Starting phenix.real_space_refine on Sat Mar 16 01:14:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_12950_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_12950.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_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_12950/03_2024/7ojg_12950_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_12950_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_12950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_12950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_12950_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojg_12950/03_2024/7ojg_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-dev-5265/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: 6.75, per 1000 atoms: 0.51 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: 4.84 Conformation dependent library (CDL) restraints added in 2.0 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: 2.02 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: 3.12 Time building geometry restraints manager: 5.18 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.660 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 34.180 Find NCS groups from input model: 0.850 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: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 73 TYR 0.006 0.001 TYR F 29 ARG 0.003 0.001 ARG D 49 *********************** 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 : 1.246 Fit side-chains REVERT: B 22 ASP cc_start: 0.8686 (t0) cc_final: 0.8405 (t0) REVERT: E 27 ASP cc_start: 0.8088 (t70) cc_final: 0.7862 (t0) REVERT: F 27 ASP cc_start: 0.8167 (t70) cc_final: 0.7824 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2425 time to fit residues: 42.3142 Evaluate side-chains 101 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 13288 Z= 0.151 Angle : 0.689 8.614 17490 Z= 0.315 Chirality : 0.050 0.252 1936 Planarity : 0.003 0.029 2123 Dihedral : 26.219 160.029 3410 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.18 % Allowed : 7.93 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.50 (0.21), residues: 1496 helix: -0.64 (0.25), residues: 429 sheet: 0.26 (0.23), residues: 506 loop : -2.44 (0.21), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE K 73 TYR 0.004 0.001 TYR E 29 ARG 0.002 0.000 ARG E 155 *********************** 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 133 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.342 Fit side-chains REVERT: B 22 ASP cc_start: 0.8583 (t0) cc_final: 0.8291 (t0) REVERT: G 22 ASP cc_start: 0.8587 (t0) cc_final: 0.8367 (t0) outliers start: 2 outliers final: 2 residues processed: 132 average time/residue: 0.1707 time to fit residues: 37.9074 Evaluate side-chains 102 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 114 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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: 0.7929 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 13288 Z= 0.255 Angle : 0.742 7.884 17490 Z= 0.340 Chirality : 0.051 0.237 1936 Planarity : 0.004 0.030 2123 Dihedral : 25.544 159.403 3410 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.08 % Allowed : 12.92 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1496 helix: -0.58 (0.25), residues: 440 sheet: -0.06 (0.21), residues: 572 loop : -2.36 (0.23), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE G 73 TYR 0.008 0.001 TYR K 29 ARG 0.002 0.000 ARG G 84 *********************** 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 175 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 118 time to evaluate : 1.339 Fit side-chains REVERT: A 27 ASP cc_start: 0.7959 (t70) cc_final: 0.7726 (t70) REVERT: B 22 ASP cc_start: 0.8679 (t0) cc_final: 0.8345 (t0) REVERT: F 27 ASP cc_start: 0.8014 (t70) cc_final: 0.7796 (t70) REVERT: H 27 ASP cc_start: 0.8025 (t70) cc_final: 0.7765 (t70) REVERT: I 27 ASP cc_start: 0.7897 (t70) cc_final: 0.7678 (t70) REVERT: J 27 ASP cc_start: 0.8032 (t70) cc_final: 0.7806 (t70) REVERT: K 22 ASP cc_start: 0.8637 (t70) cc_final: 0.8319 (t0) outliers start: 57 outliers final: 51 residues processed: 152 average time/residue: 0.2145 time to fit residues: 49.7539 Evaluate side-chains 156 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 105 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 106 MET Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 132 ASN Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 125 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 13288 Z= 0.231 Angle : 0.689 9.920 17490 Z= 0.319 Chirality : 0.050 0.214 1936 Planarity : 0.003 0.030 2123 Dihedral : 24.393 173.074 3410 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 6.06 % Allowed : 13.55 % 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: -1.31 (0.20), residues: 1496 helix: -0.49 (0.24), residues: 440 sheet: 0.39 (0.22), residues: 517 loop : -2.44 (0.21), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE K 73 TYR 0.008 0.001 TYR K 29 ARG 0.002 0.000 ARG F 155 *********************** 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 184 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 116 time to evaluate : 1.265 Fit side-chains REVERT: A 27 ASP cc_start: 0.7912 (t70) cc_final: 0.7559 (t70) REVERT: B 22 ASP cc_start: 0.8625 (t0) cc_final: 0.8290 (t0) REVERT: C 27 ASP cc_start: 0.7957 (t70) cc_final: 0.7656 (t70) REVERT: D 27 ASP cc_start: 0.8069 (t70) cc_final: 0.7814 (t70) REVERT: E 22 ASP cc_start: 0.8640 (t0) cc_final: 0.8382 (t0) REVERT: E 27 ASP cc_start: 0.7966 (t70) cc_final: 0.7733 (t70) REVERT: F 27 ASP cc_start: 0.8019 (t70) cc_final: 0.7713 (t70) REVERT: H 27 ASP cc_start: 0.8033 (t70) cc_final: 0.7706 (t70) REVERT: I 27 ASP cc_start: 0.7939 (t70) cc_final: 0.7601 (t70) REVERT: J 22 ASP cc_start: 0.8583 (t0) cc_final: 0.8332 (t0) REVERT: J 27 ASP cc_start: 0.8026 (t70) cc_final: 0.7687 (t70) REVERT: K 22 ASP cc_start: 0.8622 (t70) cc_final: 0.8317 (t0) REVERT: K 27 ASP cc_start: 0.8039 (t70) cc_final: 0.7828 (t70) outliers start: 68 outliers final: 49 residues processed: 157 average time/residue: 0.2089 time to fit residues: 50.9739 Evaluate side-chains 153 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 132 ASN Chi-restraints excluded: chain K residue 153 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.7965 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13288 Z= 0.320 Angle : 0.764 7.912 17490 Z= 0.355 Chirality : 0.052 0.213 1936 Planarity : 0.004 0.036 2123 Dihedral : 24.379 177.496 3410 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 8.11 % Allowed : 13.28 % Favored : 78.61 % 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: -1.55 (0.20), residues: 1496 helix: -0.60 (0.25), residues: 440 sheet: -0.13 (0.21), residues: 572 loop : -2.43 (0.21), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE G 73 TYR 0.008 0.001 TYR K 29 ARG 0.002 0.000 ARG K 84 *********************** 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 197 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 106 time to evaluate : 1.210 Fit side-chains REVERT: A 27 ASP cc_start: 0.7979 (t70) cc_final: 0.7619 (t70) REVERT: B 22 ASP cc_start: 0.8658 (t0) cc_final: 0.8268 (t0) REVERT: C 27 ASP cc_start: 0.8069 (t70) cc_final: 0.7756 (t70) REVERT: D 27 ASP cc_start: 0.8127 (t70) cc_final: 0.7811 (t70) REVERT: E 22 ASP cc_start: 0.8673 (t0) cc_final: 0.8400 (t0) REVERT: E 27 ASP cc_start: 0.8082 (t70) cc_final: 0.7822 (t70) REVERT: F 27 ASP cc_start: 0.8118 (t70) cc_final: 0.7783 (t70) REVERT: G 27 ASP cc_start: 0.8072 (t70) cc_final: 0.7835 (t70) REVERT: H 27 ASP cc_start: 0.8103 (t70) cc_final: 0.7745 (t70) REVERT: I 27 ASP cc_start: 0.7970 (t70) cc_final: 0.7603 (t70) REVERT: J 22 ASP cc_start: 0.8646 (t0) cc_final: 0.8355 (t0) REVERT: J 27 ASP cc_start: 0.8117 (t70) cc_final: 0.7755 (t70) REVERT: K 22 ASP cc_start: 0.8611 (t70) cc_final: 0.8035 (t0) REVERT: K 27 ASP cc_start: 0.8102 (t70) cc_final: 0.7853 (t70) outliers start: 91 outliers final: 74 residues processed: 174 average time/residue: 0.1915 time to fit residues: 52.5669 Evaluate side-chains 169 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 95 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 106 MET Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 132 ASN Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 132 ASN Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 SER 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: 3.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 0.0070 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- 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: 0.7869 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13288 Z= 0.173 Angle : 0.624 11.850 17490 Z= 0.293 Chirality : 0.047 0.190 1936 Planarity : 0.003 0.029 2123 Dihedral : 22.846 179.166 3410 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 8.29 % Allowed : 14.17 % Favored : 77.54 % 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: -1.05 (0.20), residues: 1496 helix: -0.25 (0.25), residues: 429 sheet: 0.56 (0.22), residues: 517 loop : -2.29 (0.20), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE H 73 TYR 0.007 0.001 TYR K 29 ARG 0.001 0.000 ARG G 84 *********************** 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 207 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 114 time to evaluate : 1.371 Fit side-chains REVERT: A 27 ASP cc_start: 0.7930 (t70) cc_final: 0.7515 (t70) REVERT: B 22 ASP cc_start: 0.8544 (t0) cc_final: 0.8197 (t0) REVERT: C 27 ASP cc_start: 0.7998 (t70) cc_final: 0.7669 (t70) REVERT: D 27 ASP cc_start: 0.8091 (t70) cc_final: 0.7727 (t70) REVERT: E 27 ASP cc_start: 0.8009 (t70) cc_final: 0.7687 (t70) REVERT: F 27 ASP cc_start: 0.8058 (t70) cc_final: 0.7691 (t70) REVERT: H 27 ASP cc_start: 0.8030 (t70) cc_final: 0.7654 (t70) REVERT: I 27 ASP cc_start: 0.7928 (t70) cc_final: 0.7542 (t70) REVERT: J 22 ASP cc_start: 0.8531 (t0) cc_final: 0.8261 (t0) REVERT: J 27 ASP cc_start: 0.8063 (t70) cc_final: 0.7678 (t70) REVERT: K 22 ASP cc_start: 0.8531 (t70) cc_final: 0.7990 (t0) REVERT: K 27 ASP cc_start: 0.8042 (t70) cc_final: 0.7791 (t70) outliers start: 93 outliers final: 68 residues processed: 182 average time/residue: 0.1857 time to fit residues: 53.9966 Evaluate side-chains 176 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 108 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.0030 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 77 optimal weight: 0.0040 chunk 137 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9206 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13288 Z= 0.127 Angle : 0.549 9.750 17490 Z= 0.262 Chirality : 0.045 0.165 1936 Planarity : 0.003 0.024 2123 Dihedral : 20.361 163.574 3410 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.99 % Allowed : 17.38 % Favored : 77.63 % 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: -0.55 (0.21), residues: 1496 helix: 0.03 (0.26), residues: 429 sheet: 0.95 (0.23), residues: 517 loop : -2.00 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE G 73 TYR 0.006 0.001 TYR K 29 ARG 0.003 0.000 ARG A 155 *********************** 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 167 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 111 time to evaluate : 1.184 Fit side-chains REVERT: A 27 ASP cc_start: 0.7924 (t70) cc_final: 0.7514 (t70) REVERT: B 22 ASP cc_start: 0.8555 (t0) cc_final: 0.8236 (t0) REVERT: C 27 ASP cc_start: 0.7934 (t70) cc_final: 0.7591 (t70) REVERT: D 27 ASP cc_start: 0.8018 (t70) cc_final: 0.7665 (t70) REVERT: E 27 ASP cc_start: 0.7948 (t70) cc_final: 0.7644 (t70) REVERT: F 27 ASP cc_start: 0.8014 (t70) cc_final: 0.7565 (t70) REVERT: H 27 ASP cc_start: 0.8003 (t70) cc_final: 0.7630 (t70) REVERT: I 27 ASP cc_start: 0.7852 (t70) cc_final: 0.7419 (t70) REVERT: J 27 ASP cc_start: 0.7991 (t70) cc_final: 0.7585 (t70) REVERT: K 22 ASP cc_start: 0.8494 (t70) cc_final: 0.8232 (t0) REVERT: K 27 ASP cc_start: 0.7978 (t70) cc_final: 0.7701 (t70) outliers start: 56 outliers final: 42 residues processed: 147 average time/residue: 0.1892 time to fit residues: 44.2234 Evaluate side-chains 150 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 108 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 132 ASN Chi-restraints excluded: chain K residue 142 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.7879 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13288 Z= 0.193 Angle : 0.598 9.412 17490 Z= 0.287 Chirality : 0.046 0.149 1936 Planarity : 0.003 0.027 2123 Dihedral : 20.085 151.435 3410 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.15 % Allowed : 16.13 % Favored : 77.72 % 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: -0.74 (0.21), residues: 1496 helix: -0.20 (0.25), residues: 440 sheet: 0.72 (0.22), residues: 517 loop : -1.91 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE G 73 TYR 0.007 0.001 TYR K 29 ARG 0.001 0.000 ARG E 84 *********************** 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 185 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 116 time to evaluate : 1.271 Fit side-chains REVERT: A 27 ASP cc_start: 0.7956 (t70) cc_final: 0.7556 (t70) REVERT: B 22 ASP cc_start: 0.8644 (t0) cc_final: 0.8303 (t0) REVERT: C 27 ASP cc_start: 0.8045 (t70) cc_final: 0.7711 (t70) REVERT: D 27 ASP cc_start: 0.8096 (t70) cc_final: 0.7731 (t70) REVERT: E 27 ASP cc_start: 0.7996 (t70) cc_final: 0.7653 (t70) REVERT: F 27 ASP cc_start: 0.8036 (t70) cc_final: 0.7680 (t70) REVERT: H 27 ASP cc_start: 0.8069 (t70) cc_final: 0.7681 (t70) REVERT: I 27 ASP cc_start: 0.7902 (t70) cc_final: 0.7479 (t70) REVERT: J 27 ASP cc_start: 0.8083 (t70) cc_final: 0.7702 (t70) REVERT: K 22 ASP cc_start: 0.8559 (t70) cc_final: 0.7985 (t0) REVERT: K 27 ASP cc_start: 0.8042 (t70) cc_final: 0.7766 (t70) outliers start: 69 outliers final: 65 residues processed: 163 average time/residue: 0.1969 time to fit residues: 50.3091 Evaluate side-chains 176 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 111 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.0980 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13288 Z= 0.137 Angle : 0.542 8.888 17490 Z= 0.262 Chirality : 0.044 0.141 1936 Planarity : 0.003 0.024 2123 Dihedral : 18.723 130.468 3410 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.77 % Allowed : 15.42 % Favored : 77.81 % 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: -0.44 (0.21), residues: 1496 helix: 0.03 (0.26), residues: 429 sheet: 1.02 (0.23), residues: 517 loop : -1.86 (0.23), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE H 73 TYR 0.005 0.001 TYR K 29 ARG 0.001 0.000 ARG F 84 *********************** 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 188 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 112 time to evaluate : 1.319 Fit side-chains REVERT: A 27 ASP cc_start: 0.7916 (t70) cc_final: 0.7508 (t70) REVERT: B 22 ASP cc_start: 0.8551 (t0) cc_final: 0.8217 (t0) REVERT: C 27 ASP cc_start: 0.7968 (t70) cc_final: 0.7633 (t70) REVERT: D 27 ASP cc_start: 0.8082 (t70) cc_final: 0.7726 (t70) REVERT: E 27 ASP cc_start: 0.7983 (t70) cc_final: 0.7658 (t70) REVERT: F 27 ASP cc_start: 0.8020 (t70) cc_final: 0.7660 (t70) REVERT: H 27 ASP cc_start: 0.7984 (t70) cc_final: 0.7598 (t70) REVERT: I 27 ASP cc_start: 0.7865 (t70) cc_final: 0.7431 (t70) REVERT: J 22 ASP cc_start: 0.8473 (t0) cc_final: 0.8230 (t0) REVERT: J 27 ASP cc_start: 0.8030 (t70) cc_final: 0.7651 (t70) REVERT: K 22 ASP cc_start: 0.8504 (t70) cc_final: 0.8253 (t0) REVERT: K 27 ASP cc_start: 0.8031 (t70) cc_final: 0.7727 (t70) outliers start: 76 outliers final: 68 residues processed: 162 average time/residue: 0.1819 time to fit residues: 47.6714 Evaluate side-chains 178 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 110 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 132 ASN Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.7903 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13288 Z= 0.226 Angle : 0.626 8.561 17490 Z= 0.303 Chirality : 0.047 0.144 1936 Planarity : 0.003 0.029 2123 Dihedral : 18.949 117.330 3410 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 7.04 % Allowed : 15.42 % Favored : 77.54 % 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: -0.79 (0.21), residues: 1496 helix: -0.27 (0.25), residues: 440 sheet: 0.33 (0.21), residues: 572 loop : -1.68 (0.24), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE G 73 TYR 0.008 0.001 TYR K 29 ARG 0.001 0.000 ARG G 84 ********************** 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 190 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 111 time to evaluate : 1.284 Fit side-chains REVERT: A 27 ASP cc_start: 0.7967 (t70) cc_final: 0.7589 (t70) REVERT: B 22 ASP cc_start: 0.8647 (t0) cc_final: 0.8279 (t0) REVERT: C 27 ASP cc_start: 0.8079 (t70) cc_final: 0.7738 (t70) REVERT: D 27 ASP cc_start: 0.8137 (t70) cc_final: 0.7794 (t70) REVERT: E 27 ASP cc_start: 0.8043 (t70) cc_final: 0.7699 (t70) REVERT: F 27 ASP cc_start: 0.8099 (t70) cc_final: 0.7749 (t70) REVERT: H 27 ASP cc_start: 0.8053 (t70) cc_final: 0.7678 (t70) REVERT: I 27 ASP cc_start: 0.7919 (t70) cc_final: 0.7508 (t70) REVERT: J 22 ASP cc_start: 0.8588 (t0) cc_final: 0.8322 (t0) REVERT: J 27 ASP cc_start: 0.8103 (t70) cc_final: 0.7731 (t70) REVERT: K 22 ASP cc_start: 0.8585 (t70) cc_final: 0.8025 (t0) REVERT: K 27 ASP cc_start: 0.8078 (t70) cc_final: 0.7770 (t70) outliers start: 79 outliers final: 75 residues processed: 164 average time/residue: 0.2002 time to fit residues: 51.8768 Evaluate side-chains 184 residues out of total 1122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 109 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 45 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 125 MET Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 153 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 125 MET Chi-restraints excluded: chain K residue 132 ASN Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.140568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118112 restraints weight = 15531.362| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.43 r_work: 0.3058 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13288 Z= 0.211 Angle : 0.599 8.663 17490 Z= 0.293 Chirality : 0.046 0.145 1936 Planarity : 0.003 0.029 2123 Dihedral : 17.874 93.260 3410 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.22 % Allowed : 15.51 % Favored : 77.27 % 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: -0.79 (0.21), residues: 1496 helix: -0.28 (0.25), residues: 440 sheet: 0.72 (0.22), residues: 517 loop : -1.95 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE G 73 TYR 0.007 0.001 TYR K 29 ARG 0.002 0.000 ARG E 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.12 seconds wall clock time: 42 minutes 23.61 seconds (2543.61 seconds total)