Starting phenix.real_space_refine on Sat Mar 16 01:26:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vam_21143/03_2024/6vam_21143.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vam_21143/03_2024/6vam_21143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vam_21143/03_2024/6vam_21143.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vam_21143/03_2024/6vam_21143.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vam_21143/03_2024/6vam_21143.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vam_21143/03_2024/6vam_21143.pdb" } resolution = 3.63 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= 0.045 sd= 0.520 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 8704 2.51 5 N 2248 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13360 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 7.31, per 1000 atoms: 0.55 Number of scatterers: 13360 At special positions: 0 Unit cell: (119.78, 119.78, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 2256 8.00 N 2248 7.00 C 8704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 4.61 Conformation dependent library (CDL) restraints added in 2.3 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.772A pdb=" N PHE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET A 76 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.772A pdb=" N PHE B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.696A pdb=" N ALA B 111 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.772A pdb=" N PHE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET C 76 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA C 111 " --> pdb=" O MET C 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.771A pdb=" N PHE D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN D 104 " --> pdb=" O CYS D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA D 111 " --> pdb=" O MET D 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.772A pdb=" N PHE E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA E 111 " --> pdb=" O MET E 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.772A pdb=" N PHE F 68 " --> pdb=" O PHE F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN F 104 " --> pdb=" O CYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 121 removed outlier: 3.696A pdb=" N ALA F 111 " --> pdb=" O MET F 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 171 through 201 removed outlier: 3.535A pdb=" N LEU F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP F 223 " --> pdb=" O SER F 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.772A pdb=" N PHE G 68 " --> pdb=" O PHE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 107 removed outlier: 3.842A pdb=" N GLN G 104 " --> pdb=" O CYS G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 112 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 171 through 201 removed outlier: 3.536A pdb=" N LEU G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP G 223 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.920A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.772A pdb=" N PHE H 68 " --> pdb=" O PHE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 83 removed outlier: 4.556A pdb=" N MET H 76 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 107 removed outlier: 3.841A pdb=" N GLN H 104 " --> pdb=" O CYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 121 removed outlier: 3.695A pdb=" N ALA H 111 " --> pdb=" O MET H 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 147 through 157 Processing helix chain 'H' and resid 171 through 201 removed outlier: 3.536A pdb=" N LEU H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 246 removed outlier: 3.715A pdb=" N ASP H 223 " --> pdb=" O SER H 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) 929 hydrogen bonds defined for protein. 2787 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: 3.72 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4184 1.34 - 1.46: 2675 1.46 - 1.57: 6597 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 13656 Sorted by residual: bond pdb=" N PRO C 146 " pdb=" CD PRO C 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO E 146 " pdb=" CD PRO E 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" N PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" N PRO F 146 " pdb=" CD PRO F 146 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 ... (remaining 13651 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.49: 432 106.49 - 113.39: 7422 113.39 - 120.30: 5639 120.30 - 127.21: 4891 127.21 - 134.11: 152 Bond angle restraints: 18536 Sorted by residual: angle pdb=" C LEU B 203 " pdb=" N ARG B 204 " pdb=" CA ARG B 204 " ideal model delta sigma weight residual 120.06 132.91 -12.85 1.19e+00 7.06e-01 1.17e+02 angle pdb=" C LEU F 203 " pdb=" N ARG F 204 " pdb=" CA ARG F 204 " ideal model delta sigma weight residual 120.06 132.90 -12.84 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU A 203 " pdb=" N ARG A 204 " pdb=" CA ARG A 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU C 203 " pdb=" N ARG C 204 " pdb=" CA ARG C 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 angle pdb=" C LEU E 203 " pdb=" N ARG E 204 " pdb=" CA ARG E 204 " ideal model delta sigma weight residual 120.06 132.88 -12.82 1.19e+00 7.06e-01 1.16e+02 ... (remaining 18531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 7232 16.29 - 32.59: 760 32.59 - 48.88: 120 48.88 - 65.17: 24 65.17 - 81.47: 48 Dihedral angle restraints: 8184 sinusoidal: 3152 harmonic: 5032 Sorted by residual: dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " pdb=" CB CYS G 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.76 69.76 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS H 41 " pdb=" SG CYS H 41 " pdb=" SG CYS H 126 " pdb=" CB CYS H 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS D 41 " pdb=" SG CYS D 41 " pdb=" SG CYS D 126 " pdb=" CB CYS D 126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.75 69.75 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 8181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1375 0.034 - 0.068: 620 0.068 - 0.102: 109 0.102 - 0.136: 41 0.136 - 0.170: 15 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 169 " pdb=" N ILE B 169 " pdb=" C ILE B 169 " pdb=" CB ILE B 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA ILE H 169 " pdb=" N ILE H 169 " pdb=" C ILE H 169 " pdb=" CB ILE H 169 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 2157 not shown) Planarity restraints: 2296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 59 " 0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO D 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO C 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO E 60 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.030 5.00e-02 4.00e+02 ... (remaining 2293 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3850 2.81 - 3.33: 13724 3.33 - 3.86: 20744 3.86 - 4.38: 21377 4.38 - 4.90: 37590 Nonbonded interactions: 97285 Sorted by model distance: nonbonded pdb=" OE1 GLU F 225 " pdb=" NH1 ARG F 226 " model vdw 2.290 2.520 nonbonded pdb=" OE1 GLU B 225 " pdb=" NH1 ARG B 226 " model vdw 2.290 2.520 nonbonded pdb=" OE1 GLU A 225 " pdb=" NH1 ARG A 226 " model vdw 2.290 2.520 nonbonded pdb=" OE1 GLU G 225 " pdb=" NH1 ARG G 226 " model vdw 2.290 2.520 nonbonded pdb=" OE1 GLU C 225 " pdb=" NH1 ARG C 226 " model vdw 2.290 2.520 ... (remaining 97280 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.420 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 35.540 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 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 : 0.005 0.048 13656 Z= 0.343 Angle : 0.843 12.848 18536 Z= 0.537 Chirality : 0.041 0.170 2160 Planarity : 0.005 0.053 2296 Dihedral : 14.629 81.467 4880 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.19), residues: 1664 helix: -0.64 (0.12), residues: 1304 sheet: None (None), residues: 0 loop : -3.16 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 218 HIS 0.001 0.000 HIS B 236 PHE 0.008 0.001 PHE H 229 TYR 0.014 0.002 TYR H 97 ARG 0.001 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.619 Fit side-chains REVERT: A 102 MET cc_start: 0.8083 (ttp) cc_final: 0.7852 (ttm) REVERT: B 26 MET cc_start: 0.7340 (mmm) cc_final: 0.6989 (tpt) REVERT: B 235 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8523 (mm-30) REVERT: C 102 MET cc_start: 0.8084 (ttp) cc_final: 0.7851 (ttm) REVERT: D 26 MET cc_start: 0.7335 (mmm) cc_final: 0.6978 (tpt) REVERT: D 235 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8519 (mm-30) REVERT: E 102 MET cc_start: 0.8081 (ttp) cc_final: 0.7847 (ttm) REVERT: F 26 MET cc_start: 0.7331 (mmm) cc_final: 0.6980 (tpt) REVERT: F 235 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8515 (mm-30) REVERT: G 102 MET cc_start: 0.8081 (ttp) cc_final: 0.7846 (ttm) REVERT: H 26 MET cc_start: 0.7333 (mmm) cc_final: 0.6985 (tpt) REVERT: H 235 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8520 (mm-30) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2450 time to fit residues: 96.1685 Evaluate side-chains 213 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.3980 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 48 ASN A 73 ASN A 147 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN C 73 ASN C 147 GLN D 40 ASN E 40 ASN E 48 ASN E 73 ASN E 147 GLN F 40 ASN F 48 ASN G 40 ASN G 73 ASN G 147 GLN H 40 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13656 Z= 0.201 Angle : 0.579 6.205 18536 Z= 0.311 Chirality : 0.037 0.183 2160 Planarity : 0.005 0.054 2296 Dihedral : 5.047 21.333 1856 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.77 % Allowed : 14.96 % Favored : 84.27 % 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: 0.38 (0.21), residues: 1664 helix: 1.00 (0.14), residues: 1328 sheet: None (None), residues: 0 loop : -2.75 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 218 HIS 0.000 0.000 HIS B 220 PHE 0.007 0.001 PHE B 128 TYR 0.007 0.001 TYR A 34 ARG 0.001 0.000 ARG G 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 264 time to evaluate : 1.540 Fit side-chains REVERT: B 117 THR cc_start: 0.9500 (t) cc_final: 0.9293 (t) REVERT: B 231 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8614 (mm-30) REVERT: D 26 MET cc_start: 0.7180 (mmm) cc_final: 0.6799 (tpt) REVERT: D 117 THR cc_start: 0.9500 (t) cc_final: 0.9294 (t) REVERT: D 231 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8607 (mm-30) REVERT: D 235 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8405 (mm-30) REVERT: F 26 MET cc_start: 0.7166 (mmm) cc_final: 0.6781 (tpt) REVERT: F 117 THR cc_start: 0.9500 (t) cc_final: 0.9292 (t) REVERT: F 235 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8386 (mm-30) REVERT: H 26 MET cc_start: 0.7176 (mmm) cc_final: 0.6801 (tpt) REVERT: H 117 THR cc_start: 0.9501 (t) cc_final: 0.9292 (t) REVERT: H 235 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8392 (mm-30) outliers start: 11 outliers final: 0 residues processed: 264 average time/residue: 0.2274 time to fit residues: 90.7504 Evaluate side-chains 228 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 152 optimal weight: 0.0980 chunk 165 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13656 Z= 0.367 Angle : 0.682 6.582 18536 Z= 0.367 Chirality : 0.040 0.169 2160 Planarity : 0.005 0.054 2296 Dihedral : 5.229 18.959 1856 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.97 % Allowed : 16.15 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1664 helix: 0.99 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.35 (0.42), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 218 HIS 0.001 0.000 HIS B 220 PHE 0.009 0.001 PHE G 229 TYR 0.015 0.002 TYR F 97 ARG 0.001 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 251 time to evaluate : 1.511 Fit side-chains REVERT: A 76 MET cc_start: 0.6951 (tmm) cc_final: 0.6743 (ttt) REVERT: D 231 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8622 (mm-30) REVERT: E 76 MET cc_start: 0.6959 (tmm) cc_final: 0.6734 (ttt) REVERT: F 231 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8464 (mm-30) REVERT: G 76 MET cc_start: 0.6968 (tmm) cc_final: 0.6736 (ttt) REVERT: H 231 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8471 (mm-30) outliers start: 28 outliers final: 28 residues processed: 269 average time/residue: 0.2082 time to fit residues: 84.9716 Evaluate side-chains 262 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 236 HIS ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 236 HIS ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 236 HIS ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 236 HIS ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 236 HIS ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 236 HIS ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 236 HIS ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN H 236 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13656 Z= 0.172 Angle : 0.564 7.913 18536 Z= 0.295 Chirality : 0.035 0.168 2160 Planarity : 0.005 0.056 2296 Dihedral : 4.756 20.798 1856 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.33 % Allowed : 19.38 % Favored : 79.28 % 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: 1.45 (0.21), residues: 1664 helix: 1.77 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -2.69 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 218 HIS 0.000 0.000 HIS C 236 PHE 0.006 0.001 PHE A 229 TYR 0.010 0.001 TYR G 163 ARG 0.001 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 243 time to evaluate : 1.504 Fit side-chains REVERT: A 228 LEU cc_start: 0.9008 (tt) cc_final: 0.8792 (tp) REVERT: B 76 MET cc_start: 0.6884 (ppp) cc_final: 0.6530 (ppp) REVERT: C 228 LEU cc_start: 0.8996 (tt) cc_final: 0.8783 (tp) REVERT: D 76 MET cc_start: 0.6874 (ppp) cc_final: 0.6542 (ppp) REVERT: E 228 LEU cc_start: 0.9015 (tt) cc_final: 0.8796 (tp) REVERT: F 76 MET cc_start: 0.6834 (ppp) cc_final: 0.6506 (ppp) REVERT: F 231 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8394 (mm-30) REVERT: G 228 LEU cc_start: 0.9019 (tt) cc_final: 0.8803 (tp) REVERT: H 76 MET cc_start: 0.6865 (ppp) cc_final: 0.6529 (ppp) REVERT: H 231 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 19 outliers final: 17 residues processed: 255 average time/residue: 0.2027 time to fit residues: 79.4433 Evaluate side-chains 242 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 120 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13656 Z= 0.178 Angle : 0.543 6.166 18536 Z= 0.291 Chirality : 0.036 0.165 2160 Planarity : 0.004 0.054 2296 Dihedral : 4.432 17.695 1856 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.53 % Allowed : 20.22 % Favored : 77.25 % 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: 1.99 (0.21), residues: 1664 helix: 2.01 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -2.35 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.001 0.000 HIS E 236 PHE 0.004 0.001 PHE A 229 TYR 0.025 0.001 TYR A 163 ARG 0.000 0.000 ARG G 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 241 time to evaluate : 1.551 Fit side-chains REVERT: B 76 MET cc_start: 0.6965 (ppp) cc_final: 0.6732 (ppp) REVERT: B 107 MET cc_start: 0.8437 (tpp) cc_final: 0.8218 (ttp) REVERT: D 76 MET cc_start: 0.6954 (ppp) cc_final: 0.6715 (ppp) REVERT: E 228 LEU cc_start: 0.9029 (tt) cc_final: 0.8823 (tp) REVERT: F 76 MET cc_start: 0.6968 (ppp) cc_final: 0.6733 (ppp) REVERT: F 107 MET cc_start: 0.8434 (tpp) cc_final: 0.8215 (ttp) REVERT: G 228 LEU cc_start: 0.9038 (tt) cc_final: 0.8831 (tp) REVERT: H 76 MET cc_start: 0.6959 (ppp) cc_final: 0.6713 (ppp) REVERT: H 107 MET cc_start: 0.8440 (tpp) cc_final: 0.8217 (ttp) outliers start: 36 outliers final: 25 residues processed: 270 average time/residue: 0.2123 time to fit residues: 86.5019 Evaluate side-chains 249 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 224 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 32 optimal weight: 0.0020 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 0.0020 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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: 0.7332 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13656 Z= 0.163 Angle : 0.554 6.845 18536 Z= 0.286 Chirality : 0.036 0.163 2160 Planarity : 0.004 0.053 2296 Dihedral : 4.284 17.776 1856 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.76 % Allowed : 21.98 % Favored : 76.26 % 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 (0.21), residues: 1664 helix: 2.36 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 218 HIS 0.001 0.000 HIS D 236 PHE 0.004 0.001 PHE H 212 TYR 0.018 0.001 TYR G 163 ARG 0.001 0.000 ARG G 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 1.466 Fit side-chains REVERT: B 76 MET cc_start: 0.6979 (ppp) cc_final: 0.6760 (ppp) REVERT: D 76 MET cc_start: 0.6958 (ppp) cc_final: 0.6757 (ppp) REVERT: F 76 MET cc_start: 0.7024 (ppp) cc_final: 0.6819 (ppp) outliers start: 25 outliers final: 19 residues processed: 277 average time/residue: 0.2149 time to fit residues: 89.3661 Evaluate side-chains 261 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 98 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13656 Z= 0.431 Angle : 0.753 7.206 18536 Z= 0.399 Chirality : 0.044 0.183 2160 Planarity : 0.005 0.053 2296 Dihedral : 4.996 20.858 1856 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 1.97 % Allowed : 23.67 % Favored : 74.37 % 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: 1.27 (0.20), residues: 1664 helix: 1.67 (0.13), residues: 1344 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 218 HIS 0.001 0.000 HIS E 220 PHE 0.010 0.002 PHE C 229 TYR 0.023 0.003 TYR G 163 ARG 0.003 0.000 ARG C 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 1.461 Fit side-chains REVERT: A 163 TYR cc_start: 0.7955 (t80) cc_final: 0.7710 (t80) REVERT: C 163 TYR cc_start: 0.7945 (t80) cc_final: 0.7703 (t80) REVERT: E 163 TYR cc_start: 0.7945 (t80) cc_final: 0.7707 (t80) REVERT: G 203 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7995 (mp) outliers start: 28 outliers final: 19 residues processed: 273 average time/residue: 0.2143 time to fit residues: 88.0316 Evaluate side-chains 256 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.0970 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13656 Z= 0.184 Angle : 0.593 9.077 18536 Z= 0.305 Chirality : 0.037 0.168 2160 Planarity : 0.004 0.056 2296 Dihedral : 4.577 21.548 1856 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.54 % Allowed : 23.67 % Favored : 74.79 % 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: 2.21 (0.21), residues: 1664 helix: 2.42 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -3.01 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 218 HIS 0.001 0.000 HIS A 236 PHE 0.006 0.001 PHE D 128 TYR 0.018 0.001 TYR G 163 ARG 0.001 0.000 ARG G 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 252 time to evaluate : 1.488 Fit side-chains REVERT: B 117 THR cc_start: 0.9476 (t) cc_final: 0.9239 (t) REVERT: D 107 MET cc_start: 0.8436 (ttt) cc_final: 0.8106 (ttp) REVERT: D 117 THR cc_start: 0.9478 (t) cc_final: 0.9237 (t) REVERT: F 117 THR cc_start: 0.9483 (t) cc_final: 0.9239 (t) REVERT: H 117 THR cc_start: 0.9482 (t) cc_final: 0.9245 (t) outliers start: 22 outliers final: 13 residues processed: 268 average time/residue: 0.2129 time to fit residues: 85.6234 Evaluate side-chains 252 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 239 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain F residue 203 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain H residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 chunk 118 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 159 optimal weight: 0.5980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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: 0.7349 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13656 Z= 0.178 Angle : 0.598 9.465 18536 Z= 0.302 Chirality : 0.038 0.259 2160 Planarity : 0.004 0.054 2296 Dihedral : 4.159 16.491 1856 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.40 % Allowed : 24.86 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.50 (0.22), residues: 1664 helix: 2.48 (0.14), residues: 1384 sheet: None (None), residues: 0 loop : -2.91 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 218 HIS 0.000 0.000 HIS F 236 PHE 0.004 0.001 PHE B 229 TYR 0.020 0.001 TYR G 163 ARG 0.001 0.000 ARG H 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 256 time to evaluate : 1.431 Fit side-chains REVERT: D 107 MET cc_start: 0.8410 (ttt) cc_final: 0.8165 (ttp) outliers start: 20 outliers final: 5 residues processed: 272 average time/residue: 0.2218 time to fit residues: 89.7495 Evaluate side-chains 253 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 MET Chi-restraints excluded: chain D residue 98 MET Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain F residue 98 MET Chi-restraints excluded: chain H residue 98 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 141 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13656 Z= 0.441 Angle : 0.774 8.731 18536 Z= 0.404 Chirality : 0.045 0.188 2160 Planarity : 0.005 0.053 2296 Dihedral : 4.919 19.390 1856 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.28 % Allowed : 25.56 % Favored : 74.16 % 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: 1.41 (0.21), residues: 1664 helix: 1.79 (0.13), residues: 1352 sheet: None (None), residues: 0 loop : -3.03 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 218 HIS 0.001 0.001 HIS E 236 PHE 0.010 0.002 PHE A 64 TYR 0.031 0.003 TYR G 34 ARG 0.002 0.000 ARG D 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 1.308 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 240 average time/residue: 0.2381 time to fit residues: 84.6149 Evaluate side-chains 240 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 236 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105492 restraints weight = 28379.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.108794 restraints weight = 14278.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111153 restraints weight = 9232.164| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13656 Z= 0.209 Angle : 0.635 9.013 18536 Z= 0.323 Chirality : 0.038 0.215 2160 Planarity : 0.004 0.055 2296 Dihedral : 4.538 21.248 1856 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.49 % Allowed : 25.63 % Favored : 73.88 % 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: 2.15 (0.21), residues: 1664 helix: 2.39 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -3.14 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 218 HIS 0.001 0.000 HIS A 236 PHE 0.004 0.001 PHE F 128 TYR 0.022 0.002 TYR A 34 ARG 0.001 0.000 ARG B 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2469.95 seconds wall clock time: 45 minutes 32.80 seconds (2732.80 seconds total)