Starting phenix.real_space_refine on Wed Mar 20 16:46:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/03_2024/6oee_20020_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/03_2024/6oee_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_20020/03_2024/6oee_20020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/03_2024/6oee_20020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/03_2024/6oee_20020_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oee_20020/03_2024/6oee_20020_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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-5265/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: 13.65, per 1000 atoms: 0.49 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: 9.68 Conformation dependent library (CDL) restraints added in 5.1 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: 2.36 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: 7.59 Time building geometry restraints manager: 10.46 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 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: 17.860 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: 30.980 Check model and map are aligned: 0.440 Set scattering table: 0.230 Process input model: 65.780 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 % Allowed : 14.41 % Favored : 82.02 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 89 PHE 0.017 0.003 PHE E 120 TYR 0.024 0.002 TYR D 171 ARG 0.003 0.001 ARG I 115 *********************** 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 : 3.498 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 REVERT: A 118 ILE cc_start: 0.9593 (mm) cc_final: 0.9338 (mm) REVERT: A 133 MET cc_start: 0.8671 (ppp) cc_final: 0.8450 (ttp) REVERT: A 160 MET cc_start: 0.8728 (mmt) cc_final: 0.8319 (mmm) REVERT: A 211 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.7315 (p) REVERT: A 212 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8865 (p) REVERT: A 216 ASN cc_start: 0.8564 (m110) cc_final: 0.8226 (m-40) REVERT: B 206 LYS cc_start: 0.8739 (mttt) cc_final: 0.8268 (mttm) REVERT: B 211 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8385 (p) REVERT: B 212 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8578 (p) REVERT: B 216 ASN cc_start: 0.8774 (m110) cc_final: 0.8464 (m110) REVERT: B 243 LYS cc_start: 0.6915 (mptt) cc_final: 0.6432 (mptt) REVERT: B 268 TYR cc_start: 0.7579 (t80) cc_final: 0.7346 (t80) REVERT: C 92 LYS cc_start: 0.7590 (mttm) cc_final: 0.7044 (mmtt) REVERT: C 118 ILE cc_start: 0.6794 (mm) cc_final: 0.6354 (mt) REVERT: C 119 ASP cc_start: 0.7382 (m-30) cc_final: 0.7169 (m-30) REVERT: C 134 ILE cc_start: 0.7724 (mt) cc_final: 0.6444 (mt) REVERT: C 152 ASP cc_start: 0.5246 (t70) cc_final: 0.5003 (m-30) REVERT: C 185 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8246 (t) REVERT: C 216 ASN cc_start: 0.6859 (m110) cc_final: 0.6636 (m-40) REVERT: D 118 ILE cc_start: 0.9379 (mm) cc_final: 0.9145 (mm) REVERT: D 160 MET cc_start: 0.8953 (mmt) cc_final: 0.8708 (mmm) REVERT: D 183 ASN cc_start: 0.8835 (t0) cc_final: 0.8561 (t0) REVERT: D 187 ARG cc_start: 0.5489 (tpt170) cc_final: 0.4228 (tpt-90) REVERT: D 213 ARG cc_start: 0.4610 (tpt170) cc_final: 0.4284 (tpt170) REVERT: D 215 ASN cc_start: 0.8880 (t0) cc_final: 0.8590 (t0) REVERT: D 253 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8546 (tm-30) REVERT: E 62 MET cc_start: 0.8477 (ttm) cc_final: 0.8268 (ttm) REVERT: E 96 ILE cc_start: 0.9457 (mm) cc_final: 0.9169 (mm) REVERT: E 118 ILE cc_start: 0.9504 (mm) cc_final: 0.9016 (mm) REVERT: E 212 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9269 (p) REVERT: E 232 MET cc_start: 0.4629 (ttm) cc_final: 0.3910 (ttm) REVERT: E 249 MET cc_start: 0.8925 (ttm) cc_final: 0.8558 (tmm) REVERT: E 252 LYS cc_start: 0.8518 (ptpp) cc_final: 0.8009 (pttm) REVERT: F 96 ILE cc_start: 0.9435 (mm) cc_final: 0.9171 (mm) REVERT: F 118 ILE cc_start: 0.9560 (mm) cc_final: 0.9207 (mm) REVERT: F 133 MET cc_start: 0.8532 (ppp) cc_final: 0.8136 (ttp) REVERT: F 160 MET cc_start: 0.9057 (mmt) cc_final: 0.8568 (mmm) REVERT: F 187 ARG cc_start: 0.4718 (tpt170) cc_final: 0.4344 (tpt-90) REVERT: F 212 THR cc_start: 0.9428 (OUTLIER) cc_final: 0.9197 (t) REVERT: F 215 ASN cc_start: 0.8710 (t0) cc_final: 0.8496 (t0) REVERT: F 221 LEU cc_start: 0.8091 (tp) cc_final: 0.7220 (tt) REVERT: F 255 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8613 (mm-30) REVERT: G 117 ASP cc_start: 0.8995 (p0) cc_final: 0.8529 (p0) REVERT: G 134 ILE cc_start: 0.9372 (mt) cc_final: 0.9094 (mt) REVERT: G 183 ASN cc_start: 0.9016 (t0) cc_final: 0.8494 (t0) REVERT: G 187 ARG cc_start: 0.4921 (tpt170) cc_final: 0.4071 (tpt170) REVERT: G 215 ASN cc_start: 0.8838 (t0) cc_final: 0.8455 (t0) REVERT: G 242 PHE cc_start: 0.8355 (m-80) cc_final: 0.7890 (p90) REVERT: G 264 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8295 (ttm110) REVERT: H 118 ILE cc_start: 0.9509 (mm) cc_final: 0.8995 (mm) REVERT: H 134 ILE cc_start: 0.9300 (mt) cc_final: 0.8995 (mt) REVERT: H 192 LEU cc_start: 0.9473 (tp) cc_final: 0.9260 (tt) REVERT: H 197 GLN cc_start: 0.9129 (tp40) cc_final: 0.8702 (tp40) REVERT: H 215 ASN cc_start: 0.8504 (t0) cc_final: 0.8205 (t0) REVERT: H 249 MET cc_start: 0.8891 (ttm) cc_final: 0.8333 (tmm) REVERT: I 116 SER cc_start: 0.9122 (p) cc_final: 0.8776 (p) REVERT: I 117 ASP cc_start: 0.8926 (p0) cc_final: 0.8390 (p0) REVERT: I 158 GLN cc_start: 0.8707 (pp30) cc_final: 0.8051 (pm20) REVERT: I 160 MET cc_start: 0.8857 (mmt) cc_final: 0.8567 (mmm) REVERT: I 211 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.7740 (m) REVERT: I 212 THR cc_start: 0.9395 (OUTLIER) cc_final: 0.9155 (p) REVERT: J 96 ILE cc_start: 0.9415 (mm) cc_final: 0.9136 (mm) REVERT: J 118 ILE cc_start: 0.9500 (mm) cc_final: 0.8831 (mt) REVERT: J 140 ASP cc_start: 0.6364 (m-30) cc_final: 0.6143 (m-30) REVERT: J 160 MET cc_start: 0.9082 (mmt) cc_final: 0.8571 (mmm) REVERT: J 215 ASN cc_start: 0.8772 (t0) cc_final: 0.8436 (t0) REVERT: J 232 MET cc_start: 0.3716 (ttm) cc_final: 0.3455 (ttm) REVERT: K 118 ILE cc_start: 0.9434 (mm) cc_final: 0.8948 (mm) REVERT: K 215 ASN cc_start: 0.7973 (t0) cc_final: 0.7762 (t0) REVERT: K 249 MET cc_start: 0.8783 (ttm) cc_final: 0.8567 (tmm) REVERT: K 253 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8593 (tm-30) REVERT: L 96 ILE cc_start: 0.9280 (mm) cc_final: 0.9033 (mm) REVERT: L 160 MET cc_start: 0.8892 (mmt) cc_final: 0.8335 (mmm) REVERT: L 255 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8677 (mt-10) REVERT: M 49 GLU cc_start: 0.7757 (pm20) cc_final: 0.7247 (tm-30) REVERT: M 82 LEU cc_start: 0.8188 (tt) cc_final: 0.7930 (mt) REVERT: M 108 TYR cc_start: 0.8365 (t80) cc_final: 0.7882 (t80) REVERT: M 150 THR cc_start: 0.3116 (OUTLIER) cc_final: 0.2740 (p) REVERT: N 117 ASP cc_start: 0.9042 (p0) cc_final: 0.8561 (p0) REVERT: N 118 ILE cc_start: 0.9535 (mm) cc_final: 0.9281 (mm) REVERT: N 140 ASP cc_start: 0.7274 (m-30) cc_final: 0.7013 (m-30) REVERT: N 187 ARG cc_start: 0.5505 (tpt170) cc_final: 0.5176 (tpt170) REVERT: N 232 MET cc_start: 0.3988 (ttm) cc_final: 0.3627 (ttm) REVERT: N 249 MET cc_start: 0.8997 (ttm) cc_final: 0.8375 (tmm) REVERT: N 253 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8514 (tm-30) outliers start: 112 outliers final: 34 residues processed: 899 average time/residue: 0.4366 time to fit residues: 583.2732 Evaluate side-chains 560 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 516 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 90 SER Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain N residue 131 VAL 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: 2.9990 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 0.0000 chunk 305 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 C 33 ASN C 104 GLN C 107 ASN C 141 ASN C 143 ASN C 169 HIS C 196 ASN D 33 ASN D 104 GLN D 141 ASN D 143 ASN D 164 ASN E 33 ASN E 64 GLN E 104 GLN E 141 ASN E 143 ASN E 183 ASN 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 250 GLN 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 J 33 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 GLN J 141 ASN J 143 ASN K 33 ASN K 104 GLN K 141 ASN K 143 ASN L 33 ASN ** L 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN L 141 ASN L 143 ASN L 164 ASN 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** M 208 GLN 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: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28448 Z= 0.209 Angle : 0.700 10.498 38304 Z= 0.363 Chirality : 0.043 0.190 4144 Planarity : 0.004 0.047 5054 Dihedral : 7.784 58.221 3754 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % Rotamer: Outliers : 4.75 % Allowed : 18.75 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.02 (0.13), residues: 3374 helix: 0.05 (0.13), residues: 1456 sheet: -1.73 (0.26), residues: 434 loop : -4.42 (0.12), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS M 89 PHE 0.017 0.002 PHE L 242 TYR 0.017 0.001 TYR D 40 ARG 0.005 0.001 ARG H 187 *********************** 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 733 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 584 time to evaluate : 2.981 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: A 96 ILE cc_start: 0.9263 (mm) cc_final: 0.9030 (mm) REVERT: A 103 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8763 (mm) REVERT: A 134 ILE cc_start: 0.9173 (mt) cc_final: 0.8961 (mt) REVERT: A 141 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7209 (t0) REVERT: A 160 MET cc_start: 0.8665 (mmt) cc_final: 0.8265 (mmm) REVERT: A 171 TYR cc_start: 0.4820 (OUTLIER) cc_final: 0.4031 (m-80) REVERT: A 185 VAL cc_start: 0.9058 (t) cc_final: 0.8814 (p) REVERT: A 242 PHE cc_start: 0.8443 (m-80) cc_final: 0.8218 (m-80) REVERT: A 255 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8430 (mt-10) REVERT: B 118 ILE cc_start: 0.9399 (mm) cc_final: 0.9114 (mm) REVERT: B 141 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8116 (t0) REVERT: B 160 MET cc_start: 0.8832 (mmm) cc_final: 0.8505 (mmm) REVERT: B 183 ASN cc_start: 0.9308 (t0) cc_final: 0.9043 (t0) REVERT: B 211 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8247 (p) REVERT: B 212 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9019 (p) REVERT: B 243 LYS cc_start: 0.7452 (mptt) cc_final: 0.6941 (mptt) REVERT: B 268 TYR cc_start: 0.7575 (t80) cc_final: 0.7283 (t80) REVERT: C 62 MET cc_start: 0.7681 (tmm) cc_final: 0.7339 (tmm) REVERT: C 76 ASP cc_start: 0.7437 (m-30) cc_final: 0.7128 (t0) REVERT: C 79 GLN cc_start: 0.8313 (mp10) cc_final: 0.8094 (pm20) REVERT: C 118 ILE cc_start: 0.7743 (mm) cc_final: 0.7444 (mt) REVERT: C 129 LYS cc_start: 0.8444 (tppt) cc_final: 0.8052 (tptp) REVERT: C 160 MET cc_start: 0.7219 (mmm) cc_final: 0.6358 (ptp) REVERT: C 161 LEU cc_start: 0.6163 (mm) cc_final: 0.4855 (pp) REVERT: C 196 ASN cc_start: 0.8825 (m-40) cc_final: 0.8582 (m-40) REVERT: D 141 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7014 (t0) REVERT: D 158 GLN cc_start: 0.8568 (pp30) cc_final: 0.7998 (pm20) REVERT: D 160 MET cc_start: 0.8817 (mmt) cc_final: 0.8331 (mmm) REVERT: D 171 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.3987 (m-80) REVERT: D 179 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6850 (mptt) REVERT: D 187 ARG cc_start: 0.6218 (tpt170) cc_final: 0.5078 (tpt170) REVERT: E 62 MET cc_start: 0.8442 (ttm) cc_final: 0.8229 (ttm) REVERT: E 96 ILE cc_start: 0.9461 (mm) cc_final: 0.9177 (mm) REVERT: E 105 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8389 (m-10) REVERT: E 118 ILE cc_start: 0.9391 (mm) cc_final: 0.9138 (mm) REVERT: E 171 TYR cc_start: 0.4664 (OUTLIER) cc_final: 0.4160 (m-80) REVERT: E 246 ASN cc_start: 0.8382 (p0) cc_final: 0.8145 (p0) REVERT: E 249 MET cc_start: 0.8872 (ttm) cc_final: 0.8580 (tmm) REVERT: F 96 ILE cc_start: 0.9387 (mm) cc_final: 0.9092 (mm) REVERT: F 118 ILE cc_start: 0.9438 (mm) cc_final: 0.9226 (mm) REVERT: F 160 MET cc_start: 0.8837 (mmt) cc_final: 0.8522 (mmm) REVERT: F 187 ARG cc_start: 0.5473 (tpt170) cc_final: 0.5058 (tpt-90) REVERT: F 197 GLN cc_start: 0.8974 (tp40) cc_final: 0.8559 (tp40) REVERT: G 141 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6878 (t0) REVERT: G 171 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.4928 (m-10) REVERT: G 179 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.5968 (ptpp) REVERT: G 183 ASN cc_start: 0.9117 (t0) cc_final: 0.8742 (t0) REVERT: G 187 ARG cc_start: 0.4872 (tpt170) cc_final: 0.4261 (tpt170) REVERT: G 242 PHE cc_start: 0.8533 (m-80) cc_final: 0.8084 (p90) REVERT: G 265 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: H 105 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8411 (m-10) REVERT: H 118 ILE cc_start: 0.9443 (mm) cc_final: 0.9076 (mm) REVERT: H 141 ASN cc_start: 0.7455 (OUTLIER) cc_final: 0.6769 (t0) REVERT: H 160 MET cc_start: 0.8930 (mmm) cc_final: 0.8539 (mmm) REVERT: H 171 TYR cc_start: 0.4614 (OUTLIER) cc_final: 0.4130 (m-80) REVERT: H 218 ARG cc_start: 0.5178 (tmt170) cc_final: 0.4976 (tmt170) REVERT: H 242 PHE cc_start: 0.8495 (m-80) cc_final: 0.8255 (p90) REVERT: H 249 MET cc_start: 0.8930 (ttm) cc_final: 0.8342 (tmm) REVERT: I 140 ASP cc_start: 0.7121 (m-30) cc_final: 0.6873 (m-30) REVERT: I 158 GLN cc_start: 0.8656 (pp30) cc_final: 0.8142 (pm20) REVERT: I 160 MET cc_start: 0.8887 (mmt) cc_final: 0.8537 (mmm) REVERT: I 171 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5593 (m-10) REVERT: J 96 ILE cc_start: 0.9401 (mm) cc_final: 0.9108 (mm) REVERT: J 118 ILE cc_start: 0.9317 (mm) cc_final: 0.8635 (mt) REVERT: J 140 ASP cc_start: 0.6316 (m-30) cc_final: 0.6090 (m-30) REVERT: J 141 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7465 (t0) REVERT: J 160 MET cc_start: 0.8925 (mmt) cc_final: 0.8554 (mmm) REVERT: J 171 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.4753 (m-10) REVERT: J 232 MET cc_start: 0.3689 (ttm) cc_final: 0.3364 (ttm) REVERT: K 105 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8228 (m-10) REVERT: K 118 ILE cc_start: 0.9231 (mm) cc_final: 0.8850 (mm) REVERT: K 160 MET cc_start: 0.8766 (mmm) cc_final: 0.8207 (mmm) REVERT: K 171 TYR cc_start: 0.5709 (OUTLIER) cc_final: 0.5226 (m-10) REVERT: K 218 ARG cc_start: 0.5689 (tmt170) cc_final: 0.5422 (tmt170) REVERT: L 96 ILE cc_start: 0.9337 (mm) cc_final: 0.9013 (mm) REVERT: L 134 ILE cc_start: 0.9468 (mt) cc_final: 0.9253 (mt) REVERT: L 141 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.6616 (t0) REVERT: L 160 MET cc_start: 0.8753 (mmt) cc_final: 0.7816 (mmm) REVERT: L 171 TYR cc_start: 0.4935 (OUTLIER) cc_final: 0.3991 (m-80) REVERT: L 185 VAL cc_start: 0.8985 (t) cc_final: 0.8704 (p) REVERT: L 197 GLN cc_start: 0.8991 (tp40) cc_final: 0.8400 (tp40) REVERT: L 243 LYS cc_start: 0.7367 (mptt) cc_final: 0.7068 (mptt) REVERT: L 255 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8665 (mt-10) REVERT: M 48 SER cc_start: 0.7778 (p) cc_final: 0.7555 (t) REVERT: M 49 GLU cc_start: 0.7966 (pm20) cc_final: 0.7160 (tm-30) REVERT: M 82 LEU cc_start: 0.8655 (tt) cc_final: 0.8209 (mp) REVERT: M 85 LYS cc_start: 0.7144 (tppt) cc_final: 0.6727 (ttmt) REVERT: M 96 ILE cc_start: 0.7849 (mm) cc_final: 0.7605 (mm) REVERT: M 141 ASN cc_start: 0.5920 (OUTLIER) cc_final: 0.5326 (t0) REVERT: M 150 THR cc_start: 0.2527 (OUTLIER) cc_final: 0.2068 (p) REVERT: M 249 MET cc_start: 0.9109 (tpp) cc_final: 0.8864 (tmm) REVERT: N 140 ASP cc_start: 0.7306 (m-30) cc_final: 0.6983 (m-30) REVERT: N 171 TYR cc_start: 0.5282 (OUTLIER) cc_final: 0.4675 (m-10) REVERT: N 187 ARG cc_start: 0.6008 (tpt170) cc_final: 0.4747 (tpt170) REVERT: N 232 MET cc_start: 0.4230 (ttm) cc_final: 0.3841 (ttm) REVERT: N 249 MET cc_start: 0.8943 (ttm) cc_final: 0.8286 (tmm) REVERT: N 253 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8575 (tm-30) outliers start: 149 outliers final: 58 residues processed: 705 average time/residue: 0.4503 time to fit residues: 479.3881 Evaluate side-chains 589 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 503 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 ASN Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 141 ASN Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 171 TYR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 133 MET Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 182 ILE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 127 ASN Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 83 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 141 ASN Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 208 GLN Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 255 GLU Chi-restraints excluded: chain N residue 105 TYR Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 171 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 305 optimal weight: 0.0050 chunk 330 optimal weight: 6.9990 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** A 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 53 ASN B 216 ASN B 250 GLN C 215 ASN D 53 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 GLN E 53 ASN F 53 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 GLN H 53 ASN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS H 183 ASN H 191 GLN I 53 ASN ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 GLN J 53 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN L 53 ASN ** M 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN N 53 ASN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 28448 Z= 0.421 Angle : 0.862 12.592 38304 Z= 0.450 Chirality : 0.047 0.224 4144 Planarity : 0.005 0.054 5054 Dihedral : 7.710 59.930 3738 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.50 % Favored : 84.50 % Rotamer: Outliers : 6.66 % Allowed : 19.13 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -2.41 (0.14), residues: 3374 helix: 0.66 (0.14), residues: 1456 sheet: -1.28 (0.26), residues: 434 loop : -4.27 (0.12), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 89 PHE 0.019 0.002 PHE L 242 TYR 0.022 0.002 TYR B 171 ARG 0.010 0.001 ARG L 264 *********************** 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 734 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 525 time to evaluate : 3.302 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: A 117 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8450 (p0) REVERT: A 141 ASN cc_start: 0.7541 (OUTLIER) cc_final: 0.7112 (t0) REVERT: A 160 MET cc_start: 0.8749 (mmt) cc_final: 0.8300 (mmm) REVERT: A 171 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.4099 (m-80) REVERT: A 185 VAL cc_start: 0.9110 (t) cc_final: 0.8782 (p) REVERT: A 259 LYS cc_start: 0.2282 (OUTLIER) cc_final: 0.1749 (tttm) REVERT: B 105 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8865 (m-10) REVERT: B 118 ILE cc_start: 0.9400 (mm) cc_final: 0.9106 (mm) REVERT: B 160 MET cc_start: 0.8977 (mmm) cc_final: 0.8558 (mmm) REVERT: B 161 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8579 (mm) REVERT: B 171 TYR cc_start: 0.5197 (t80) cc_final: 0.4651 (m-80) REVERT: B 183 ASN cc_start: 0.9264 (t0) cc_final: 0.9034 (t0) REVERT: B 211 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8412 (p) REVERT: B 243 LYS cc_start: 0.7130 (mptt) cc_final: 0.6871 (mptt) REVERT: B 268 TYR cc_start: 0.7583 (t80) cc_final: 0.7184 (t80) REVERT: C 62 MET cc_start: 0.8409 (tmm) cc_final: 0.7509 (tmm) REVERT: C 96 ILE cc_start: 0.9243 (mm) cc_final: 0.8982 (mm) REVERT: C 103 LEU cc_start: 0.9094 (tt) cc_final: 0.8689 (mt) REVERT: C 116 SER cc_start: 0.8793 (p) cc_final: 0.8441 (p) REVERT: C 118 ILE cc_start: 0.8675 (mm) cc_final: 0.8222 (mm) REVERT: C 161 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8603 (mm) REVERT: D 116 SER cc_start: 0.8796 (p) cc_final: 0.8453 (p) REVERT: D 133 MET cc_start: 0.8957 (ttp) cc_final: 0.8710 (tmm) REVERT: D 141 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.6985 (t0) REVERT: D 171 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4023 (m-80) REVERT: D 185 VAL cc_start: 0.8974 (p) cc_final: 0.8113 (t) REVERT: D 187 ARG cc_start: 0.5820 (tpt170) cc_final: 0.4159 (tpt-90) REVERT: E 62 MET cc_start: 0.8483 (ttm) cc_final: 0.8182 (ttm) REVERT: E 96 ILE cc_start: 0.9152 (mm) cc_final: 0.8889 (mm) REVERT: E 105 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: E 118 ILE cc_start: 0.9423 (mm) cc_final: 0.9196 (mm) REVERT: E 171 TYR cc_start: 0.4362 (t80) cc_final: 0.3564 (m-80) REVERT: E 179 LYS cc_start: 0.7312 (ptpp) cc_final: 0.7094 (ptpp) REVERT: E 180 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8661 (tm-30) REVERT: E 249 MET cc_start: 0.8911 (ttm) cc_final: 0.8286 (tmm) REVERT: F 96 ILE cc_start: 0.9408 (mm) cc_final: 0.9154 (mm) REVERT: F 116 SER cc_start: 0.9247 (p) cc_final: 0.9043 (p) REVERT: F 118 ILE cc_start: 0.9503 (mm) cc_final: 0.9302 (mm) REVERT: F 160 MET cc_start: 0.8923 (mmt) cc_final: 0.8538 (mmm) REVERT: F 197 GLN cc_start: 0.8909 (tp40) cc_final: 0.8464 (tp40) REVERT: G 171 TYR cc_start: 0.5706 (OUTLIER) cc_final: 0.4486 (m-10) REVERT: G 179 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6461 (ptpp) REVERT: G 183 ASN cc_start: 0.9091 (t0) cc_final: 0.8656 (t0) REVERT: G 187 ARG cc_start: 0.6020 (tpt170) cc_final: 0.5506 (tpt170) REVERT: G 264 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7954 (ttp-110) REVERT: G 265 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: H 105 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8578 (m-10) REVERT: H 118 ILE cc_start: 0.9406 (mm) cc_final: 0.9157 (mm) REVERT: H 171 TYR cc_start: 0.4215 (t80) cc_final: 0.3469 (m-80) REVERT: H 185 VAL cc_start: 0.9020 (p) cc_final: 0.8819 (t) REVERT: H 213 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5307 (tpt170) REVERT: H 218 ARG cc_start: 0.5154 (tmt170) cc_final: 0.4943 (tmt170) REVERT: H 249 MET cc_start: 0.8925 (ttm) cc_final: 0.8345 (tmm) REVERT: H 259 LYS cc_start: 0.3034 (OUTLIER) cc_final: 0.2449 (tttm) REVERT: I 160 MET cc_start: 0.8914 (mmt) cc_final: 0.8438 (mmm) REVERT: J 96 ILE cc_start: 0.9353 (mm) cc_final: 0.9057 (mm) REVERT: J 141 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7492 (t0) REVERT: J 160 MET cc_start: 0.9027 (mmt) cc_final: 0.8372 (mmm) REVERT: J 161 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8625 (mm) REVERT: J 171 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5129 (m-80) REVERT: K 54 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7749 (p0) REVERT: K 105 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8409 (m-10) REVERT: K 118 ILE cc_start: 0.9246 (mm) cc_final: 0.8913 (mm) REVERT: K 160 MET cc_start: 0.8909 (mmm) cc_final: 0.8250 (mmm) REVERT: K 161 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8614 (mm) REVERT: K 171 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.5122 (m-10) REVERT: K 187 ARG cc_start: 0.5069 (tpt170) cc_final: 0.3878 (tpt-90) REVERT: K 259 LYS cc_start: 0.3049 (OUTLIER) cc_final: 0.2321 (tttm) REVERT: L 96 ILE cc_start: 0.9300 (mm) cc_final: 0.9096 (mm) REVERT: L 134 ILE cc_start: 0.9251 (mt) cc_final: 0.9048 (mt) REVERT: L 141 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6916 (t0) REVERT: L 160 MET cc_start: 0.8750 (mmt) cc_final: 0.8171 (mmm) REVERT: L 171 TYR cc_start: 0.5317 (OUTLIER) cc_final: 0.4264 (m-80) REVERT: L 185 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8751 (p) REVERT: L 244 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7870 (p0) REVERT: L 255 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8779 (mt-10) REVERT: L 264 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7405 (ttp-110) REVERT: M 49 GLU cc_start: 0.8013 (pm20) cc_final: 0.7550 (tm-30) REVERT: M 62 MET cc_start: 0.8492 (ttm) cc_final: 0.8236 (ttm) REVERT: M 78 LYS cc_start: 0.8167 (tppt) cc_final: 0.7912 (tptm) REVERT: M 96 ILE cc_start: 0.9293 (mm) cc_final: 0.9020 (mm) REVERT: M 150 THR cc_start: 0.3401 (OUTLIER) cc_final: 0.3026 (p) REVERT: M 172 ASP cc_start: 0.4328 (m-30) cc_final: 0.4086 (m-30) REVERT: M 218 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6430 (mpp80) REVERT: N 140 ASP cc_start: 0.6872 (m-30) cc_final: 0.6621 (m-30) REVERT: N 171 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.4736 (m-10) REVERT: N 249 MET cc_start: 0.8937 (ttm) cc_final: 0.8369 (tmm) outliers start: 209 outliers final: 125 residues processed: 693 average time/residue: 0.4304 time to fit residues: 444.2161 Evaluate side-chains 630 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 474 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 141 ASN Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 76 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 172 ASP Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 213 ARG Chi-restraints excluded: chain H residue 259 LYS Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 58 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 133 MET Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 127 ASN Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 259 LYS Chi-restraints excluded: chain K residue 268 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 244 ASN Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 255 GLU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 150 THR Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 215 ASN Chi-restraints excluded: chain N residue 244 ASN Chi-restraints excluded: chain N residue 255 GLU Chi-restraints excluded: chain N residue 258 GLU Chi-restraints excluded: chain N residue 268 TYR 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: 0.0770 chunk 158 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 290 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 261 GLN D 141 ASN D 183 ASN E 250 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 ASN G 250 GLN ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN J 141 ASN K 250 GLN L 141 ASN ** 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** M 226 ASN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 261 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28448 Z= 0.181 Angle : 0.683 11.017 38304 Z= 0.349 Chirality : 0.043 0.295 4144 Planarity : 0.004 0.043 5054 Dihedral : 6.929 59.884 3733 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 5.61 % Allowed : 20.98 % Favored : 73.41 % 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: -1.86 (0.15), residues: 3374 helix: 1.21 (0.14), residues: 1456 sheet: -1.07 (0.26), residues: 434 loop : -4.07 (0.13), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 89 PHE 0.010 0.001 PHE L 242 TYR 0.010 0.001 TYR M 70 ARG 0.008 0.001 ARG C 213 *********************** 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 714 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 538 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8197 (p0) REVERT: A 141 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7481 (t0) REVERT: A 171 TYR cc_start: 0.5021 (OUTLIER) cc_final: 0.4164 (m-80) REVERT: A 185 VAL cc_start: 0.9199 (t) cc_final: 0.8963 (p) REVERT: A 197 GLN cc_start: 0.8933 (tp40) cc_final: 0.8538 (tp40) REVERT: A 255 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 105 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8600 (m-10) REVERT: B 118 ILE cc_start: 0.9340 (mm) cc_final: 0.9034 (mm) REVERT: B 160 MET cc_start: 0.8873 (mmm) cc_final: 0.8274 (mmm) REVERT: B 211 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 243 LYS cc_start: 0.7586 (mptt) cc_final: 0.7266 (mptt) REVERT: C 62 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7055 (tmm) REVERT: C 116 SER cc_start: 0.8785 (p) cc_final: 0.8367 (p) REVERT: C 118 ILE cc_start: 0.8610 (mm) cc_final: 0.8366 (mm) REVERT: C 255 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8669 (tt0) REVERT: D 133 MET cc_start: 0.8733 (ttp) cc_final: 0.8501 (tmm) REVERT: D 140 ASP cc_start: 0.7541 (m-30) cc_final: 0.7323 (m-30) REVERT: D 160 MET cc_start: 0.8841 (mmt) cc_final: 0.8335 (mmm) REVERT: D 171 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.3976 (m-80) REVERT: D 179 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6902 (ptpp) REVERT: D 185 VAL cc_start: 0.8855 (p) cc_final: 0.8388 (t) REVERT: D 187 ARG cc_start: 0.6410 (tpt170) cc_final: 0.5378 (tpm170) REVERT: D 259 LYS cc_start: 0.3600 (OUTLIER) cc_final: 0.3186 (tttm) REVERT: E 50 ILE cc_start: 0.4200 (OUTLIER) cc_final: 0.3535 (tp) REVERT: E 62 MET cc_start: 0.8389 (ttm) cc_final: 0.8176 (ttm) REVERT: E 105 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8369 (m-10) REVERT: E 140 ASP cc_start: 0.7299 (m-30) cc_final: 0.7097 (m-30) REVERT: E 171 TYR cc_start: 0.4287 (OUTLIER) cc_final: 0.3665 (m-80) REVERT: E 180 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8344 (tm-30) REVERT: E 249 MET cc_start: 0.8869 (ttm) cc_final: 0.8222 (tmm) REVERT: F 96 ILE cc_start: 0.9403 (mm) cc_final: 0.9111 (mm) REVERT: F 116 SER cc_start: 0.9112 (p) cc_final: 0.8514 (p) REVERT: F 117 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7973 (p0) REVERT: F 160 MET cc_start: 0.8840 (mmt) cc_final: 0.8376 (mmm) REVERT: F 171 TYR cc_start: 0.6500 (m-80) cc_final: 0.5917 (m-10) REVERT: F 197 GLN cc_start: 0.8866 (tp40) cc_final: 0.8507 (tp40) REVERT: G 117 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8669 (p0) REVERT: G 141 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6577 (t0) REVERT: G 171 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.4931 (m-10) REVERT: G 179 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6945 (ptpp) REVERT: G 183 ASN cc_start: 0.9176 (t0) cc_final: 0.8777 (t0) REVERT: G 187 ARG cc_start: 0.5656 (tpt170) cc_final: 0.4876 (mtp-110) REVERT: H 105 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.8398 (m-10) REVERT: H 171 TYR cc_start: 0.4206 (OUTLIER) cc_final: 0.3632 (m-80) REVERT: H 213 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.4898 (tpt170) REVERT: H 218 ARG cc_start: 0.5540 (tmt170) cc_final: 0.5305 (tmt170) REVERT: H 249 MET cc_start: 0.8880 (ttm) cc_final: 0.8298 (tmm) REVERT: I 117 ASP cc_start: 0.9016 (OUTLIER) cc_final: 0.8392 (p0) REVERT: I 133 MET cc_start: 0.8818 (ttp) cc_final: 0.8488 (tmm) REVERT: I 160 MET cc_start: 0.8962 (mmt) cc_final: 0.8633 (mmm) REVERT: J 96 ILE cc_start: 0.9337 (mm) cc_final: 0.9017 (mm) REVERT: J 141 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7271 (t0) REVERT: J 160 MET cc_start: 0.8915 (mmt) cc_final: 0.8341 (mmm) REVERT: J 171 TYR cc_start: 0.6182 (OUTLIER) cc_final: 0.4886 (m-80) REVERT: J 252 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8405 (ptpp) REVERT: J 264 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7410 (ttp-110) REVERT: K 105 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8292 (m-10) REVERT: K 160 MET cc_start: 0.8816 (mmm) cc_final: 0.8192 (mmm) REVERT: K 171 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.4965 (m-10) REVERT: K 187 ARG cc_start: 0.4619 (tpt170) cc_final: 0.3837 (tpt170) REVERT: L 96 ILE cc_start: 0.9432 (mm) cc_final: 0.9176 (mm) REVERT: L 134 ILE cc_start: 0.9275 (mt) cc_final: 0.9059 (mt) REVERT: L 141 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.6599 (t0) REVERT: L 160 MET cc_start: 0.8722 (mmt) cc_final: 0.8275 (mmm) REVERT: L 171 TYR cc_start: 0.5082 (OUTLIER) cc_final: 0.4135 (m-80) REVERT: L 185 VAL cc_start: 0.8971 (t) cc_final: 0.8752 (p) REVERT: L 197 GLN cc_start: 0.8890 (tp40) cc_final: 0.8416 (tp40) REVERT: L 255 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8750 (mt-10) REVERT: L 257 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8126 (ttp80) REVERT: L 264 ARG cc_start: 0.7583 (ttp-110) cc_final: 0.7188 (ttp-110) REVERT: M 49 GLU cc_start: 0.7869 (pm20) cc_final: 0.7573 (tm-30) REVERT: M 150 THR cc_start: 0.3129 (OUTLIER) cc_final: 0.2920 (p) REVERT: M 160 MET cc_start: 0.8828 (mmt) cc_final: 0.8340 (mmm) REVERT: M 218 ARG cc_start: 0.7228 (mtt180) cc_final: 0.6525 (mpp80) REVERT: M 246 ASN cc_start: 0.8980 (t0) cc_final: 0.8776 (p0) REVERT: N 45 GLU cc_start: 0.7502 (pp20) cc_final: 0.7189 (pp20) REVERT: N 102 ILE cc_start: 0.9307 (pt) cc_final: 0.9099 (pt) REVERT: N 117 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8634 (p0) REVERT: N 140 ASP cc_start: 0.6846 (m-30) cc_final: 0.6593 (m-30) REVERT: N 161 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (mm) REVERT: N 171 TYR cc_start: 0.5540 (OUTLIER) cc_final: 0.4766 (m-10) REVERT: N 249 MET cc_start: 0.8893 (ttm) cc_final: 0.8177 (tmm) REVERT: N 259 LYS cc_start: 0.2226 (OUTLIER) cc_final: 0.2005 (tptt) outliers start: 176 outliers final: 104 residues processed: 676 average time/residue: 0.4356 time to fit residues: 440.9025 Evaluate side-chains 628 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 492 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 50 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 105 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 141 ASN Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 213 ARG Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain K residue 268 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 84 PHE Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 84 PHE Chi-restraints excluded: chain N residue 105 TYR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 255 GLU Chi-restraints excluded: chain N residue 259 LYS Chi-restraints excluded: chain N residue 268 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 241 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 277 optimal weight: 0.5980 chunk 224 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 291 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN D 191 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 ASN H 143 ASN H 217 GLN L 183 ASN L 197 GLN M 141 ASN ** 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: 0.7476 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28448 Z= 0.205 Angle : 0.693 11.592 38304 Z= 0.351 Chirality : 0.043 0.256 4144 Planarity : 0.004 0.042 5054 Dihedral : 6.644 56.757 3733 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.32 % Favored : 85.68 % Rotamer: Outliers : 5.68 % Allowed : 21.78 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 3374 helix: 1.35 (0.14), residues: 1470 sheet: -0.91 (0.26), residues: 434 loop : -3.91 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 89 PHE 0.010 0.001 PHE M 151 TYR 0.023 0.001 TYR L 199 ARG 0.007 0.001 ARG C 264 *********************** 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 692 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 514 time to evaluate : 3.272 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: A 50 ILE cc_start: 0.5971 (OUTLIER) cc_final: 0.5245 (tp) REVERT: A 117 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8246 (p0) REVERT: A 171 TYR cc_start: 0.5094 (OUTLIER) cc_final: 0.4203 (m-80) REVERT: A 197 GLN cc_start: 0.8956 (tp40) cc_final: 0.8500 (tp40) REVERT: A 255 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 118 ILE cc_start: 0.9347 (mm) cc_final: 0.9046 (mm) REVERT: B 160 MET cc_start: 0.8884 (mmm) cc_final: 0.8329 (mmm) REVERT: B 161 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8375 (mm) REVERT: B 243 LYS cc_start: 0.7605 (mptt) cc_final: 0.7297 (mptt) REVERT: B 259 LYS cc_start: 0.2664 (OUTLIER) cc_final: 0.2115 (tttm) REVERT: C 62 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.6973 (tmm) REVERT: C 116 SER cc_start: 0.8856 (p) cc_final: 0.8429 (p) REVERT: C 118 ILE cc_start: 0.8746 (mm) cc_final: 0.8162 (mt) REVERT: C 213 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7796 (ttp80) REVERT: C 218 ARG cc_start: 0.6180 (mtt180) cc_final: 0.5790 (tmt170) REVERT: C 244 ASN cc_start: 0.8502 (p0) cc_final: 0.7766 (t0) REVERT: D 133 MET cc_start: 0.8752 (ttp) cc_final: 0.8546 (tmm) REVERT: D 171 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.4046 (m-80) REVERT: D 179 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6562 (ptpp) REVERT: D 230 TYR cc_start: 0.7011 (t80) cc_final: 0.6809 (t80) REVERT: D 259 LYS cc_start: 0.3822 (OUTLIER) cc_final: 0.2754 (tttm) REVERT: E 62 MET cc_start: 0.8465 (ttm) cc_final: 0.8188 (ttm) REVERT: E 105 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8359 (m-10) REVERT: E 171 TYR cc_start: 0.4345 (OUTLIER) cc_final: 0.3714 (m-80) REVERT: E 180 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8301 (tm-30) REVERT: E 249 MET cc_start: 0.8881 (ttm) cc_final: 0.8227 (tmm) REVERT: E 264 ARG cc_start: 0.7301 (ttp80) cc_final: 0.7057 (tmm-80) REVERT: F 55 LYS cc_start: 0.9152 (tptt) cc_final: 0.8911 (tptt) REVERT: F 96 ILE cc_start: 0.9399 (mm) cc_final: 0.9151 (mm) REVERT: F 116 SER cc_start: 0.9127 (p) cc_final: 0.8532 (p) REVERT: F 117 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8015 (p0) REVERT: F 160 MET cc_start: 0.8811 (mmt) cc_final: 0.8335 (mmm) REVERT: F 171 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.6240 (m-10) REVERT: F 197 GLN cc_start: 0.8899 (tp40) cc_final: 0.8519 (tp40) REVERT: G 117 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8568 (p0) REVERT: G 171 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.4967 (m-10) REVERT: G 179 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6826 (ptpp) REVERT: G 183 ASN cc_start: 0.9158 (t0) cc_final: 0.8906 (t0) REVERT: G 187 ARG cc_start: 0.5666 (tpt170) cc_final: 0.4848 (mtp-110) REVERT: H 105 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: H 171 TYR cc_start: 0.4303 (OUTLIER) cc_final: 0.3719 (m-80) REVERT: H 213 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.5331 (tpt170) REVERT: H 218 ARG cc_start: 0.5671 (tmt170) cc_final: 0.5400 (tmt170) REVERT: H 249 MET cc_start: 0.8881 (ttm) cc_final: 0.8277 (tmm) REVERT: H 264 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7295 (tmm-80) REVERT: I 117 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8344 (p0) REVERT: I 133 MET cc_start: 0.8789 (ttp) cc_final: 0.8540 (tmm) REVERT: I 160 MET cc_start: 0.8929 (mmt) cc_final: 0.8539 (mmm) REVERT: J 96 ILE cc_start: 0.9346 (mm) cc_final: 0.9061 (mm) REVERT: J 160 MET cc_start: 0.8945 (mmt) cc_final: 0.8376 (mmm) REVERT: J 171 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.4969 (m-80) REVERT: K 105 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8300 (m-10) REVERT: K 118 ILE cc_start: 0.9214 (mm) cc_final: 0.8971 (mm) REVERT: K 160 MET cc_start: 0.8852 (mmm) cc_final: 0.8264 (mmm) REVERT: K 161 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8314 (mm) REVERT: K 171 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: K 187 ARG cc_start: 0.4653 (tpt170) cc_final: 0.3844 (tpt170) REVERT: L 96 ILE cc_start: 0.9448 (mm) cc_final: 0.9205 (mm) REVERT: L 160 MET cc_start: 0.8793 (mmt) cc_final: 0.8299 (mmm) REVERT: L 171 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.4173 (m-80) REVERT: L 185 VAL cc_start: 0.8919 (t) cc_final: 0.8647 (p) REVERT: L 255 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8753 (mt-10) REVERT: L 264 ARG cc_start: 0.7733 (ttp-110) cc_final: 0.7342 (ttp-110) REVERT: M 49 GLU cc_start: 0.7875 (pm20) cc_final: 0.7598 (tm-30) REVERT: M 96 ILE cc_start: 0.9325 (mm) cc_final: 0.8995 (mm) REVERT: M 216 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.7924 (t0) REVERT: M 218 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6511 (mpp80) REVERT: M 248 ASN cc_start: 0.8217 (m110) cc_final: 0.7808 (p0) REVERT: N 117 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8682 (p0) REVERT: N 140 ASP cc_start: 0.6831 (m-30) cc_final: 0.6595 (m-30) REVERT: N 161 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8215 (mm) REVERT: N 171 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.4785 (m-10) REVERT: N 213 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5575 (mtt180) outliers start: 178 outliers final: 125 residues processed: 650 average time/residue: 0.4387 time to fit residues: 424.9827 Evaluate side-chains 644 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 489 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 268 TYR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 171 TYR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 213 ARG Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 133 MET Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 PHE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 244 ASN Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 161 LEU Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain K residue 268 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 84 PHE Chi-restraints excluded: chain N residue 105 TYR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 182 ILE Chi-restraints excluded: chain N residue 213 ARG Chi-restraints excluded: chain N residue 255 GLU Chi-restraints excluded: chain N residue 268 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 0.0670 chunk 292 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 325 optimal weight: 0.0060 chunk 269 optimal weight: 0.0670 chunk 150 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN F 250 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 ASN H 250 GLN I 250 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 250 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN ** 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: 0.7415 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28448 Z= 0.162 Angle : 0.661 11.211 38304 Z= 0.333 Chirality : 0.042 0.246 4144 Planarity : 0.004 0.044 5054 Dihedral : 6.112 45.742 3730 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 5.29 % Allowed : 22.83 % Favored : 71.88 % 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: -1.34 (0.15), residues: 3374 helix: 1.61 (0.14), residues: 1470 sheet: -0.87 (0.26), residues: 434 loop : -3.78 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 89 PHE 0.013 0.001 PHE M 151 TYR 0.021 0.001 TYR L 199 ARG 0.008 0.001 ARG L 257 *********************** 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 704 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 538 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 revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8423 (mm) REVERT: A 117 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8112 (p0) REVERT: A 136 SER cc_start: 0.9225 (p) cc_final: 0.9010 (p) REVERT: A 171 TYR cc_start: 0.5006 (OUTLIER) cc_final: 0.4143 (m-80) REVERT: A 197 GLN cc_start: 0.8885 (tp40) cc_final: 0.8516 (tp40) REVERT: A 255 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8250 (mt-10) REVERT: B 105 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8507 (m-10) REVERT: B 118 ILE cc_start: 0.9362 (mm) cc_final: 0.9078 (mm) REVERT: B 160 MET cc_start: 0.8923 (mmm) cc_final: 0.8437 (mmm) REVERT: B 243 LYS cc_start: 0.7404 (mptt) cc_final: 0.7170 (mptt) REVERT: B 257 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8091 (ttp80) REVERT: C 62 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7335 (tmm) REVERT: C 116 SER cc_start: 0.8845 (p) cc_final: 0.8428 (p) REVERT: C 118 ILE cc_start: 0.8776 (mm) cc_final: 0.8473 (mt) REVERT: C 213 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7554 (ttp80) REVERT: C 218 ARG cc_start: 0.6126 (mtt180) cc_final: 0.5814 (tmt170) REVERT: C 244 ASN cc_start: 0.8466 (p0) cc_final: 0.7759 (t0) REVERT: D 133 MET cc_start: 0.8659 (ttp) cc_final: 0.8452 (tmm) REVERT: D 140 ASP cc_start: 0.7416 (m-30) cc_final: 0.7212 (m-30) REVERT: D 160 MET cc_start: 0.8947 (mmt) cc_final: 0.8588 (mmp) REVERT: D 171 TYR cc_start: 0.5181 (OUTLIER) cc_final: 0.4174 (m-80) REVERT: D 179 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6858 (mptt) REVERT: D 259 LYS cc_start: 0.3656 (OUTLIER) cc_final: 0.2718 (tttm) REVERT: E 62 MET cc_start: 0.8332 (ttm) cc_final: 0.7929 (ttm) REVERT: E 84 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8407 (t80) REVERT: E 105 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: E 171 TYR cc_start: 0.4388 (OUTLIER) cc_final: 0.3702 (m-80) REVERT: E 179 LYS cc_start: 0.6995 (ptpp) cc_final: 0.6779 (mppt) REVERT: E 180 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8287 (tm-30) REVERT: E 249 MET cc_start: 0.8860 (ttm) cc_final: 0.8205 (tmm) REVERT: F 96 ILE cc_start: 0.9379 (mm) cc_final: 0.9103 (mm) REVERT: F 116 SER cc_start: 0.9053 (p) cc_final: 0.8477 (p) REVERT: F 117 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7933 (p0) REVERT: F 160 MET cc_start: 0.8801 (mmt) cc_final: 0.8282 (mmm) REVERT: F 197 GLN cc_start: 0.8844 (tp40) cc_final: 0.8533 (tp40) REVERT: G 117 ASP cc_start: 0.8953 (OUTLIER) cc_final: 0.8590 (p0) REVERT: G 171 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.4928 (m-10) REVERT: G 179 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6782 (ptpp) REVERT: G 187 ARG cc_start: 0.5522 (tpt170) cc_final: 0.4940 (mtp-110) REVERT: G 243 LYS cc_start: 0.6561 (mmtt) cc_final: 0.5845 (mptt) REVERT: G 265 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6343 (pm20) REVERT: H 84 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8372 (t80) REVERT: H 105 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: H 150 THR cc_start: 0.3679 (OUTLIER) cc_final: 0.3472 (p) REVERT: H 171 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.4383 (m-80) REVERT: H 213 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5596 (tpt170) REVERT: H 249 MET cc_start: 0.8870 (ttm) cc_final: 0.8278 (tmm) REVERT: H 264 ARG cc_start: 0.7571 (ttp80) cc_final: 0.7189 (ttp80) REVERT: I 117 ASP cc_start: 0.8926 (OUTLIER) cc_final: 0.8278 (p0) REVERT: I 133 MET cc_start: 0.8700 (ttp) cc_final: 0.8457 (tmm) REVERT: I 150 THR cc_start: 0.2974 (OUTLIER) cc_final: 0.2711 (p) REVERT: I 264 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7343 (ttp80) REVERT: J 96 ILE cc_start: 0.9349 (mm) cc_final: 0.9031 (mm) REVERT: J 160 MET cc_start: 0.8674 (mmt) cc_final: 0.8261 (mmm) REVERT: J 171 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.4582 (m-80) REVERT: K 105 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8217 (m-10) REVERT: K 118 ILE cc_start: 0.9272 (mm) cc_final: 0.9012 (mm) REVERT: K 160 MET cc_start: 0.8808 (mmm) cc_final: 0.8234 (mmm) REVERT: K 171 TYR cc_start: 0.5324 (OUTLIER) cc_final: 0.4587 (m-10) REVERT: K 187 ARG cc_start: 0.4759 (tpt170) cc_final: 0.4162 (tpt170) REVERT: K 243 LYS cc_start: 0.7442 (mptt) cc_final: 0.7091 (mptt) REVERT: L 96 ILE cc_start: 0.9449 (mm) cc_final: 0.9101 (mm) REVERT: L 117 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8151 (p0) REVERT: L 160 MET cc_start: 0.8701 (mmt) cc_final: 0.8233 (mmm) REVERT: L 171 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.4152 (m-80) REVERT: L 197 GLN cc_start: 0.8720 (tp40) cc_final: 0.8254 (tp40) REVERT: L 255 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8701 (mt-10) REVERT: L 257 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8215 (ttp80) REVERT: M 96 ILE cc_start: 0.9297 (mm) cc_final: 0.8980 (mm) REVERT: M 160 MET cc_start: 0.8806 (mmt) cc_final: 0.8093 (mmm) REVERT: M 161 LEU cc_start: 0.6646 (mm) cc_final: 0.5881 (pp) REVERT: M 218 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6775 (mpp80) REVERT: M 248 ASN cc_start: 0.8090 (m110) cc_final: 0.7699 (p0) REVERT: M 249 MET cc_start: 0.9124 (ttm) cc_final: 0.8688 (tmm) REVERT: N 117 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8665 (p0) REVERT: N 161 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7573 (mm) REVERT: N 171 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.4761 (m-10) REVERT: N 213 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5167 (ttm170) outliers start: 166 outliers final: 99 residues processed: 651 average time/residue: 0.4328 time to fit residues: 420.9852 Evaluate side-chains 643 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 511 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 268 TYR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 213 ARG Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 PHE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain M residue 70 TYR Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 84 PHE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 213 ARG Chi-restraints excluded: chain N residue 255 GLU Chi-restraints excluded: chain N residue 258 GLU Chi-restraints excluded: chain N residue 268 TYR 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: 0.7980 chunk 185 optimal weight: 7.9990 chunk 237 optimal weight: 0.3980 chunk 183 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 202 optimal weight: 0.0980 chunk 197 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 261 GLN ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN ** N 64 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: 0.7416 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28448 Z= 0.166 Angle : 0.673 11.396 38304 Z= 0.338 Chirality : 0.042 0.276 4144 Planarity : 0.004 0.041 5054 Dihedral : 5.830 47.400 3726 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 5.04 % Allowed : 23.53 % Favored : 71.43 % 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: -1.15 (0.15), residues: 3374 helix: 1.79 (0.15), residues: 1470 sheet: -0.81 (0.26), residues: 434 loop : -3.67 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 89 PHE 0.013 0.001 PHE M 151 TYR 0.019 0.001 TYR L 199 ARG 0.012 0.001 ARG G 264 *********************** 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 694 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 536 time to evaluate : 3.538 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: A 103 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 117 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8157 (p0) REVERT: A 136 SER cc_start: 0.9240 (p) cc_final: 0.8968 (p) REVERT: A 171 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.4215 (m-80) REVERT: A 197 GLN cc_start: 0.9012 (tp40) cc_final: 0.8584 (tp40) REVERT: A 255 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 105 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.8485 (m-10) REVERT: B 118 ILE cc_start: 0.9369 (mm) cc_final: 0.9114 (mm) REVERT: B 160 MET cc_start: 0.8983 (mmm) cc_final: 0.8480 (mmm) REVERT: B 171 TYR cc_start: 0.5866 (t80) cc_final: 0.5501 (m-80) REVERT: B 243 LYS cc_start: 0.7397 (mptt) cc_final: 0.7166 (mptt) REVERT: B 257 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8101 (ttp80) REVERT: B 259 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2549 (tttm) REVERT: C 62 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7139 (tmm) REVERT: C 116 SER cc_start: 0.8867 (p) cc_final: 0.8436 (p) REVERT: C 118 ILE cc_start: 0.9098 (mm) cc_final: 0.8780 (mm) REVERT: C 161 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.6528 (pp) REVERT: C 218 ARG cc_start: 0.6388 (mtt180) cc_final: 0.6051 (tmt170) REVERT: C 244 ASN cc_start: 0.8495 (p0) cc_final: 0.7799 (t0) REVERT: D 133 MET cc_start: 0.8671 (ttp) cc_final: 0.8457 (tmm) REVERT: D 160 MET cc_start: 0.9063 (mmt) cc_final: 0.8716 (mmp) REVERT: D 171 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.4590 (m-10) REVERT: D 179 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6621 (ptpp) REVERT: D 259 LYS cc_start: 0.3016 (OUTLIER) cc_final: 0.2163 (tttm) REVERT: E 62 MET cc_start: 0.8358 (ttm) cc_final: 0.8100 (ttm) REVERT: E 84 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8439 (t80) REVERT: E 105 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: E 171 TYR cc_start: 0.4988 (OUTLIER) cc_final: 0.4320 (m-80) REVERT: E 179 LYS cc_start: 0.6936 (ptpp) cc_final: 0.6686 (mppt) REVERT: E 249 MET cc_start: 0.8862 (ttm) cc_final: 0.8219 (tmm) REVERT: F 96 ILE cc_start: 0.9381 (mm) cc_final: 0.9116 (mm) REVERT: F 116 SER cc_start: 0.9056 (p) cc_final: 0.8464 (p) REVERT: F 117 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7942 (p0) REVERT: F 160 MET cc_start: 0.8806 (mmt) cc_final: 0.8281 (mmm) REVERT: F 197 GLN cc_start: 0.8876 (tp40) cc_final: 0.8523 (tp40) REVERT: G 171 TYR cc_start: 0.5489 (OUTLIER) cc_final: 0.4667 (m-10) REVERT: G 179 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.6671 (ptpp) REVERT: G 187 ARG cc_start: 0.5538 (tpt170) cc_final: 0.4991 (mtp-110) REVERT: G 243 LYS cc_start: 0.6572 (mmtt) cc_final: 0.5848 (mptt) REVERT: H 84 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8445 (t80) REVERT: H 105 TYR cc_start: 0.8921 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: H 171 TYR cc_start: 0.4454 (OUTLIER) cc_final: 0.3772 (m-80) REVERT: H 249 MET cc_start: 0.8906 (ttm) cc_final: 0.8254 (tmm) REVERT: H 264 ARG cc_start: 0.7392 (ttp80) cc_final: 0.6973 (ttp80) REVERT: I 117 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8247 (p0) REVERT: I 133 MET cc_start: 0.8711 (ttp) cc_final: 0.8414 (tmm) REVERT: I 150 THR cc_start: 0.3041 (OUTLIER) cc_final: 0.2698 (p) REVERT: I 264 ARG cc_start: 0.7406 (ttp80) cc_final: 0.6863 (ttp80) REVERT: J 160 MET cc_start: 0.8839 (mmt) cc_final: 0.8483 (mmm) REVERT: J 171 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4615 (m-80) REVERT: K 105 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: K 118 ILE cc_start: 0.9301 (mm) cc_final: 0.9045 (mm) REVERT: K 160 MET cc_start: 0.8953 (mmm) cc_final: 0.8297 (mmm) REVERT: K 171 TYR cc_start: 0.5230 (OUTLIER) cc_final: 0.4669 (m-10) REVERT: K 187 ARG cc_start: 0.4773 (tpt170) cc_final: 0.4172 (tpt170) REVERT: L 96 ILE cc_start: 0.9386 (mm) cc_final: 0.9138 (mm) REVERT: L 117 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8221 (p0) REVERT: L 136 SER cc_start: 0.9317 (p) cc_final: 0.9024 (p) REVERT: L 141 ASN cc_start: 0.6429 (OUTLIER) cc_final: 0.5424 (t0) REVERT: L 160 MET cc_start: 0.8770 (mmt) cc_final: 0.8248 (mmm) REVERT: L 171 TYR cc_start: 0.5281 (OUTLIER) cc_final: 0.4391 (m-80) REVERT: L 197 GLN cc_start: 0.8818 (tp40) cc_final: 0.8316 (tp40) REVERT: L 255 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8753 (mt-10) REVERT: M 96 ILE cc_start: 0.9303 (mm) cc_final: 0.8980 (mm) REVERT: M 160 MET cc_start: 0.8705 (mmt) cc_final: 0.8093 (mmm) REVERT: M 161 LEU cc_start: 0.6482 (mm) cc_final: 0.5893 (pp) REVERT: M 218 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6755 (mpp80) REVERT: M 249 MET cc_start: 0.9112 (ttm) cc_final: 0.8740 (tmm) REVERT: N 117 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8703 (p0) REVERT: N 161 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7642 (mm) REVERT: N 171 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.4797 (m-10) REVERT: N 188 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8221 (mm-30) outliers start: 158 outliers final: 107 residues processed: 641 average time/residue: 0.4398 time to fit residues: 422.7682 Evaluate side-chains 653 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 515 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 151 PHE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 PHE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 244 ASN Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 127 ASN Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain M residue 84 PHE Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 105 TYR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 268 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.8980 chunk 129 optimal weight: 0.0270 chunk 193 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 220 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28448 Z= 0.175 Angle : 0.676 11.455 38304 Z= 0.339 Chirality : 0.042 0.226 4144 Planarity : 0.004 0.042 5054 Dihedral : 5.705 49.635 3723 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 4.88 % Allowed : 23.66 % Favored : 71.46 % 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: -1.01 (0.16), residues: 3374 helix: 1.90 (0.15), residues: 1470 sheet: -0.76 (0.26), residues: 434 loop : -3.59 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 89 PHE 0.010 0.001 PHE M 151 TYR 0.019 0.001 TYR L 199 ARG 0.014 0.001 ARG G 264 *********************** 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 691 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 538 time to evaluate : 3.439 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: A 103 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 117 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 136 SER cc_start: 0.9208 (p) cc_final: 0.8968 (p) REVERT: A 171 TYR cc_start: 0.5073 (OUTLIER) cc_final: 0.4233 (m-80) REVERT: A 197 GLN cc_start: 0.8991 (tp40) cc_final: 0.8555 (tp40) REVERT: A 255 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8258 (mt-10) REVERT: B 105 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: B 118 ILE cc_start: 0.9388 (mm) cc_final: 0.9120 (mm) REVERT: B 160 MET cc_start: 0.8929 (mmm) cc_final: 0.8451 (mmm) REVERT: B 171 TYR cc_start: 0.5884 (t80) cc_final: 0.5505 (m-10) REVERT: B 243 LYS cc_start: 0.7389 (mptt) cc_final: 0.7143 (mptt) REVERT: B 257 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8134 (ttp80) REVERT: B 259 LYS cc_start: 0.3086 (OUTLIER) cc_final: 0.2426 (tttm) REVERT: B 264 ARG cc_start: 0.8068 (ttm110) cc_final: 0.7700 (ttt-90) REVERT: C 62 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7204 (tmm) REVERT: C 116 SER cc_start: 0.8929 (p) cc_final: 0.8533 (p) REVERT: C 118 ILE cc_start: 0.9154 (mm) cc_final: 0.8872 (mm) REVERT: C 161 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.6483 (pp) REVERT: C 205 ASP cc_start: 0.6880 (m-30) cc_final: 0.4375 (t70) REVERT: C 244 ASN cc_start: 0.8515 (p0) cc_final: 0.7830 (t0) REVERT: C 257 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8636 (mmp80) REVERT: D 133 MET cc_start: 0.8692 (ttp) cc_final: 0.8475 (tmm) REVERT: D 160 MET cc_start: 0.8883 (mmt) cc_final: 0.8655 (mmp) REVERT: D 171 TYR cc_start: 0.5126 (OUTLIER) cc_final: 0.4551 (m-10) REVERT: D 179 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6687 (ptpp) REVERT: E 84 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8370 (t80) REVERT: E 105 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: E 171 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.4339 (m-80) REVERT: E 249 MET cc_start: 0.8865 (ttm) cc_final: 0.8231 (tmm) REVERT: F 96 ILE cc_start: 0.9328 (mm) cc_final: 0.9069 (mm) REVERT: F 116 SER cc_start: 0.9075 (p) cc_final: 0.8495 (p) REVERT: F 117 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7925 (p0) REVERT: F 160 MET cc_start: 0.8816 (mmt) cc_final: 0.8257 (mmm) REVERT: F 197 GLN cc_start: 0.8877 (tp40) cc_final: 0.8523 (tp40) REVERT: G 117 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8660 (p0) REVERT: G 171 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.4671 (m-10) REVERT: G 179 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6758 (ptpp) REVERT: G 187 ARG cc_start: 0.5547 (tpt170) cc_final: 0.5302 (ttp-170) REVERT: G 243 LYS cc_start: 0.6575 (mmtt) cc_final: 0.5858 (mptt) REVERT: G 257 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8039 (ttp80) REVERT: H 84 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8439 (t80) REVERT: H 105 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: H 171 TYR cc_start: 0.4501 (OUTLIER) cc_final: 0.3792 (m-80) REVERT: H 179 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.5378 (ptpp) REVERT: H 249 MET cc_start: 0.8916 (ttm) cc_final: 0.8269 (tmm) REVERT: H 264 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7002 (ttp80) REVERT: I 117 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8114 (p0) REVERT: I 133 MET cc_start: 0.8732 (ttp) cc_final: 0.8408 (tmm) REVERT: I 150 THR cc_start: 0.3198 (OUTLIER) cc_final: 0.2814 (p) REVERT: I 264 ARG cc_start: 0.7378 (ttp80) cc_final: 0.6856 (ttp80) REVERT: J 96 ILE cc_start: 0.9232 (mm) cc_final: 0.8907 (mm) REVERT: J 160 MET cc_start: 0.8897 (mmt) cc_final: 0.8551 (mmm) REVERT: J 171 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4877 (m-80) REVERT: K 105 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8212 (m-10) REVERT: K 118 ILE cc_start: 0.9313 (mm) cc_final: 0.9058 (mm) REVERT: K 160 MET cc_start: 0.9042 (mmm) cc_final: 0.8424 (mmm) REVERT: K 171 TYR cc_start: 0.5245 (OUTLIER) cc_final: 0.4664 (m-10) REVERT: K 187 ARG cc_start: 0.4794 (tpt170) cc_final: 0.4203 (tpt170) REVERT: K 243 LYS cc_start: 0.7419 (mptt) cc_final: 0.7079 (mptt) REVERT: L 96 ILE cc_start: 0.9382 (mm) cc_final: 0.9133 (mm) REVERT: L 117 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8214 (p0) REVERT: L 136 SER cc_start: 0.9322 (p) cc_final: 0.9050 (p) REVERT: L 141 ASN cc_start: 0.6445 (OUTLIER) cc_final: 0.5731 (t0) REVERT: L 160 MET cc_start: 0.8754 (mmt) cc_final: 0.8238 (mmm) REVERT: L 171 TYR cc_start: 0.5310 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: L 197 GLN cc_start: 0.8815 (tp40) cc_final: 0.8349 (tp40) REVERT: L 255 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8749 (mt-10) REVERT: M 96 ILE cc_start: 0.9290 (mm) cc_final: 0.9009 (mm) REVERT: M 160 MET cc_start: 0.8736 (mmt) cc_final: 0.8157 (mmm) REVERT: M 161 LEU cc_start: 0.6446 (mm) cc_final: 0.5927 (pp) REVERT: M 214 LYS cc_start: 0.9029 (tttt) cc_final: 0.8786 (ttpt) REVERT: M 248 ASN cc_start: 0.8407 (m-40) cc_final: 0.7876 (m110) REVERT: M 249 MET cc_start: 0.9114 (ttm) cc_final: 0.8723 (tmm) REVERT: N 117 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8663 (p0) REVERT: N 161 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7616 (mm) REVERT: N 171 TYR cc_start: 0.5571 (OUTLIER) cc_final: 0.4940 (m-10) outliers start: 153 outliers final: 110 residues processed: 636 average time/residue: 0.4325 time to fit residues: 410.7978 Evaluate side-chains 670 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 528 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 151 PHE Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 151 PHE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 PHE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 244 ASN Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain K residue 268 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 141 ASN Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 134 ILE Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 84 PHE Chi-restraints excluded: chain N residue 105 TYR Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 255 GLU Chi-restraints excluded: chain N residue 268 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 4.9990 chunk 310 optimal weight: 10.0000 chunk 283 optimal weight: 0.7980 chunk 301 optimal weight: 0.0270 chunk 181 optimal weight: 0.5980 chunk 131 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 overall best weight: 1.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN B 215 ASN C 215 ASN C 217 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 250 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28448 Z= 0.274 Angle : 0.766 11.779 38304 Z= 0.386 Chirality : 0.044 0.302 4144 Planarity : 0.004 0.044 5054 Dihedral : 6.069 56.026 3722 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.64 % Favored : 85.36 % Rotamer: Outliers : 4.91 % Allowed : 23.85 % Favored : 71.24 % 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: -1.08 (0.15), residues: 3374 helix: 1.87 (0.15), residues: 1456 sheet: -0.70 (0.26), residues: 434 loop : -3.64 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 89 PHE 0.015 0.002 PHE M 151 TYR 0.020 0.001 TYR C 198 ARG 0.017 0.001 ARG G 264 *********************** 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 700 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 546 time to evaluate : 3.549 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: A 117 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8317 (p0) REVERT: A 171 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4407 (m-80) REVERT: A 197 GLN cc_start: 0.9079 (tp40) cc_final: 0.8619 (tp40) REVERT: A 255 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8424 (mt-10) REVERT: B 105 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: B 118 ILE cc_start: 0.9411 (mm) cc_final: 0.9153 (mm) REVERT: B 160 MET cc_start: 0.8946 (mmm) cc_final: 0.8412 (mmm) REVERT: B 171 TYR cc_start: 0.5112 (t80) cc_final: 0.4826 (m-80) REVERT: B 257 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8202 (ttp80) REVERT: B 259 LYS cc_start: 0.2750 (OUTLIER) cc_final: 0.2304 (tttm) REVERT: C 62 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.6654 (tmm) REVERT: C 116 SER cc_start: 0.9182 (p) cc_final: 0.8846 (p) REVERT: C 118 ILE cc_start: 0.9311 (mm) cc_final: 0.8765 (mt) REVERT: C 164 ASN cc_start: 0.8764 (t0) cc_final: 0.8532 (t0) REVERT: D 133 MET cc_start: 0.8861 (ttp) cc_final: 0.8613 (tmm) REVERT: D 171 TYR cc_start: 0.5388 (OUTLIER) cc_final: 0.4676 (m-80) REVERT: D 179 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6827 (ptpp) REVERT: E 62 MET cc_start: 0.7882 (ttm) cc_final: 0.7675 (ttm) REVERT: E 105 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8425 (m-10) REVERT: E 171 TYR cc_start: 0.4535 (t80) cc_final: 0.3897 (m-80) REVERT: E 249 MET cc_start: 0.8947 (ttm) cc_final: 0.8274 (tmm) REVERT: F 96 ILE cc_start: 0.9328 (mm) cc_final: 0.9079 (mm) REVERT: F 116 SER cc_start: 0.9217 (p) cc_final: 0.8724 (p) REVERT: F 117 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8029 (p0) REVERT: F 160 MET cc_start: 0.8813 (mmt) cc_final: 0.8260 (mmm) REVERT: F 197 GLN cc_start: 0.8912 (tp40) cc_final: 0.8436 (tp40) REVERT: G 117 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8662 (p0) REVERT: G 171 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5007 (m-10) REVERT: G 179 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6987 (ptpp) REVERT: G 243 LYS cc_start: 0.6495 (mmtt) cc_final: 0.5664 (mptt) REVERT: G 257 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8173 (ttp80) REVERT: G 264 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7566 (ptm-80) REVERT: H 105 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8406 (m-10) REVERT: H 171 TYR cc_start: 0.4554 (t80) cc_final: 0.3949 (m-80) REVERT: H 179 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6251 (ptpp) REVERT: H 248 ASN cc_start: 0.8781 (m-40) cc_final: 0.8384 (m110) REVERT: H 249 MET cc_start: 0.8947 (ttm) cc_final: 0.8319 (tmm) REVERT: H 264 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7344 (tmm-80) REVERT: I 117 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8276 (p0) REVERT: I 264 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7513 (ttp80) REVERT: J 96 ILE cc_start: 0.9256 (mm) cc_final: 0.8979 (mm) REVERT: J 160 MET cc_start: 0.8911 (mmt) cc_final: 0.8312 (mmm) REVERT: J 171 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: K 105 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: K 118 ILE cc_start: 0.9326 (mm) cc_final: 0.9077 (mm) REVERT: K 160 MET cc_start: 0.8974 (mmm) cc_final: 0.8272 (mmm) REVERT: K 171 TYR cc_start: 0.5481 (OUTLIER) cc_final: 0.4642 (m-10) REVERT: K 187 ARG cc_start: 0.4699 (tpt170) cc_final: 0.3881 (tpt170) REVERT: L 96 ILE cc_start: 0.9417 (mm) cc_final: 0.9192 (mm) REVERT: L 117 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8353 (p0) REVERT: L 136 SER cc_start: 0.9224 (p) cc_final: 0.8929 (p) REVERT: L 160 MET cc_start: 0.8687 (mmt) cc_final: 0.8182 (mmm) REVERT: L 171 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4338 (m-80) REVERT: L 185 VAL cc_start: 0.8935 (t) cc_final: 0.8623 (p) REVERT: L 255 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8732 (mt-10) REVERT: M 84 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9120 (t80) REVERT: M 96 ILE cc_start: 0.9261 (mm) cc_final: 0.8953 (mm) REVERT: M 160 MET cc_start: 0.8833 (mmt) cc_final: 0.8350 (mmm) REVERT: M 197 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8950 (tp40) REVERT: M 214 LYS cc_start: 0.8975 (tttt) cc_final: 0.8697 (ttpt) REVERT: M 249 MET cc_start: 0.9070 (ttm) cc_final: 0.8614 (tmm) REVERT: M 259 LYS cc_start: 0.1152 (mttt) cc_final: 0.0641 (tttp) REVERT: N 117 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8708 (p0) REVERT: N 138 TYR cc_start: 0.5593 (m-10) cc_final: 0.5372 (m-80) REVERT: N 161 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8372 (mm) REVERT: N 171 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.4988 (m-10) outliers start: 154 outliers final: 114 residues processed: 645 average time/residue: 0.4210 time to fit residues: 406.1394 Evaluate side-chains 669 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 530 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 105 TYR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 127 ASN Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 172 ASP Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 244 ASN Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 127 ASN Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain K residue 268 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 76 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain M residue 84 PHE Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 132 VAL Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 237 ILE Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 84 PHE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 268 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 4.9990 chunk 319 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 221 optimal weight: 0.6980 chunk 334 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 266 optimal weight: 0.0040 chunk 27 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 250 GLN ** K 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28448 Z= 0.183 Angle : 0.714 11.299 38304 Z= 0.355 Chirality : 0.043 0.243 4144 Planarity : 0.004 0.041 5054 Dihedral : 5.877 56.406 3722 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 4.30 % Allowed : 25.13 % Favored : 70.57 % 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: -1.01 (0.15), residues: 3374 helix: 1.92 (0.15), residues: 1456 sheet: -0.75 (0.26), residues: 434 loop : -3.57 (0.14), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 89 PHE 0.010 0.001 PHE M 120 TYR 0.018 0.001 TYR L 199 ARG 0.018 0.001 ARG C 213 ********************** 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 682 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 547 time to evaluate : 3.294 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: A 117 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8122 (p0) REVERT: A 136 SER cc_start: 0.9116 (p) cc_final: 0.8871 (p) REVERT: A 171 TYR cc_start: 0.5002 (OUTLIER) cc_final: 0.4416 (m-80) REVERT: A 197 GLN cc_start: 0.8963 (tp40) cc_final: 0.8470 (tp40) REVERT: A 255 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8367 (mt-10) REVERT: A 260 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7882 (pp) REVERT: B 105 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8484 (m-10) REVERT: B 118 ILE cc_start: 0.9398 (mm) cc_final: 0.9149 (mm) REVERT: B 160 MET cc_start: 0.8858 (mmm) cc_final: 0.8337 (mmm) REVERT: B 171 TYR cc_start: 0.5848 (t80) cc_final: 0.5506 (m-10) REVERT: B 257 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8132 (ttp80) REVERT: B 259 LYS cc_start: 0.2657 (OUTLIER) cc_final: 0.1926 (tttm) REVERT: C 62 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7317 (tmm) REVERT: C 116 SER cc_start: 0.9141 (p) cc_final: 0.8774 (p) REVERT: C 118 ILE cc_start: 0.9302 (mm) cc_final: 0.8878 (mm) REVERT: C 179 LYS cc_start: 0.6908 (tttt) cc_final: 0.6547 (ptpp) REVERT: C 213 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7299 (ttp80) REVERT: D 133 MET cc_start: 0.8707 (ttp) cc_final: 0.8489 (tmm) REVERT: D 171 TYR cc_start: 0.5139 (OUTLIER) cc_final: 0.4541 (m-10) REVERT: D 179 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6772 (ptpp) REVERT: E 84 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8307 (t80) REVERT: E 105 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8362 (m-80) REVERT: E 171 TYR cc_start: 0.4578 (t80) cc_final: 0.3738 (m-80) REVERT: E 249 MET cc_start: 0.8929 (ttm) cc_final: 0.8250 (tmm) REVERT: F 96 ILE cc_start: 0.9314 (mm) cc_final: 0.9053 (mm) REVERT: F 116 SER cc_start: 0.9116 (p) cc_final: 0.8557 (p) REVERT: F 117 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7863 (p0) REVERT: F 160 MET cc_start: 0.8771 (mmt) cc_final: 0.8148 (mmm) REVERT: F 197 GLN cc_start: 0.8873 (tp40) cc_final: 0.8467 (tp40) REVERT: G 117 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8699 (p0) REVERT: G 171 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.4621 (m-10) REVERT: G 179 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6710 (ptpp) REVERT: G 187 ARG cc_start: 0.5518 (tpt170) cc_final: 0.5264 (ttp-170) REVERT: G 243 LYS cc_start: 0.6370 (mmtt) cc_final: 0.5607 (mptt) REVERT: G 257 ARG cc_start: 0.8437 (ttm170) cc_final: 0.8101 (ttp80) REVERT: H 84 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8446 (t80) REVERT: H 105 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: H 171 TYR cc_start: 0.4499 (t80) cc_final: 0.3774 (m-80) REVERT: H 179 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.5918 (ptpp) REVERT: H 249 MET cc_start: 0.8935 (ttm) cc_final: 0.8288 (tmm) REVERT: H 264 ARG cc_start: 0.7419 (ttp80) cc_final: 0.6996 (ttp80) REVERT: I 117 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8084 (p0) REVERT: I 133 MET cc_start: 0.8668 (ttp) cc_final: 0.8411 (tmm) REVERT: I 264 ARG cc_start: 0.7407 (ttp80) cc_final: 0.6883 (ttp80) REVERT: J 160 MET cc_start: 0.8769 (mmt) cc_final: 0.8332 (mmm) REVERT: J 171 TYR cc_start: 0.5797 (OUTLIER) cc_final: 0.4807 (m-80) REVERT: J 213 ARG cc_start: 0.5030 (tpt170) cc_final: 0.4809 (ttm170) REVERT: K 105 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: K 118 ILE cc_start: 0.9311 (mm) cc_final: 0.9061 (mm) REVERT: K 160 MET cc_start: 0.9049 (mmm) cc_final: 0.8429 (mmm) REVERT: K 171 TYR cc_start: 0.5208 (OUTLIER) cc_final: 0.4621 (m-10) REVERT: K 187 ARG cc_start: 0.4774 (tpt170) cc_final: 0.4199 (tpt170) REVERT: K 243 LYS cc_start: 0.7482 (mptt) cc_final: 0.7092 (mptt) REVERT: L 96 ILE cc_start: 0.9405 (mm) cc_final: 0.9165 (mm) REVERT: L 117 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8217 (p0) REVERT: L 136 SER cc_start: 0.9247 (p) cc_final: 0.8956 (p) REVERT: L 160 MET cc_start: 0.8694 (mmt) cc_final: 0.8161 (mmm) REVERT: L 171 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.4223 (m-80) REVERT: L 197 GLN cc_start: 0.8670 (tp40) cc_final: 0.8222 (tp40) REVERT: L 255 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8720 (mt-10) REVERT: M 84 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.9056 (t80) REVERT: M 85 LYS cc_start: 0.5890 (tptt) cc_final: 0.5520 (tptt) REVERT: M 96 ILE cc_start: 0.9288 (mm) cc_final: 0.9001 (mm) REVERT: M 160 MET cc_start: 0.8827 (mmt) cc_final: 0.8337 (mmm) REVERT: M 197 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8851 (tp40) REVERT: M 214 LYS cc_start: 0.9011 (tttt) cc_final: 0.8782 (ttpt) REVERT: M 233 ARG cc_start: 0.4032 (ttm170) cc_final: 0.3481 (tpt-90) REVERT: M 249 MET cc_start: 0.8792 (ttm) cc_final: 0.8390 (tmm) REVERT: N 117 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8697 (p0) REVERT: N 161 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7828 (mm) REVERT: N 171 TYR cc_start: 0.5556 (OUTLIER) cc_final: 0.4920 (m-10) outliers start: 135 outliers final: 97 residues processed: 635 average time/residue: 0.4342 time to fit residues: 411.3277 Evaluate side-chains 659 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 534 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 257 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 151 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 171 TYR Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 268 TYR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain E residue 127 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 268 TYR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 151 PHE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 171 TYR Chi-restraints excluded: chain G residue 179 LYS Chi-restraints excluded: chain G residue 212 THR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 179 LYS Chi-restraints excluded: chain H residue 268 TYR Chi-restraints excluded: chain I residue 39 VAL Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 117 ASP Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 131 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 151 PHE Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 268 TYR Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 117 ASP Chi-restraints excluded: chain J residue 127 ASN Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 171 TYR Chi-restraints excluded: chain J residue 268 TYR Chi-restraints excluded: chain K residue 80 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 105 TYR Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 127 ASN Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 133 MET Chi-restraints excluded: chain K residue 151 PHE Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 171 TYR Chi-restraints excluded: chain K residue 268 TYR Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 105 TYR Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 131 VAL Chi-restraints excluded: chain L residue 151 PHE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 171 TYR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain M residue 84 PHE Chi-restraints excluded: chain M residue 117 ASP Chi-restraints excluded: chain M residue 153 VAL Chi-restraints excluded: chain M residue 268 TYR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 84 PHE Chi-restraints excluded: chain N residue 117 ASP Chi-restraints excluded: chain N residue 131 VAL Chi-restraints excluded: chain N residue 151 PHE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 171 TYR Chi-restraints excluded: chain N residue 268 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.7980 chunk 283 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 245 optimal weight: 0.0060 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** D 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 261 GLN ** K 180 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.117211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105724 restraints weight = 92761.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107296 restraints weight = 50730.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108366 restraints weight = 33795.735| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28448 Z= 0.179 Angle : 0.704 11.338 38304 Z= 0.350 Chirality : 0.042 0.221 4144 Planarity : 0.004 0.042 5054 Dihedral : 5.697 57.955 3722 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 4.18 % Allowed : 25.32 % Favored : 70.50 % 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: -0.94 (0.16), residues: 3374 helix: 1.98 (0.15), residues: 1456 sheet: -0.71 (0.26), residues: 434 loop : -3.52 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 89 PHE 0.011 0.001 PHE M 120 TYR 0.017 0.001 TYR L 199 ARG 0.013 0.001 ARG G 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7634.76 seconds wall clock time: 141 minutes 13.52 seconds (8473.52 seconds total)