.180 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: 5.610 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 36.250 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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 : 0.025 0.224 13288 Z= 1.323 Angle : 2.596 36.215 17490 Z= 0.916 Chirality : 0.066 0.384 1936 Planarity : 0.013 0.111 2123 Dihedral : 26.096 152.899 5632 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -2.38 (0.19), residues: 1496 helix: -0.88 (0.25), residues: 396 sheet: -0.83 (0.22), residues: 462 loop : -2.57 (0.19), residues: 638 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.307 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2505 time to fit residues: 43.8326 Evaluate side-chains 101 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.0270 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 0.0020 chunk 83 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 overall best weight: 1.0050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 13288 Z= 0.147 Angle : 0.688 8.465 17490 Z= 0.315 Chirality : 0.049 0.229 1936 Planarity : 0.003 0.029 2123 Dihedral : 26.362 159.561 3410 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.18 % Allowed : 7.31 % Favored : 92.51 % 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: -1.51 (0.21), residues: 1496 helix: -0.64 (0.25), residues: 429 sheet: 0.23 (0.23), residues: 506 loop : -2.44 (0.21), residues: 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.213 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 130 average time/residue: 0.1665 time to fit residues: 36.5297 Evaluate side-chains 102 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1163 time to fit residues: 2.1470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 13288 Z= 0.297 Angle : 0.768 8.014 17490 Z= 0.353 Chirality : 0.052 0.237 1936 Planarity : 0.004 0.033 2123 Dihedral : 25.792 160.490 3410 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.08 % Allowed : 12.30 % Favored : 82.62 % 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: -1.57 (0.20), residues: 1496 helix: -0.66 (0.24), residues: 440 sheet: -0.10 (0.21), residues: 572 loop : -2.45 (0.22), residues: 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 115 time to evaluate : 1.229 Fit side-chains outliers start: 57 outliers final: 53 residues processed: 151 average time/residue: 0.2209 time to fit residues: 51.0521 Evaluate side-chains 157 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 104 time to evaluate : 1.338 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.1259 time to fit residues: 14.2944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13288 Z= 0.173 Angle : 0.644 9.989 17490 Z= 0.299 Chirality : 0.048 0.204 1936 Planarity : 0.003 0.030 2123 Dihedral : 24.254 168.310 3410 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.16 % Allowed : 13.99 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.21), residues: 1496 helix: -0.26 (0.25), residues: 429 sheet: 0.53 (0.23), residues: 517 loop : -2.36 (0.21), residues: 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.226 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 124 average time/residue: 0.1682 time to fit residues: 35.1404 Evaluate side-chains 108 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 1.273 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1293 time to fit residues: 2.4399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13288 Z= 0.267 Angle : 0.721 10.805 17490 Z= 0.333 Chirality : 0.051 0.211 1936 Planarity : 0.004 0.035 2123 Dihedral : 24.170 178.629 3410 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.55 % Allowed : 13.55 % Favored : 81.91 % 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: -1.33 (0.20), residues: 1496 helix: -0.48 (0.25), residues: 440 sheet: 0.01 (0.21), residues: 572 loop : -2.24 (0.22), residues: 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 110 time to evaluate : 1.286 Fit side-chains outliers start: 51 outliers final: 38 residues processed: 142 average time/residue: 0.2229 time to fit residues: 48.2435 Evaluate side-chains 140 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 102 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.1144 time to fit residues: 9.7909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13288 Z= 0.231 Angle : 0.673 8.729 17490 Z= 0.318 Chirality : 0.049 0.193 1936 Planarity : 0.003 0.033 2123 Dihedral : 23.178 177.643 3410 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.30 % Allowed : 15.51 % Favored : 81.19 % 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: -1.18 (0.20), residues: 1496 helix: -0.43 (0.25), residues: 440 sheet: 0.46 (0.22), residues: 517 loop : -2.31 (0.21), residues: 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.238 Fit side-chains outliers start: 37 outliers final: 15 residues processed: 144 average time/residue: 0.2164 time to fit residues: 48.0838 Evaluate side-chains 118 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1138 time to fit residues: 4.9681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 137 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13288 Z= 0.132 Angle : 0.570 11.998 17490 Z= 0.273 Chirality : 0.045 0.170 1936 Planarity : 0.003 0.025 2123 Dihedral : 20.856 169.830 3410 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.23 % Allowed : 16.58 % Favored : 81.19 % 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: -0.51 (0.21), residues: 1496 helix: 0.03 (0.26), residues: 429 sheet: 1.01 (0.23), residues: 517 loop : -1.98 (0.22), residues: 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.278 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 129 average time/residue: 0.1844 time to fit residues: 39.5376 Evaluate side-chains 112 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1205 time to fit residues: 3.6209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 27 optimal weight: 0.0170 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13288 Z= 0.137 Angle : 0.551 10.318 17490 Z= 0.266 Chirality : 0.044 0.144 1936 Planarity : 0.003 0.022 2123 Dihedral : 18.969 142.741 3410 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.16 % Allowed : 18.45 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1496 helix: 0.25 (0.27), residues: 418 sheet: 1.08 (0.23), residues: 517 loop : -1.84 (0.23), residues: 561 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.339 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 103 average time/residue: 0.2070 time to fit residues: 34.2418 Evaluate side-chains 109 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1130 time to fit residues: 4.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13288 Z= 0.172 Angle : 0.581 9.589 17490 Z= 0.282 Chirality : 0.045 0.140 1936 Planarity : 0.003 0.025 2123 Dihedral : 18.554 119.428 3410 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.89 % Allowed : 19.07 % Favored : 80.04 % 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: -0.46 (0.22), residues: 1496 helix: 0.04 (0.26), residues: 429 sheet: 0.92 (0.23), residues: 517 loop : -1.79 (0.24), residues: 550 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.275 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 109 average time/residue: 0.2149 time to fit residues: 36.3406 Evaluate side-chains 108 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1108 time to fit residues: 3.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13288 Z= 0.223 Angle : 0.623 9.392 17490 Z= 0.303 Chirality : 0.046 0.145 1936 Planarity : 0.003 0.030 2123 Dihedral : 18.194 94.170 3410 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.80 % Allowed : 19.34 % Favored : 79.86 % 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: -0.70 (0.21), residues: 1496 helix: -0.21 (0.25), residues: 440 sheet: 0.67 (0.22), residues: 517 loop : -1.78 (0.24), residues: 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.194 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 106 average time/residue: 0.2070 time to fit residues: 34.3702 Evaluate side-chains 105 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1090 time to fit residues: 2.7505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.140408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117045 restraints weight = 15521.153| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.57 r_work: 0.3088 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13288 Z= 0.159 Angle : 0.560 9.274 17490 Z= 0.276 Chirality : 0.044 0.144 1936 Planarity : 0.003 0.026 2123 Dihedral : 16.886 83.684 3410 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.16 % Allowed : 19.07 % Favored : 79.77 % 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: -0.46 (0.21), residues: 1496 helix: 0.04 (0.26), residues: 429 sheet: 0.96 (0.23), residues: 517 loop : -1.83 (0.24), residues: 550 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2147.64 seconds wall clock time: 40 minutes 5.80 seconds (2405.80 seconds total)