Starting phenix.real_space_refine (version: dev) on Sun Feb 26 11:59:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/02_2023/6oee_20020_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/02_2023/6oee_20020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/02_2023/6oee_20020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/02_2023/6oee_20020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/02_2023/6oee_20020_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/02_2023/6oee_20020_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 187": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "F ARG 187": "NH1" <-> "NH2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F GLU 253": "OE1" <-> "OE2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G GLU 188": "OE1" <-> "OE2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "H ARG 187": "NH1" <-> "NH2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 253": "OE1" <-> "OE2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "I GLU 253": "OE1" <-> "OE2" Residue "J ARG 187": "NH1" <-> "NH2" Residue "J GLU 188": "OE1" <-> "OE2" Residue "J GLU 253": "OE1" <-> "OE2" Residue "K ARG 187": "NH1" <-> "NH2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K GLU 253": "OE1" <-> "OE2" Residue "L ARG 187": "NH1" <-> "NH2" Residue "L GLU 188": "OE1" <-> "OE2" Residue "L GLU 253": "OE1" <-> "OE2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M GLU 253": "OE1" <-> "OE2" Residue "N ARG 187": "NH1" <-> "NH2" Residue "N GLU 188": "OE1" <-> "OE2" Residue "N GLU 253": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 28000 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "B" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "C" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "D" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "E" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "F" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "G" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "H" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "I" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "J" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "K" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "L" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "M" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "N" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2000 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Time building chain proxies: 15.15, per 1000 atoms: 0.54 Number of scatterers: 28000 At special positions: 0 Unit cell: (323.08, 323.08, 90.2, 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 70 16.00 O 5432 8.00 N 4900 7.00 C 17598 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=0, symmetry=0 Time building additional restraints: 11.47 Conformation dependent library (CDL) restraints added in 4.6 seconds 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6552 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 14 sheets defined 44.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.818A pdb=" N ASP A 152 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 198 Processing helix chain 'A' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.816A pdb=" N ASP B 152 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 198 Processing helix chain 'B' and resid 207 through 234 removed outlier: 3.865A pdb=" N ARG B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.979A pdb=" N MET B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 87 " --> pdb=" O THR C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 113 Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.818A pdb=" N ASP C 152 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 198 Processing helix chain 'C' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.979A pdb=" N MET C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.990A pdb=" N LEU D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.818A pdb=" N ASP D 152 " --> pdb=" O GLN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 198 Processing helix chain 'D' and resid 207 through 234 removed outlier: 3.867A pdb=" N ARG D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 3.988A pdb=" N LEU E 86 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 113 Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP E 152 " --> pdb=" O GLN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 198 Processing helix chain 'E' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU F 86 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 113 Processing helix chain 'F' and resid 148 through 152 removed outlier: 3.818A pdb=" N ASP F 152 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 198 Processing helix chain 'F' and resid 207 through 234 removed outlier: 3.865A pdb=" N ARG F 213 " --> pdb=" O GLU F 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 266 removed outlier: 3.979A pdb=" N MET F 249 " --> pdb=" O GLY F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL G 87 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 113 Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP G 152 " --> pdb=" O GLN G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 198 Processing helix chain 'G' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET G 249 " --> pdb=" O GLY G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 113 Processing helix chain 'H' and resid 148 through 152 removed outlier: 3.818A pdb=" N ASP H 152 " --> pdb=" O GLN H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 198 Processing helix chain 'H' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN H 234 " --> pdb=" O TYR H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 266 removed outlier: 3.979A pdb=" N MET H 249 " --> pdb=" O GLY H 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 113 Processing helix chain 'I' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 198 Processing helix chain 'I' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN I 234 " --> pdb=" O TYR I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET I 249 " --> pdb=" O GLY I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU J 86 " --> pdb=" O LEU J 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 113 Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP J 152 " --> pdb=" O GLN J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 198 Processing helix chain 'J' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG J 213 " --> pdb=" O GLU J 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN J 234 " --> pdb=" O TYR J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET J 249 " --> pdb=" O GLY J 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL K 87 " --> pdb=" O THR K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 113 Processing helix chain 'K' and resid 148 through 152 removed outlier: 3.818A pdb=" N ASP K 152 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 198 Processing helix chain 'K' and resid 207 through 234 removed outlier: 3.865A pdb=" N ARG K 213 " --> pdb=" O GLU K 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN K 234 " --> pdb=" O TYR K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 266 removed outlier: 3.979A pdb=" N MET K 249 " --> pdb=" O GLY K 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 removed outlier: 3.990A pdb=" N LEU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL L 87 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 113 Processing helix chain 'L' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP L 152 " --> pdb=" O GLN L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 198 Processing helix chain 'L' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG L 213 " --> pdb=" O GLU L 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN L 234 " --> pdb=" O TYR L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET L 249 " --> pdb=" O GLY L 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 90 removed outlier: 3.989A pdb=" N LEU M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL M 87 " --> pdb=" O THR M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 113 Processing helix chain 'M' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP M 152 " --> pdb=" O GLN M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 198 Processing helix chain 'M' and resid 207 through 234 removed outlier: 3.865A pdb=" N ARG M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN M 234 " --> pdb=" O TYR M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 266 removed outlier: 3.979A pdb=" N MET M 249 " --> pdb=" O GLY M 245 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 removed outlier: 3.988A pdb=" N LEU N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL N 87 " --> pdb=" O THR N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 148 through 152 removed outlier: 3.817A pdb=" N ASP N 152 " --> pdb=" O GLN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 198 Processing helix chain 'N' and resid 207 through 234 removed outlier: 3.866A pdb=" N ARG N 213 " --> pdb=" O GLU N 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN N 234 " --> pdb=" O TYR N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 242 through 266 removed outlier: 3.978A pdb=" N MET N 249 " --> pdb=" O GLY N 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE A 93 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN A 123 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 95 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 62 through 67 removed outlier: 6.679A pdb=" N ILE B 93 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN B 123 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU B 95 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE C 93 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN C 123 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU C 95 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE D 93 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLN D 123 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU D 95 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE E 93 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN E 123 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU E 95 " --> pdb=" O GLN E 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE F 93 " --> pdb=" O TYR F 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN F 123 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU F 95 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE G 93 " --> pdb=" O TYR G 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN G 123 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU G 95 " --> pdb=" O GLN G 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE H 93 " --> pdb=" O TYR H 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN H 123 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU H 95 " --> pdb=" O GLN H 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE I 93 " --> pdb=" O TYR I 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN I 123 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU I 95 " --> pdb=" O GLN I 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 62 through 67 removed outlier: 6.679A pdb=" N ILE J 93 " --> pdb=" O TYR J 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN J 123 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU J 95 " --> pdb=" O GLN J 123 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE K 93 " --> pdb=" O TYR K 121 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN K 123 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU K 95 " --> pdb=" O GLN K 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 62 through 67 removed outlier: 6.677A pdb=" N ILE L 93 " --> pdb=" O TYR L 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN L 123 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU L 95 " --> pdb=" O GLN L 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE M 93 " --> pdb=" O TYR M 121 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLN M 123 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU M 95 " --> pdb=" O GLN M 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 62 through 67 removed outlier: 6.678A pdb=" N ILE N 93 " --> pdb=" O TYR N 121 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLN N 123 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU N 95 " --> pdb=" O GLN N 123 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3654 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: 7.47 Time building geometry restraints manager: 12.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9284 1.34 - 1.46: 4323 1.46 - 1.57: 14701 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 28448 Sorted by residual: bond pdb=" CG LEU F 221 " pdb=" CD2 LEU F 221 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.94e+00 bond pdb=" CG LEU D 221 " pdb=" CD2 LEU D 221 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.93e+00 bond pdb=" CG LEU H 221 " pdb=" CD2 LEU H 221 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.91e+00 bond pdb=" CG LEU K 221 " pdb=" CD2 LEU K 221 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.87e+00 bond pdb=" CG LEU N 221 " pdb=" CD2 LEU N 221 " ideal model delta sigma weight residual 1.521 1.435 0.086 3.30e-02 9.18e+02 6.86e+00 ... (remaining 28443 not shown) Histogram of bond angle deviations from ideal: 86.57 - 95.76: 14 95.76 - 104.95: 364 104.95 - 114.14: 16290 114.14 - 123.34: 20567 123.34 - 132.53: 1069 Bond angle restraints: 38304 Sorted by residual: angle pdb=" CB LEU I 221 " pdb=" CG LEU I 221 " pdb=" CD2 LEU I 221 " ideal model delta sigma weight residual 110.70 86.57 24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" CB LEU A 221 " pdb=" CG LEU A 221 " pdb=" CD2 LEU A 221 " ideal model delta sigma weight residual 110.70 86.57 24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" CB LEU G 221 " pdb=" CG LEU G 221 " pdb=" CD2 LEU G 221 " ideal model delta sigma weight residual 110.70 86.58 24.12 3.00e+00 1.11e-01 6.47e+01 angle pdb=" CB LEU N 221 " pdb=" CG LEU N 221 " pdb=" CD2 LEU N 221 " ideal model delta sigma weight residual 110.70 86.59 24.11 3.00e+00 1.11e-01 6.46e+01 angle pdb=" CB LEU D 221 " pdb=" CG LEU D 221 " pdb=" CD2 LEU D 221 " ideal model delta sigma weight residual 110.70 86.59 24.11 3.00e+00 1.11e-01 6.46e+01 ... (remaining 38299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 14714 16.70 - 33.40: 2282 33.40 - 50.10: 574 50.10 - 66.80: 154 66.80 - 83.50: 28 Dihedral angle restraints: 17752 sinusoidal: 7602 harmonic: 10150 Sorted by residual: dihedral pdb=" CA LYS L 166 " pdb=" C LYS L 166 " pdb=" N ASN L 167 " pdb=" CA ASN L 167 " ideal model delta harmonic sigma weight residual 180.00 144.58 35.42 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LYS E 166 " pdb=" C LYS E 166 " pdb=" N ASN E 167 " pdb=" CA ASN E 167 " ideal model delta harmonic sigma weight residual 180.00 144.58 35.42 0 5.00e+00 4.00e-02 5.02e+01 dihedral pdb=" CA LYS F 166 " pdb=" C LYS F 166 " pdb=" N ASN F 167 " pdb=" CA ASN F 167 " ideal model delta harmonic sigma weight residual 180.00 144.61 35.39 0 5.00e+00 4.00e-02 5.01e+01 ... (remaining 17749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2719 0.048 - 0.097: 975 0.097 - 0.145: 296 0.145 - 0.194: 108 0.194 - 0.242: 46 Chirality restraints: 4144 Sorted by residual: chirality pdb=" CB ILE H 50 " pdb=" CA ILE H 50 " pdb=" CG1 ILE H 50 " pdb=" CG2 ILE H 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE I 50 " pdb=" CA ILE I 50 " pdb=" CG1 ILE I 50 " pdb=" CG2 ILE I 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE K 50 " pdb=" CA ILE K 50 " pdb=" CG1 ILE K 50 " pdb=" CG2 ILE K 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4141 not shown) Planarity restraints: 5054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE N 220 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ILE N 220 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE N 220 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU N 221 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 220 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ILE H 220 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE H 220 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU H 221 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 220 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ILE D 220 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE D 220 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D 221 " 0.013 2.00e-02 2.50e+03 ... (remaining 5051 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1216 2.71 - 3.26: 27001 3.26 - 3.80: 42454 3.80 - 4.35: 48098 4.35 - 4.90: 79328 Nonbonded interactions: 198097 Sorted by model distance: nonbonded pdb=" ND1 HIS M 169 " pdb=" O ASN N 112 " model vdw 2.159 2.520 nonbonded pdb=" O GLN N 208 " pdb=" OG1 THR N 212 " model vdw 2.215 2.440 nonbonded pdb=" O GLN J 208 " pdb=" OG1 THR J 212 " model vdw 2.215 2.440 nonbonded pdb=" O GLN H 208 " pdb=" OG1 THR H 212 " model vdw 2.215 2.440 nonbonded pdb=" O GLN M 208 " pdb=" OG1 THR M 212 " model vdw 2.216 2.440 ... (remaining 198092 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 17598 2.51 5 N 4900 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 8.380 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: 30.770 Check model and map are aligned: 0.440 Process input model: 68.100 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.008 0.087 28448 Z= 0.521 Angle : 1.190 24.135 38304 Z= 0.627 Chirality : 0.061 0.242 4144 Planarity : 0.006 0.038 5054 Dihedral : 17.188 83.504 11200 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.11), residues: 3374 helix: -1.81 (0.11), residues: 1428 sheet: -2.23 (0.24), residues: 434 loop : -4.68 (0.10), residues: 1512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 801 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 34 residues processed: 899 average time/residue: 0.4425 time to fit residues: 588.9442 Evaluate side-chains 535 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 501 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2157 time to fit residues: 18.6078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 141 ASN A 143 ASN A 164 ASN A 217 GLN B 33 ASN B 104 GLN B 141 ASN B 143 ASN B 216 ASN C 33 ASN C 104 GLN C 107 ASN C 141 ASN C 143 ASN ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN D 141 ASN D 143 ASN D 164 ASN D 183 ASN E 33 ASN E 64 GLN E 104 GLN E 141 ASN E 143 ASN E 183 ASN E 217 GLN F 33 ASN F 104 GLN F 141 ASN F 143 ASN F 164 ASN G 33 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 141 ASN G 143 ASN G 164 ASN G 217 GLN G 250 GLN ** G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 64 GLN H 104 GLN H 141 ASN H 143 ASN I 33 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN I 141 ASN I 143 ASN I 164 ASN ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 GLN J 141 ASN J 143 ASN J 183 ASN J 217 GLN K 33 ASN K 104 GLN K 141 ASN K 143 ASN K 217 GLN L 33 ASN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN L 141 ASN L 143 ASN L 164 ASN L 217 GLN M 33 ASN M 53 ASN M 79 GLN M 104 GLN M 141 ASN M 143 ASN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN N 141 ASN N 143 ASN N 217 GLN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 28448 Z= 0.265 Angle : 0.750 11.631 38304 Z= 0.386 Chirality : 0.044 0.210 4144 Planarity : 0.004 0.050 5054 Dihedral : 6.720 31.465 3710 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.01 (0.13), residues: 3374 helix: 0.07 (0.13), residues: 1456 sheet: -1.77 (0.25), residues: 434 loop : -4.41 (0.12), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 575 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 53 residues processed: 676 average time/residue: 0.4553 time to fit residues: 460.5557 Evaluate side-chains 557 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 504 time to evaluate : 3.471 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.2368 time to fit residues: 28.6968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 250 GLN B 261 GLN C 169 HIS ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS H 183 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN I 217 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 28448 Z= 0.263 Angle : 0.735 11.673 38304 Z= 0.380 Chirality : 0.044 0.190 4144 Planarity : 0.004 0.042 5054 Dihedral : 6.322 28.766 3710 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.49 % Favored : 85.51 % Rotamer Outliers : 3.35 % 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: -2.24 (0.14), residues: 3374 helix: 0.89 (0.14), residues: 1456 sheet: -1.37 (0.26), residues: 434 loop : -4.22 (0.13), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 558 time to evaluate : 3.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 60 residues processed: 638 average time/residue: 0.4543 time to fit residues: 430.0547 Evaluate side-chains 557 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 497 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2381 time to fit residues: 31.5103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 7.9990 chunk 229 optimal weight: 0.0170 chunk 158 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 306 optimal weight: 0.7980 chunk 324 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 290 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN C 196 ASN E 250 GLN F 250 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN H 217 GLN K 250 GLN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 28448 Z= 0.173 Angle : 0.672 10.710 38304 Z= 0.343 Chirality : 0.042 0.180 4144 Planarity : 0.004 0.036 5054 Dihedral : 5.917 25.286 3710 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3374 helix: 1.25 (0.14), residues: 1470 sheet: -1.14 (0.26), residues: 434 loop : -4.00 (0.13), residues: 1470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 560 time to evaluate : 3.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 30 residues processed: 625 average time/residue: 0.4715 time to fit residues: 435.1276 Evaluate side-chains 544 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 514 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2517 time to fit residues: 18.8300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 241 optimal weight: 0.1980 chunk 134 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN C 110 GLN C 127 ASN C 196 ASN D 53 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 250 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN ** G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 261 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 28448 Z= 0.272 Angle : 0.751 11.760 38304 Z= 0.383 Chirality : 0.044 0.348 4144 Planarity : 0.004 0.086 5054 Dihedral : 5.949 26.476 3710 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer Outliers : 2.68 % 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: -1.56 (0.15), residues: 3374 helix: 1.47 (0.14), residues: 1456 sheet: -0.94 (0.26), residues: 434 loop : -3.91 (0.14), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 519 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 49 residues processed: 574 average time/residue: 0.4488 time to fit residues: 382.3928 Evaluate side-chains 541 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 492 time to evaluate : 3.609 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2446 time to fit residues: 26.8813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 325 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 261 GLN F 250 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 250 GLN I 250 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 ASN ** M 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 28448 Z= 0.196 Angle : 0.701 11.490 38304 Z= 0.355 Chirality : 0.043 0.319 4144 Planarity : 0.004 0.041 5054 Dihedral : 5.767 24.203 3710 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer Outliers : 1.37 % 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: -1.39 (0.15), residues: 3374 helix: 1.66 (0.14), residues: 1456 sheet: -0.91 (0.26), residues: 434 loop : -3.84 (0.14), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 524 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 555 average time/residue: 0.5019 time to fit residues: 412.6104 Evaluate side-chains 527 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 497 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2627 time to fit residues: 19.5598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 185 optimal weight: 7.9990 chunk 237 optimal weight: 0.0970 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 197 optimal weight: 0.5980 chunk 149 optimal weight: 0.4980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 GLN J 250 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 GLN L 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 28448 Z= 0.177 Angle : 0.693 11.474 38304 Z= 0.348 Chirality : 0.042 0.289 4144 Planarity : 0.004 0.040 5054 Dihedral : 5.542 23.887 3710 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.72 % Favored : 86.28 % Rotamer Outliers : 1.15 % 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: -1.25 (0.15), residues: 3374 helix: 1.70 (0.15), residues: 1470 sheet: -0.84 (0.26), residues: 434 loop : -3.72 (0.14), residues: 1470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 528 time to evaluate : 3.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 548 average time/residue: 0.4889 time to fit residues: 395.6586 Evaluate side-chains 526 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 501 time to evaluate : 3.805 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2639 time to fit residues: 17.2016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 205 optimal weight: 0.0010 chunk 220 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 254 optimal weight: 7.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN C 127 ASN C 215 ASN C 217 GLN E 261 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 261 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 28448 Z= 0.198 Angle : 0.712 11.273 38304 Z= 0.358 Chirality : 0.043 0.371 4144 Planarity : 0.004 0.040 5054 Dihedral : 5.499 21.884 3710 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.22 % Favored : 86.78 % Rotamer Outliers : 1.12 % 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: -1.16 (0.15), residues: 3374 helix: 1.85 (0.15), residues: 1456 sheet: -0.83 (0.26), residues: 434 loop : -3.70 (0.14), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 522 time to evaluate : 3.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 21 residues processed: 543 average time/residue: 0.4998 time to fit residues: 403.3134 Evaluate side-chains 520 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 499 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2567 time to fit residues: 14.8915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 131 optimal weight: 0.0470 chunk 236 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 chunk 300 optimal weight: 0.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN F 250 GLN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 28448 Z= 0.244 Angle : 0.757 12.761 38304 Z= 0.380 Chirality : 0.044 0.310 4144 Planarity : 0.004 0.044 5054 Dihedral : 5.580 23.318 3710 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.15), residues: 3374 helix: 1.81 (0.14), residues: 1456 sheet: -0.84 (0.26), residues: 434 loop : -3.69 (0.14), residues: 1484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 519 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 527 average time/residue: 0.4874 time to fit residues: 377.5585 Evaluate side-chains 515 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 501 time to evaluate : 3.595 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2714 time to fit residues: 11.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 0.7980 chunk 319 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 chunk 334 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 266 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 205 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 250 GLN J 261 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28448 Z= 0.182 Angle : 0.713 11.304 38304 Z= 0.357 Chirality : 0.043 0.298 4144 Planarity : 0.004 0.040 5054 Dihedral : 5.410 20.811 3710 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer Outliers : 0.35 % 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: -1.11 (0.15), residues: 3374 helix: 1.86 (0.15), residues: 1456 sheet: -0.84 (0.26), residues: 434 loop : -3.64 (0.14), residues: 1484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 538 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 540 average time/residue: 0.4854 time to fit residues: 384.4229 Evaluate side-chains 524 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 518 time to evaluate : 3.395 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2399 time to fit residues: 7.2645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 0.4980 chunk 81 optimal weight: 0.4980 chunk 245 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 266 optimal weight: 0.2980 chunk 111 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 127 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN J 137 ASN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.117918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.106490 restraints weight = 93560.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.108044 restraints weight = 51955.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.109108 restraints weight = 34829.592| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 28448 Z= 0.180 Angle : 0.716 11.002 38304 Z= 0.357 Chirality : 0.042 0.371 4144 Planarity : 0.004 0.041 5054 Dihedral : 5.261 19.284 3710 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.74 % Favored : 87.26 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3374 helix: 1.80 (0.15), residues: 1470 sheet: -0.81 (0.26), residues: 434 loop : -3.56 (0.14), residues: 1470 =============================================================================== Job complete usr+sys time: 7329.08 seconds wall clock time: 133 minutes 53.28 seconds (8033.28 seconds total)