Starting phenix.real_space_refine on Sat Mar 7 09:36:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yto_10920/03_2026/6yto_10920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yto_10920/03_2026/6yto_10920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6yto_10920/03_2026/6yto_10920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yto_10920/03_2026/6yto_10920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yto_10920/03_2026/6yto_10920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yto_10920/03_2026/6yto_10920.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.005 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 400 5.16 5 C 26800 2.51 5 N 6980 2.21 5 O 7440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41620 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "E" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "F" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "G" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "I" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "J" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "K" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "M" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "O" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "P" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "Q" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "T" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Time building chain proxies: 10.38, per 1000 atoms: 0.25 Number of scatterers: 41620 At special positions: 0 Unit cell: (135.34, 135.34, 210.38, 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 400 16.00 O 7440 8.00 N 6980 7.00 C 26800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.04 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.04 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.04 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.04 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.04 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.04 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.04 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.04 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10160 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.755A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 167 through 210 Processing helix chain 'A' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.755A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 167 through 210 Processing helix chain 'B' and resid 214 through 253 removed outlier: 3.582A pdb=" N HIS B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.905A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.755A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.610A pdb=" N GLY C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 167 through 210 Processing helix chain 'C' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.905A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.755A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 167 through 210 Processing helix chain 'D' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.754A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 167 through 210 Processing helix chain 'E' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.755A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 167 through 210 Processing helix chain 'F' and resid 214 through 253 removed outlier: 3.582A pdb=" N HIS F 218 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.754A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 76 " --> pdb=" O SER G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY G 126 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 167 through 210 Processing helix chain 'G' and resid 214 through 253 removed outlier: 3.582A pdb=" N HIS G 218 " --> pdb=" O THR G 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 276 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.905A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.754A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 167 through 210 Processing helix chain 'H' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS H 218 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS H 219 " --> pdb=" O SER H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 276 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.754A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY I 126 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 167 through 210 Processing helix chain 'I' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS I 218 " --> pdb=" O THR I 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 276 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.904A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.755A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 76 " --> pdb=" O SER J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 167 through 210 Processing helix chain 'J' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS J 218 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 276 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.898A pdb=" N PHE K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.738A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY K 126 " --> pdb=" O THR K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.831A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE K 160 " --> pdb=" O ILE K 156 " (cutoff:3.500A) Proline residue: K 161 - end of helix Processing helix chain 'K' and resid 167 through 210 Processing helix chain 'K' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS K 218 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS K 219 " --> pdb=" O SER K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 276 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 removed outlier: 3.898A pdb=" N PHE L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.737A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 112 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY L 126 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE L 160 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Proline residue: L 161 - end of helix Processing helix chain 'L' and resid 167 through 210 Processing helix chain 'L' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS L 218 " --> pdb=" O THR L 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS L 219 " --> pdb=" O SER L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 276 Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 70 removed outlier: 3.899A pdb=" N PHE M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.738A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 112 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE M 160 " --> pdb=" O ILE M 156 " (cutoff:3.500A) Proline residue: M 161 - end of helix Processing helix chain 'M' and resid 167 through 210 Processing helix chain 'M' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS M 218 " --> pdb=" O THR M 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 276 Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 removed outlier: 3.899A pdb=" N PHE N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.738A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 112 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY N 126 " --> pdb=" O THR N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) Proline residue: N 161 - end of helix Processing helix chain 'N' and resid 167 through 210 Processing helix chain 'N' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS N 219 " --> pdb=" O SER N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 276 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 38 removed outlier: 3.686A pdb=" N ILE O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 70 removed outlier: 3.898A pdb=" N PHE O 55 " --> pdb=" O TYR O 51 " (cutoff:3.500A) Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.737A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 112 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY O 126 " --> pdb=" O THR O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.831A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE O 160 " --> pdb=" O ILE O 156 " (cutoff:3.500A) Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 167 through 210 Processing helix chain 'O' and resid 214 through 253 removed outlier: 3.601A pdb=" N HIS O 218 " --> pdb=" O THR O 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS O 219 " --> pdb=" O SER O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 38 removed outlier: 3.686A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.899A pdb=" N PHE P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.737A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 112 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY P 126 " --> pdb=" O THR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE P 160 " --> pdb=" O ILE P 156 " (cutoff:3.500A) Proline residue: P 161 - end of helix Processing helix chain 'P' and resid 167 through 210 Processing helix chain 'P' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS P 218 " --> pdb=" O THR P 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 276 Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 70 removed outlier: 3.898A pdb=" N PHE Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.738A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 112 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.607A pdb=" N GLY Q 126 " --> pdb=" O THR Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE Q 160 " --> pdb=" O ILE Q 156 " (cutoff:3.500A) Proline residue: Q 161 - end of helix Processing helix chain 'Q' and resid 167 through 210 Processing helix chain 'Q' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS Q 218 " --> pdb=" O THR Q 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 276 Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE R 19 " --> pdb=" O ASN R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 removed outlier: 3.899A pdb=" N PHE R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.738A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 112 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE R 160 " --> pdb=" O ILE R 156 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'R' and resid 214 through 253 removed outlier: 3.601A pdb=" N HIS R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 276 Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE S 19 " --> pdb=" O ASN S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 removed outlier: 3.898A pdb=" N PHE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.738A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 112 Processing helix chain 'S' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY S 126 " --> pdb=" O THR S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE S 160 " --> pdb=" O ILE S 156 " (cutoff:3.500A) Proline residue: S 161 - end of helix Processing helix chain 'S' and resid 167 through 210 Processing helix chain 'S' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS S 218 " --> pdb=" O THR S 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS S 219 " --> pdb=" O SER S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 276 Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE T 19 " --> pdb=" O ASN T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 removed outlier: 3.899A pdb=" N PHE T 55 " --> pdb=" O TYR T 51 " (cutoff:3.500A) Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.737A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 112 Processing helix chain 'T' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY T 126 " --> pdb=" O THR T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 3.831A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE T 160 " --> pdb=" O ILE T 156 " (cutoff:3.500A) Proline residue: T 161 - end of helix Processing helix chain 'T' and resid 167 through 210 Processing helix chain 'T' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS T 218 " --> pdb=" O THR T 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS T 219 " --> pdb=" O SER T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 276 3171 hydrogen bonds defined for protein. 9513 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: 7.75 Time building geometry restraints manager: 4.88 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: 13125 1.34 - 1.46: 8828 1.46 - 1.58: 20127 1.58 - 1.70: 0 1.70 - 1.82: 500 Bond restraints: 42580 Sorted by residual: bond pdb=" CB CYS O 41 " pdb=" SG CYS O 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CB CYS P 41 " pdb=" SG CYS P 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB CYS R 41 " pdb=" SG CYS R 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB CYS Q 41 " pdb=" SG CYS Q 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB CYS N 41 " pdb=" SG CYS N 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.37e+00 ... (remaining 42575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 55983 1.60 - 3.19: 1474 3.19 - 4.79: 167 4.79 - 6.39: 146 6.39 - 7.99: 50 Bond angle restraints: 57820 Sorted by residual: angle pdb=" CA ARG M 164 " pdb=" CB ARG M 164 " pdb=" CG ARG M 164 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA ARG N 164 " pdb=" CB ARG N 164 " pdb=" CG ARG N 164 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG S 164 " pdb=" CB ARG S 164 " pdb=" CG ARG S 164 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG R 164 " pdb=" CB ARG R 164 " pdb=" CG ARG R 164 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG L 164 " pdb=" CB ARG L 164 " pdb=" CG ARG L 164 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 ... (remaining 57815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 22968 17.60 - 35.20: 2002 35.20 - 52.80: 390 52.80 - 70.40: 20 70.40 - 88.00: 60 Dihedral angle restraints: 25440 sinusoidal: 9820 harmonic: 15620 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 131 " pdb=" CB CYS B 131 " ideal model delta sinusoidal sigma weight residual -86.00 -174.00 88.00 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS A 41 " pdb=" SG CYS A 41 " pdb=" SG CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sinusoidal sigma weight residual -86.00 -174.00 88.00 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 131 " pdb=" CB CYS G 131 " ideal model delta sinusoidal sigma weight residual -86.00 -173.99 87.99 1 1.00e+01 1.00e-02 9.26e+01 ... (remaining 25437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4161 0.036 - 0.071: 2017 0.071 - 0.107: 396 0.107 - 0.143: 134 0.143 - 0.178: 32 Chirality restraints: 6740 Sorted by residual: chirality pdb=" CA CYS A 43 " pdb=" N CYS A 43 " pdb=" C CYS A 43 " pdb=" CB CYS A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA CYS J 43 " pdb=" N CYS J 43 " pdb=" C CYS J 43 " pdb=" CB CYS J 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA CYS F 43 " pdb=" N CYS F 43 " pdb=" C CYS F 43 " pdb=" CB CYS F 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 6737 not shown) Planarity restraints: 7180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE S 160 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.30e+00 pdb=" CG PHE S 160 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE S 160 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE S 160 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE S 160 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE S 160 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE S 160 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 160 " 0.019 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE P 160 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE P 160 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE P 160 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE P 160 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE P 160 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE P 160 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 160 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE T 160 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE T 160 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE T 160 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE T 160 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE T 160 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE T 160 " -0.000 2.00e-02 2.50e+03 ... (remaining 7177 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 11152 2.81 - 3.33: 44227 3.33 - 3.85: 66822 3.85 - 4.38: 67509 4.38 - 4.90: 121056 Nonbonded interactions: 310766 Sorted by model distance: nonbonded pdb=" OH TYR B 142 " pdb=" OE1 GLU B 176 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR G 142 " pdb=" OE1 GLU G 176 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR I 142 " pdb=" OE1 GLU I 176 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR H 142 " pdb=" OE1 GLU H 176 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 142 " pdb=" OE1 GLU A 176 " model vdw 2.283 3.040 ... (remaining 310761 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 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' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.060 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 36.840 Find NCS groups from input model: 0.780 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 42620 Z= 0.230 Angle : 0.709 7.985 57900 Z= 0.389 Chirality : 0.043 0.178 6740 Planarity : 0.005 0.054 7180 Dihedral : 13.409 80.955 15160 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.11), residues: 5260 helix: 0.79 (0.08), residues: 4040 sheet: None (None), residues: 0 loop : -2.89 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 164 TYR 0.011 0.002 TYR K 81 PHE 0.040 0.002 PHE S 160 TRP 0.016 0.002 TRP O 190 HIS 0.003 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00497 (42580) covalent geometry : angle 0.70392 (57820) SS BOND : bond 0.00446 ( 40) SS BOND : angle 2.39776 ( 80) hydrogen bonds : bond 0.12148 ( 3171) hydrogen bonds : angle 4.74129 ( 9513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1303 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 CYS cc_start: 0.6847 (m) cc_final: 0.6536 (p) REVERT: A 174 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8550 (tmm-80) REVERT: A 184 GLN cc_start: 0.8941 (mt0) cc_final: 0.8617 (tp40) REVERT: B 15 ASN cc_start: 0.8516 (t0) cc_final: 0.8221 (t0) REVERT: B 104 PHE cc_start: 0.7699 (t80) cc_final: 0.7475 (t80) REVERT: B 153 ARG cc_start: 0.9053 (ttp80) cc_final: 0.8750 (ttt180) REVERT: B 172 LEU cc_start: 0.8977 (tt) cc_final: 0.8677 (tp) REVERT: B 174 ARG cc_start: 0.8524 (ttp80) cc_final: 0.7744 (ttp-170) REVERT: B 183 TYR cc_start: 0.9311 (t80) cc_final: 0.8920 (t80) REVERT: B 184 GLN cc_start: 0.8998 (mt0) cc_final: 0.8536 (tp40) REVERT: B 233 GLU cc_start: 0.8494 (tp30) cc_final: 0.8130 (tm-30) REVERT: B 237 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8247 (tm-30) REVERT: B 245 MET cc_start: 0.8260 (ttm) cc_final: 0.7955 (mtm) REVERT: C 74 MET cc_start: 0.8050 (tmm) cc_final: 0.7444 (tmm) REVERT: C 153 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8895 (ttt180) REVERT: C 162 CYS cc_start: 0.7512 (p) cc_final: 0.7175 (t) REVERT: C 184 GLN cc_start: 0.9037 (mt0) cc_final: 0.8474 (tp40) REVERT: D 51 TYR cc_start: 0.9217 (t80) cc_final: 0.8963 (t80) REVERT: D 154 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8805 (mm-30) REVERT: D 183 TYR cc_start: 0.9130 (t80) cc_final: 0.8714 (t80) REVERT: D 245 MET cc_start: 0.8144 (ttm) cc_final: 0.7864 (mtm) REVERT: D 249 LYS cc_start: 0.8728 (tttt) cc_final: 0.8302 (ttmm) REVERT: E 104 PHE cc_start: 0.7909 (t80) cc_final: 0.7365 (t80) REVERT: E 128 TYR cc_start: 0.8887 (m-10) cc_final: 0.8634 (m-80) REVERT: E 201 LEU cc_start: 0.9000 (tp) cc_final: 0.8790 (tt) REVERT: E 265 ARG cc_start: 0.7841 (ttt90) cc_final: 0.6781 (tpt170) REVERT: F 78 THR cc_start: 0.7688 (m) cc_final: 0.7265 (t) REVERT: F 153 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8739 (ttt180) REVERT: F 162 CYS cc_start: 0.7786 (p) cc_final: 0.7352 (t) REVERT: F 174 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8523 (ptm-80) REVERT: G 74 MET cc_start: 0.8412 (tmm) cc_final: 0.7919 (tmm) REVERT: G 153 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8784 (ttt180) REVERT: G 174 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8090 (ttp-170) REVERT: H 128 TYR cc_start: 0.8625 (m-10) cc_final: 0.8228 (m-80) REVERT: H 174 ARG cc_start: 0.8549 (ttp80) cc_final: 0.7772 (ttp-170) REVERT: H 187 MET cc_start: 0.9151 (mmp) cc_final: 0.8804 (mmm) REVERT: H 192 LEU cc_start: 0.9170 (tp) cc_final: 0.8894 (tt) REVERT: H 237 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8429 (tm-30) REVERT: I 74 MET cc_start: 0.8172 (tmm) cc_final: 0.7259 (tmm) REVERT: I 107 ILE cc_start: 0.9214 (mm) cc_final: 0.8827 (tp) REVERT: I 146 ASP cc_start: 0.7777 (p0) cc_final: 0.7575 (p0) REVERT: I 153 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8802 (ttt180) REVERT: I 174 ARG cc_start: 0.8697 (ttp80) cc_final: 0.7510 (ttp-170) REVERT: J 78 THR cc_start: 0.7826 (m) cc_final: 0.7497 (t) REVERT: J 174 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8543 (ttp80) REVERT: J 184 GLN cc_start: 0.8913 (mt0) cc_final: 0.8627 (tp40) REVERT: J 244 MET cc_start: 0.9108 (tpt) cc_final: 0.8892 (tpt) REVERT: J 262 LYS cc_start: 0.8432 (mmmm) cc_final: 0.8135 (mmmm) REVERT: K 26 LEU cc_start: 0.9146 (tp) cc_final: 0.8890 (tp) REVERT: K 74 MET cc_start: 0.8313 (tmm) cc_final: 0.7932 (tmm) REVERT: K 107 ILE cc_start: 0.9392 (mm) cc_final: 0.9087 (tp) REVERT: K 152 LYS cc_start: 0.9310 (tptt) cc_final: 0.9107 (tppp) REVERT: K 153 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8705 (ttt180) REVERT: K 221 TRP cc_start: 0.8953 (t60) cc_final: 0.8730 (t60) REVERT: K 245 MET cc_start: 0.8226 (ttm) cc_final: 0.7932 (mtm) REVERT: L 153 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8500 (ttt180) REVERT: L 160 PHE cc_start: 0.8550 (m-80) cc_final: 0.8196 (m-80) REVERT: L 183 TYR cc_start: 0.9277 (t80) cc_final: 0.9062 (t80) REVERT: L 184 GLN cc_start: 0.8825 (mt0) cc_final: 0.8401 (tp40) REVERT: L 187 MET cc_start: 0.8924 (mmp) cc_final: 0.8656 (mmt) REVERT: L 255 ILE cc_start: 0.9439 (mm) cc_final: 0.9230 (mp) REVERT: M 153 ARG cc_start: 0.9085 (ttp80) cc_final: 0.8752 (ttt180) REVERT: M 160 PHE cc_start: 0.8307 (m-80) cc_final: 0.7431 (m-80) REVERT: M 245 MET cc_start: 0.8128 (ttm) cc_final: 0.7682 (mtm) REVERT: N 15 ASN cc_start: 0.8388 (t0) cc_final: 0.8065 (t0) REVERT: N 183 TYR cc_start: 0.8991 (t80) cc_final: 0.8647 (t80) REVERT: N 184 GLN cc_start: 0.8961 (mt0) cc_final: 0.8202 (mm-40) REVERT: O 237 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8651 (tm-30) REVERT: O 249 LYS cc_start: 0.8797 (tttt) cc_final: 0.8553 (ttpp) REVERT: P 74 MET cc_start: 0.7884 (tmm) cc_final: 0.7515 (tmm) REVERT: P 128 TYR cc_start: 0.8753 (m-10) cc_final: 0.8515 (m-80) REVERT: P 245 MET cc_start: 0.8353 (ttm) cc_final: 0.8063 (mtm) REVERT: Q 153 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8785 (ttt180) REVERT: Q 160 PHE cc_start: 0.8277 (m-80) cc_final: 0.7826 (m-80) REVERT: Q 174 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8431 (ttp80) REVERT: Q 184 GLN cc_start: 0.9055 (mt0) cc_final: 0.8511 (tp40) REVERT: Q 245 MET cc_start: 0.8232 (ttm) cc_final: 0.7827 (mtm) REVERT: R 70 LEU cc_start: 0.9111 (mp) cc_final: 0.8829 (tt) REVERT: R 74 MET cc_start: 0.8194 (tmm) cc_final: 0.7382 (tmm) REVERT: R 146 ASP cc_start: 0.7893 (p0) cc_final: 0.7655 (p0) REVERT: R 153 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8605 (ttt180) REVERT: R 174 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8556 (ttp80) REVERT: R 201 LEU cc_start: 0.9011 (tp) cc_final: 0.8790 (tt) REVERT: R 233 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8439 (tm-30) REVERT: R 249 LYS cc_start: 0.8948 (tttt) cc_final: 0.8702 (ttmm) REVERT: S 61 LEU cc_start: 0.8572 (tt) cc_final: 0.8330 (mt) REVERT: S 245 MET cc_start: 0.8280 (ttm) cc_final: 0.8056 (mtm) REVERT: T 61 LEU cc_start: 0.8524 (tt) cc_final: 0.8208 (mt) REVERT: T 62 ILE cc_start: 0.9261 (mm) cc_final: 0.9031 (tp) REVERT: T 174 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8387 (ttp80) REVERT: T 237 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8603 (tm-30) REVERT: T 245 MET cc_start: 0.8241 (ttm) cc_final: 0.7993 (mtm) REVERT: T 249 LYS cc_start: 0.8735 (tttt) cc_final: 0.8510 (ttpp) outliers start: 0 outliers final: 0 residues processed: 1303 average time/residue: 0.2622 time to fit residues: 540.8398 Evaluate side-chains 675 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 675 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 4.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.0970 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 516 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 184 GLN A 227 ASN B 20 ASN B 48 ASN B 184 GLN B 217 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 184 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 184 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN G 20 ASN G 184 GLN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN H 184 GLN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 ASN I 184 GLN ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 ASN J 184 GLN J 227 ASN K 184 GLN L 20 ASN L 184 GLN M 20 ASN M 184 GLN M 227 ASN N 20 ASN N 184 GLN O 20 ASN O 184 GLN P 184 GLN Q 20 ASN Q 48 ASN Q 184 GLN R 184 GLN R 227 ASN S 20 ASN S 184 GLN S 234 GLN T 20 ASN T 184 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105283 restraints weight = 75375.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107614 restraints weight = 46853.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109113 restraints weight = 34755.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110104 restraints weight = 28881.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.110822 restraints weight = 25825.270| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 42620 Z= 0.146 Angle : 0.568 6.341 57900 Z= 0.297 Chirality : 0.039 0.164 6740 Planarity : 0.004 0.054 7180 Dihedral : 3.828 15.318 5700 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.12), residues: 5260 helix: 1.79 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.97 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 174 TYR 0.021 0.002 TYR I 51 PHE 0.019 0.001 PHE L 232 TRP 0.011 0.001 TRP H 75 HIS 0.002 0.001 HIS T 246 Details of bonding type rmsd covalent geometry : bond 0.00293 (42580) covalent geometry : angle 0.56350 (57820) SS BOND : bond 0.00570 ( 40) SS BOND : angle 1.93526 ( 80) hydrogen bonds : bond 0.05530 ( 3171) hydrogen bonds : angle 3.97927 ( 9513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1086 time to evaluate : 1.462 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 14 ARG cc_start: 0.8028 (ptt90) cc_final: 0.7536 (ptt90) REVERT: A 122 THR cc_start: 0.9213 (t) cc_final: 0.8899 (t) REVERT: A 128 TYR cc_start: 0.9047 (m-10) cc_final: 0.8514 (m-80) REVERT: A 184 GLN cc_start: 0.9002 (mt0) cc_final: 0.8507 (tp40) REVERT: A 208 LYS cc_start: 0.8838 (tppt) cc_final: 0.8118 (tmmt) REVERT: B 41 CYS cc_start: 0.5983 (t) cc_final: 0.5687 (t) REVERT: B 51 TYR cc_start: 0.9215 (t80) cc_final: 0.8902 (t80) REVERT: B 104 PHE cc_start: 0.7688 (t80) cc_final: 0.7164 (t80) REVERT: B 128 TYR cc_start: 0.8912 (m-10) cc_final: 0.8708 (m-80) REVERT: B 183 TYR cc_start: 0.9156 (t80) cc_final: 0.8928 (t80) REVERT: B 184 GLN cc_start: 0.8991 (mt0) cc_final: 0.8507 (tp-100) REVERT: B 233 GLU cc_start: 0.8416 (tp30) cc_final: 0.8073 (tm-30) REVERT: B 279 THR cc_start: 0.7581 (m) cc_final: 0.7247 (p) REVERT: C 14 ARG cc_start: 0.7910 (ptt90) cc_final: 0.7673 (ppt170) REVERT: C 41 CYS cc_start: 0.5870 (t) cc_final: 0.5400 (t) REVERT: C 77 ILE cc_start: 0.8787 (tp) cc_final: 0.8549 (mm) REVERT: C 128 TYR cc_start: 0.9073 (m-10) cc_final: 0.8813 (m-80) REVERT: C 184 GLN cc_start: 0.8983 (mt0) cc_final: 0.8484 (tp-100) REVERT: C 237 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8407 (tm-30) REVERT: C 259 GLU cc_start: 0.6439 (mp0) cc_final: 0.6207 (mm-30) REVERT: D 41 CYS cc_start: 0.5532 (t) cc_final: 0.5049 (t) REVERT: D 76 THR cc_start: 0.9071 (p) cc_final: 0.8833 (t) REVERT: D 128 TYR cc_start: 0.8955 (m-10) cc_final: 0.8719 (m-80) REVERT: D 153 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8427 (ttt180) REVERT: D 183 TYR cc_start: 0.8991 (t80) cc_final: 0.8541 (t80) REVERT: D 237 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8357 (tm-30) REVERT: D 245 MET cc_start: 0.8047 (ttm) cc_final: 0.7715 (mtm) REVERT: E 77 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8038 (mm) REVERT: E 104 PHE cc_start: 0.8005 (t80) cc_final: 0.7350 (t80) REVERT: E 128 TYR cc_start: 0.9004 (m-10) cc_final: 0.8730 (m-80) REVERT: E 152 LYS cc_start: 0.9117 (tptm) cc_final: 0.8861 (tppp) REVERT: E 155 GLU cc_start: 0.8858 (tp30) cc_final: 0.8604 (tm-30) REVERT: E 184 GLN cc_start: 0.9181 (mt0) cc_final: 0.8616 (mm-40) REVERT: E 201 LEU cc_start: 0.9098 (tp) cc_final: 0.8860 (tt) REVERT: E 233 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8333 (tm-30) REVERT: E 249 LYS cc_start: 0.8304 (tttm) cc_final: 0.8091 (tttm) REVERT: F 128 TYR cc_start: 0.8985 (m-10) cc_final: 0.8434 (m-80) REVERT: F 153 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8532 (ttt180) REVERT: F 174 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8399 (ptm-80) REVERT: F 184 GLN cc_start: 0.8952 (mt0) cc_final: 0.8553 (tp-100) REVERT: F 244 MET cc_start: 0.8951 (tpt) cc_final: 0.8613 (tpp) REVERT: G 245 MET cc_start: 0.8330 (ttm) cc_final: 0.8084 (mtm) REVERT: H 187 MET cc_start: 0.8998 (mmp) cc_final: 0.8729 (mmm) REVERT: H 237 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8439 (tm-30) REVERT: I 51 TYR cc_start: 0.9322 (t80) cc_final: 0.9089 (t80) REVERT: I 249 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8348 (ttmm) REVERT: J 128 TYR cc_start: 0.8846 (m-10) cc_final: 0.8633 (m-80) REVERT: J 184 GLN cc_start: 0.8959 (mt0) cc_final: 0.8387 (tp40) REVERT: J 208 LYS cc_start: 0.8800 (tppt) cc_final: 0.8296 (tmmt) REVERT: J 244 MET cc_start: 0.9077 (tpt) cc_final: 0.8850 (tpp) REVERT: J 262 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8118 (mmmm) REVERT: K 26 LEU cc_start: 0.9150 (tp) cc_final: 0.8907 (tp) REVERT: K 77 ILE cc_start: 0.8773 (tp) cc_final: 0.8448 (tp) REVERT: K 78 THR cc_start: 0.6930 (m) cc_final: 0.6444 (m) REVERT: K 107 ILE cc_start: 0.9387 (mm) cc_final: 0.8963 (tp) REVERT: K 160 PHE cc_start: 0.8527 (m-80) cc_final: 0.8294 (m-80) REVERT: K 221 TRP cc_start: 0.8844 (t60) cc_final: 0.8451 (t60) REVERT: K 245 MET cc_start: 0.8138 (ttm) cc_final: 0.7833 (mtm) REVERT: L 129 TYR cc_start: 0.9317 (t80) cc_final: 0.9035 (t80) REVERT: L 160 PHE cc_start: 0.8340 (m-80) cc_final: 0.8011 (m-80) REVERT: L 174 ARG cc_start: 0.8602 (ptm-80) cc_final: 0.8301 (ptm160) REVERT: L 184 GLN cc_start: 0.8935 (mt0) cc_final: 0.8521 (tp40) REVERT: L 208 LYS cc_start: 0.8683 (tppt) cc_final: 0.8174 (tmmt) REVERT: L 244 MET cc_start: 0.9010 (tpt) cc_final: 0.8736 (tpt) REVERT: M 74 MET cc_start: 0.8181 (tmm) cc_final: 0.7916 (tpt) REVERT: M 160 PHE cc_start: 0.8329 (m-80) cc_final: 0.7622 (m-80) REVERT: M 184 GLN cc_start: 0.9140 (mt0) cc_final: 0.8647 (tp-100) REVERT: M 245 MET cc_start: 0.7918 (ttm) cc_final: 0.7659 (mtm) REVERT: M 271 ASP cc_start: 0.9066 (m-30) cc_final: 0.8836 (m-30) REVERT: N 17 ILE cc_start: 0.9013 (tp) cc_final: 0.8809 (tp) REVERT: N 41 CYS cc_start: 0.5021 (t) cc_final: 0.4721 (t) REVERT: N 116 LEU cc_start: 0.8799 (tt) cc_final: 0.8572 (tt) REVERT: N 183 TYR cc_start: 0.8947 (t80) cc_final: 0.8585 (t80) REVERT: N 184 GLN cc_start: 0.9012 (mt0) cc_final: 0.8221 (mm-40) REVERT: O 187 MET cc_start: 0.9209 (mmp) cc_final: 0.8959 (mmt) REVERT: O 241 ARG cc_start: 0.9026 (tpp80) cc_final: 0.8756 (tpp80) REVERT: O 249 LYS cc_start: 0.8678 (tttt) cc_final: 0.8475 (ttpp) REVERT: P 77 ILE cc_start: 0.8377 (tp) cc_final: 0.8093 (pt) REVERT: P 103 ARG cc_start: 0.8800 (ttp-170) cc_final: 0.8487 (mtm-85) REVERT: P 128 TYR cc_start: 0.8914 (m-10) cc_final: 0.8513 (m-80) REVERT: P 154 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8523 (mm-30) REVERT: P 187 MET cc_start: 0.8999 (mmm) cc_final: 0.8769 (mmm) REVERT: P 245 MET cc_start: 0.8301 (ttm) cc_final: 0.8042 (mtm) REVERT: Q 160 PHE cc_start: 0.8240 (m-80) cc_final: 0.7720 (m-80) REVERT: Q 184 GLN cc_start: 0.9042 (mt0) cc_final: 0.8548 (tp40) REVERT: Q 187 MET cc_start: 0.9130 (mmp) cc_final: 0.8850 (mmt) REVERT: Q 230 GLU cc_start: 0.8447 (tp30) cc_final: 0.8139 (tp30) REVERT: Q 234 GLN cc_start: 0.8305 (mt0) cc_final: 0.8051 (mt0) REVERT: R 187 MET cc_start: 0.8817 (mmm) cc_final: 0.8252 (mmm) REVERT: S 61 LEU cc_start: 0.8644 (tt) cc_final: 0.8334 (mt) REVERT: S 74 MET cc_start: 0.8462 (tpt) cc_final: 0.8198 (tpt) REVERT: S 96 GLU cc_start: 0.5827 (pm20) cc_final: 0.4101 (tm-30) REVERT: T 61 LEU cc_start: 0.8576 (tt) cc_final: 0.8252 (mt) REVERT: T 174 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8200 (ttp80) REVERT: T 187 MET cc_start: 0.9215 (mmp) cc_final: 0.8982 (mmt) REVERT: T 249 LYS cc_start: 0.8619 (tttt) cc_final: 0.8394 (ttpp) outliers start: 4 outliers final: 0 residues processed: 1089 average time/residue: 0.2238 time to fit residues: 406.2100 Evaluate side-chains 701 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 700 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 348 optimal weight: 0.6980 chunk 307 optimal weight: 4.9990 chunk 326 optimal weight: 0.0470 chunk 299 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN B 227 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 48 ASN M 48 ASN M 227 ASN N 227 ASN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099162 restraints weight = 76800.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101429 restraints weight = 48286.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102800 restraints weight = 35801.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.103866 restraints weight = 29803.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104278 restraints weight = 26454.051| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42620 Z= 0.131 Angle : 0.538 6.504 57900 Z= 0.283 Chirality : 0.039 0.155 6740 Planarity : 0.004 0.054 7180 Dihedral : 3.781 22.678 5700 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.12), residues: 5260 helix: 2.19 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.89 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 247 TYR 0.013 0.001 TYR O 81 PHE 0.024 0.001 PHE S 160 TRP 0.011 0.001 TRP G 75 HIS 0.003 0.001 HIS F 246 Details of bonding type rmsd covalent geometry : bond 0.00260 (42580) covalent geometry : angle 0.53563 (57820) SS BOND : bond 0.00229 ( 40) SS BOND : angle 1.39855 ( 80) hydrogen bonds : bond 0.05060 ( 3171) hydrogen bonds : angle 3.75702 ( 9513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1075 time to evaluate : 1.504 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: A 14 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7520 (ptt90) REVERT: A 184 GLN cc_start: 0.9009 (mt0) cc_final: 0.8403 (tp40) REVERT: A 208 LYS cc_start: 0.8847 (tppt) cc_final: 0.8128 (tmmt) REVERT: A 228 GLU cc_start: 0.8925 (pp20) cc_final: 0.8636 (tm-30) REVERT: B 41 CYS cc_start: 0.6120 (t) cc_final: 0.5845 (t) REVERT: B 51 TYR cc_start: 0.9197 (t80) cc_final: 0.8991 (t80) REVERT: B 74 MET cc_start: 0.8271 (tpt) cc_final: 0.8067 (tpp) REVERT: B 78 THR cc_start: 0.7323 (m) cc_final: 0.7017 (m) REVERT: B 128 TYR cc_start: 0.8875 (m-10) cc_final: 0.8674 (m-80) REVERT: B 184 GLN cc_start: 0.8883 (mt0) cc_final: 0.8427 (tp-100) REVERT: B 233 GLU cc_start: 0.8460 (tp30) cc_final: 0.8206 (tm-30) REVERT: C 41 CYS cc_start: 0.5825 (t) cc_final: 0.5434 (t) REVERT: C 51 TYR cc_start: 0.9161 (t80) cc_final: 0.8889 (t80) REVERT: C 128 TYR cc_start: 0.9049 (m-10) cc_final: 0.8826 (m-80) REVERT: C 184 GLN cc_start: 0.8951 (mt0) cc_final: 0.8367 (tp40) REVERT: D 41 CYS cc_start: 0.5711 (t) cc_final: 0.5225 (t) REVERT: D 51 TYR cc_start: 0.9158 (t80) cc_final: 0.8953 (t80) REVERT: D 76 THR cc_start: 0.9249 (p) cc_final: 0.8959 (t) REVERT: D 128 TYR cc_start: 0.8946 (m-10) cc_final: 0.8717 (m-80) REVERT: D 183 TYR cc_start: 0.8999 (t80) cc_final: 0.8358 (t80) REVERT: D 184 GLN cc_start: 0.9182 (mt0) cc_final: 0.8274 (tp40) REVERT: D 233 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 237 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 271 ASP cc_start: 0.8864 (m-30) cc_final: 0.8649 (m-30) REVERT: E 77 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8038 (mm) REVERT: E 152 LYS cc_start: 0.9150 (tptm) cc_final: 0.8880 (tppp) REVERT: E 155 GLU cc_start: 0.8878 (tp30) cc_final: 0.8520 (tm-30) REVERT: E 184 GLN cc_start: 0.9227 (mt0) cc_final: 0.8593 (mm-40) REVERT: E 249 LYS cc_start: 0.8136 (tttm) cc_final: 0.7798 (ttmm) REVERT: F 128 TYR cc_start: 0.8945 (m-10) cc_final: 0.8396 (m-80) REVERT: F 129 TYR cc_start: 0.9434 (t80) cc_final: 0.9226 (t80) REVERT: F 174 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8347 (ptm-80) REVERT: F 184 GLN cc_start: 0.9056 (mt0) cc_final: 0.8576 (tp-100) REVERT: G 74 MET cc_start: 0.8515 (tpt) cc_final: 0.8309 (tpp) REVERT: H 61 LEU cc_start: 0.8343 (mt) cc_final: 0.8077 (tt) REVERT: H 74 MET cc_start: 0.8433 (tpt) cc_final: 0.8142 (tpp) REVERT: H 221 TRP cc_start: 0.8051 (t60) cc_final: 0.7412 (t60) REVERT: H 237 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8403 (tm-30) REVERT: H 248 ILE cc_start: 0.8657 (mm) cc_final: 0.8199 (tp) REVERT: I 51 TYR cc_start: 0.9398 (t80) cc_final: 0.9185 (t80) REVERT: J 104 PHE cc_start: 0.7283 (t80) cc_final: 0.7018 (t80) REVERT: J 128 TYR cc_start: 0.8876 (m-10) cc_final: 0.8667 (m-80) REVERT: J 183 TYR cc_start: 0.8995 (t80) cc_final: 0.8500 (t80) REVERT: J 184 GLN cc_start: 0.8918 (mt0) cc_final: 0.8391 (tp40) REVERT: J 208 LYS cc_start: 0.8822 (tppt) cc_final: 0.8305 (tmmt) REVERT: J 244 MET cc_start: 0.9089 (tpt) cc_final: 0.8881 (tpp) REVERT: J 262 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8121 (mmmm) REVERT: K 198 ILE cc_start: 0.8323 (mm) cc_final: 0.8048 (tp) REVERT: K 245 MET cc_start: 0.8190 (ttm) cc_final: 0.7989 (mtm) REVERT: L 129 TYR cc_start: 0.9278 (t80) cc_final: 0.8956 (t80) REVERT: L 160 PHE cc_start: 0.8508 (m-80) cc_final: 0.8287 (m-80) REVERT: L 184 GLN cc_start: 0.8892 (mt0) cc_final: 0.8556 (tp40) REVERT: L 208 LYS cc_start: 0.8630 (tppt) cc_final: 0.8104 (tmmt) REVERT: L 244 MET cc_start: 0.8948 (tpt) cc_final: 0.8615 (tpt) REVERT: M 153 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8798 (ttt180) REVERT: M 160 PHE cc_start: 0.8458 (m-80) cc_final: 0.7770 (m-80) REVERT: M 184 GLN cc_start: 0.9181 (mt0) cc_final: 0.8460 (tp-100) REVERT: M 241 ARG cc_start: 0.8901 (tpp80) cc_final: 0.8639 (tpp80) REVERT: M 271 ASP cc_start: 0.9083 (m-30) cc_final: 0.8715 (m-30) REVERT: N 116 LEU cc_start: 0.8709 (tt) cc_final: 0.8455 (tt) REVERT: N 152 LYS cc_start: 0.9072 (tppp) cc_final: 0.8809 (tppp) REVERT: N 155 GLU cc_start: 0.8748 (tp30) cc_final: 0.8516 (tm-30) REVERT: N 183 TYR cc_start: 0.8966 (t80) cc_final: 0.8726 (t80) REVERT: N 184 GLN cc_start: 0.8925 (mt0) cc_final: 0.7960 (tp40) REVERT: N 233 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8470 (tm-30) REVERT: N 249 LYS cc_start: 0.7954 (tttp) cc_final: 0.7683 (ttmm) REVERT: O 128 TYR cc_start: 0.8669 (m-10) cc_final: 0.8380 (m-80) REVERT: P 103 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.8450 (mtm-85) REVERT: P 128 TYR cc_start: 0.8931 (m-10) cc_final: 0.8487 (m-80) REVERT: P 187 MET cc_start: 0.8923 (mmm) cc_final: 0.8686 (mmm) REVERT: P 245 MET cc_start: 0.8243 (ttm) cc_final: 0.8010 (mtm) REVERT: Q 31 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8776 (tm-30) REVERT: Q 130 GLU cc_start: 0.8876 (pt0) cc_final: 0.8612 (pt0) REVERT: Q 160 PHE cc_start: 0.8402 (m-80) cc_final: 0.7951 (m-80) REVERT: Q 184 GLN cc_start: 0.9051 (mt0) cc_final: 0.8552 (tp40) REVERT: R 74 MET cc_start: 0.8516 (tpp) cc_final: 0.8294 (tpt) REVERT: R 153 ARG cc_start: 0.9085 (ttp80) cc_final: 0.8782 (ttt180) REVERT: R 187 MET cc_start: 0.8628 (mmm) cc_final: 0.8182 (mmm) REVERT: R 251 LEU cc_start: 0.9288 (tp) cc_final: 0.9031 (tt) REVERT: S 74 MET cc_start: 0.8495 (tpt) cc_final: 0.8186 (tpp) REVERT: S 160 PHE cc_start: 0.8077 (m-80) cc_final: 0.7625 (m-80) REVERT: S 221 TRP cc_start: 0.8420 (t60) cc_final: 0.8136 (t60) REVERT: S 279 THR cc_start: 0.6879 (m) cc_final: 0.6670 (p) REVERT: T 61 LEU cc_start: 0.8556 (tt) cc_final: 0.8229 (mt) REVERT: T 128 TYR cc_start: 0.8604 (m-10) cc_final: 0.8218 (m-80) REVERT: T 160 PHE cc_start: 0.7945 (m-80) cc_final: 0.7611 (m-80) REVERT: T 248 ILE cc_start: 0.8769 (mm) cc_final: 0.8530 (tp) outliers start: 4 outliers final: 2 residues processed: 1077 average time/residue: 0.2280 time to fit residues: 407.2454 Evaluate side-chains 728 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 725 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 226 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 410 optimal weight: 0.0770 chunk 126 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 chunk 460 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN F 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN J 48 ASN J 227 ASN L 48 ASN M 227 ASN N 48 ASN N 217 GLN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094488 restraints weight = 78267.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.096614 restraints weight = 49981.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097902 restraints weight = 37482.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098908 restraints weight = 31462.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099386 restraints weight = 28067.315| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 42620 Z= 0.166 Angle : 0.582 6.014 57900 Z= 0.307 Chirality : 0.040 0.161 6740 Planarity : 0.004 0.068 7180 Dihedral : 3.782 22.810 5700 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.13 % Allowed : 3.35 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.12), residues: 5260 helix: 2.37 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.95 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 247 TYR 0.012 0.001 TYR I 81 PHE 0.018 0.002 PHE D 232 TRP 0.013 0.001 TRP C 190 HIS 0.004 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00364 (42580) covalent geometry : angle 0.57990 (57820) SS BOND : bond 0.00529 ( 40) SS BOND : angle 1.42630 ( 80) hydrogen bonds : bond 0.05415 ( 3171) hydrogen bonds : angle 3.86646 ( 9513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1024 time to evaluate : 1.578 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: A 14 ARG cc_start: 0.8087 (ptt90) cc_final: 0.7823 (ppt170) REVERT: A 184 GLN cc_start: 0.9053 (mt0) cc_final: 0.8527 (tp40) REVERT: A 208 LYS cc_start: 0.8845 (tppt) cc_final: 0.8220 (tmmt) REVERT: B 41 CYS cc_start: 0.6112 (t) cc_final: 0.5843 (t) REVERT: B 51 TYR cc_start: 0.9306 (t80) cc_final: 0.9068 (t80) REVERT: B 74 MET cc_start: 0.8285 (tpt) cc_final: 0.8004 (tpp) REVERT: B 128 TYR cc_start: 0.8911 (m-10) cc_final: 0.8673 (m-80) REVERT: B 174 ARG cc_start: 0.8678 (ptm-80) cc_final: 0.8453 (ptt180) REVERT: B 184 GLN cc_start: 0.9025 (mt0) cc_final: 0.8636 (tp40) REVERT: B 228 GLU cc_start: 0.8970 (pp20) cc_final: 0.8768 (pp20) REVERT: B 233 GLU cc_start: 0.8504 (tp30) cc_final: 0.8274 (tm-30) REVERT: B 241 ARG cc_start: 0.9141 (tpp80) cc_final: 0.8697 (mmm-85) REVERT: C 41 CYS cc_start: 0.5629 (t) cc_final: 0.5340 (t) REVERT: C 48 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7546 (t0) REVERT: C 51 TYR cc_start: 0.9371 (t80) cc_final: 0.9049 (t80) REVERT: C 172 LEU cc_start: 0.8653 (tt) cc_final: 0.8436 (mt) REVERT: C 184 GLN cc_start: 0.8944 (mt0) cc_final: 0.8475 (tp40) REVERT: C 271 ASP cc_start: 0.8857 (m-30) cc_final: 0.8609 (m-30) REVERT: D 41 CYS cc_start: 0.5576 (t) cc_final: 0.5333 (t) REVERT: D 128 TYR cc_start: 0.9016 (m-10) cc_final: 0.8784 (m-80) REVERT: D 155 GLU cc_start: 0.8689 (tp30) cc_final: 0.7939 (tm-30) REVERT: D 184 GLN cc_start: 0.9160 (mt0) cc_final: 0.8580 (tp-100) REVERT: D 233 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 241 ARG cc_start: 0.9061 (tpp80) cc_final: 0.8749 (tpp80) REVERT: D 271 ASP cc_start: 0.8768 (m-30) cc_final: 0.8510 (m-30) REVERT: E 155 GLU cc_start: 0.8850 (tp30) cc_final: 0.8518 (tm-30) REVERT: E 184 GLN cc_start: 0.9167 (mt0) cc_final: 0.8678 (mm-40) REVERT: F 74 MET cc_start: 0.8321 (tpt) cc_final: 0.8053 (tpt) REVERT: F 128 TYR cc_start: 0.8992 (m-10) cc_final: 0.8446 (m-80) REVERT: F 129 TYR cc_start: 0.9499 (t80) cc_final: 0.9260 (t80) REVERT: F 184 GLN cc_start: 0.9035 (mt0) cc_final: 0.8600 (tp-100) REVERT: F 233 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8225 (tm-30) REVERT: F 244 MET cc_start: 0.9194 (tpt) cc_final: 0.8977 (tpp) REVERT: F 245 MET cc_start: 0.8591 (tpp) cc_final: 0.8266 (tpp) REVERT: G 74 MET cc_start: 0.8554 (tpt) cc_final: 0.8339 (tpt) REVERT: G 233 GLU cc_start: 0.8224 (tm-30) cc_final: 0.8002 (tm-30) REVERT: G 271 ASP cc_start: 0.8536 (m-30) cc_final: 0.8258 (m-30) REVERT: H 184 GLN cc_start: 0.8925 (mt0) cc_final: 0.8500 (tp40) REVERT: H 237 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8408 (tm-30) REVERT: H 248 ILE cc_start: 0.8730 (mm) cc_final: 0.8222 (tp) REVERT: J 184 GLN cc_start: 0.8998 (mt0) cc_final: 0.8417 (tp40) REVERT: J 208 LYS cc_start: 0.8941 (tppt) cc_final: 0.8401 (tmmt) REVERT: J 244 MET cc_start: 0.8969 (tpt) cc_final: 0.8737 (tpp) REVERT: J 249 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8336 (ttmm) REVERT: J 262 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8165 (mmmm) REVERT: K 174 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8142 (tmm-80) REVERT: K 198 ILE cc_start: 0.8380 (mm) cc_final: 0.8055 (tp) REVERT: K 221 TRP cc_start: 0.8679 (t60) cc_final: 0.8248 (t60) REVERT: K 279 THR cc_start: 0.7626 (m) cc_final: 0.7332 (p) REVERT: L 129 TYR cc_start: 0.9388 (t80) cc_final: 0.9053 (t80) REVERT: L 183 TYR cc_start: 0.9175 (t80) cc_final: 0.8719 (t80) REVERT: L 184 GLN cc_start: 0.8970 (mt0) cc_final: 0.8608 (tp40) REVERT: L 208 LYS cc_start: 0.8724 (tppt) cc_final: 0.8229 (tmmt) REVERT: L 244 MET cc_start: 0.9023 (tpt) cc_final: 0.8695 (tpt) REVERT: M 51 TYR cc_start: 0.9218 (t80) cc_final: 0.8905 (t80) REVERT: M 74 MET cc_start: 0.8711 (tpt) cc_final: 0.8423 (tpt) REVERT: M 160 PHE cc_start: 0.8315 (m-80) cc_final: 0.8078 (m-80) REVERT: M 184 GLN cc_start: 0.9136 (mt0) cc_final: 0.8621 (tp-100) REVERT: M 241 ARG cc_start: 0.9112 (tpp80) cc_final: 0.8849 (tpp80) REVERT: M 245 MET cc_start: 0.7909 (mtm) cc_final: 0.7682 (mtm) REVERT: M 271 ASP cc_start: 0.9004 (m-30) cc_final: 0.8567 (m-30) REVERT: N 128 TYR cc_start: 0.9064 (m-10) cc_final: 0.8862 (m-80) REVERT: N 152 LYS cc_start: 0.9159 (tppp) cc_final: 0.8869 (tppp) REVERT: N 155 GLU cc_start: 0.8744 (tp30) cc_final: 0.8502 (tm-30) REVERT: N 174 ARG cc_start: 0.8496 (ttp80) cc_final: 0.8292 (ttp80) REVERT: N 183 TYR cc_start: 0.9123 (t80) cc_final: 0.8802 (t80) REVERT: N 184 GLN cc_start: 0.9066 (mt0) cc_final: 0.8175 (tp40) REVERT: O 184 GLN cc_start: 0.9010 (mt0) cc_final: 0.8650 (tp40) REVERT: P 74 MET cc_start: 0.8385 (tpp) cc_final: 0.8076 (tpt) REVERT: P 128 TYR cc_start: 0.8977 (m-10) cc_final: 0.8604 (m-80) REVERT: P 249 LYS cc_start: 0.8671 (tttp) cc_final: 0.8466 (tttm) REVERT: Q 160 PHE cc_start: 0.8507 (m-80) cc_final: 0.8037 (m-80) REVERT: Q 184 GLN cc_start: 0.9082 (mt0) cc_final: 0.8586 (tp40) REVERT: R 74 MET cc_start: 0.8497 (tpp) cc_final: 0.8159 (tpt) REVERT: R 153 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8861 (ttt180) REVERT: R 187 MET cc_start: 0.8763 (mmm) cc_final: 0.8460 (mmm) REVERT: R 249 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8369 (ttmm) REVERT: R 251 LEU cc_start: 0.9326 (tp) cc_final: 0.9088 (tt) REVERT: S 74 MET cc_start: 0.8395 (tpt) cc_final: 0.8121 (tpt) REVERT: S 160 PHE cc_start: 0.8231 (m-80) cc_final: 0.7995 (m-80) REVERT: S 192 LEU cc_start: 0.9036 (tt) cc_final: 0.8834 (tp) REVERT: T 184 GLN cc_start: 0.8970 (mt0) cc_final: 0.8709 (tp-100) REVERT: T 241 ARG cc_start: 0.9063 (tpp80) cc_final: 0.8732 (tpp80) REVERT: T 249 LYS cc_start: 0.8608 (tttt) cc_final: 0.8402 (ttpp) outliers start: 6 outliers final: 0 residues processed: 1029 average time/residue: 0.2274 time to fit residues: 387.5093 Evaluate side-chains 714 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 713 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 119 optimal weight: 0.0050 chunk 91 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 451 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 334 optimal weight: 0.9990 chunk 511 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN D 48 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN G 227 ASN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN N 48 ASN N 217 GLN N 227 ASN P 48 ASN R 227 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097475 restraints weight = 77025.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099624 restraints weight = 48947.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100855 restraints weight = 36777.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101924 restraints weight = 31164.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.102341 restraints weight = 27680.141| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 42620 Z= 0.128 Angle : 0.538 6.665 57900 Z= 0.281 Chirality : 0.039 0.155 6740 Planarity : 0.004 0.084 7180 Dihedral : 3.795 34.444 5700 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.12), residues: 5260 helix: 2.60 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.88 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 14 TYR 0.012 0.001 TYR L 81 PHE 0.027 0.001 PHE L 160 TRP 0.009 0.001 TRP O 221 HIS 0.003 0.001 HIS E 246 Details of bonding type rmsd covalent geometry : bond 0.00258 (42580) covalent geometry : angle 0.53547 (57820) SS BOND : bond 0.00363 ( 40) SS BOND : angle 1.58015 ( 80) hydrogen bonds : bond 0.04887 ( 3171) hydrogen bonds : angle 3.69572 ( 9513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1033 time to evaluate : 1.116 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.8929 (mt0) cc_final: 0.8345 (tp40) REVERT: A 208 LYS cc_start: 0.8820 (tppt) cc_final: 0.8126 (tmmt) REVERT: A 248 ILE cc_start: 0.9200 (tp) cc_final: 0.8997 (tp) REVERT: B 74 MET cc_start: 0.8243 (tpt) cc_final: 0.7930 (tpp) REVERT: B 128 TYR cc_start: 0.8916 (m-10) cc_final: 0.8655 (m-80) REVERT: B 174 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8374 (ptt180) REVERT: B 184 GLN cc_start: 0.9005 (mt0) cc_final: 0.8621 (tp40) REVERT: B 241 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8784 (mmm-85) REVERT: C 31 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8696 (tm-30) REVERT: C 41 CYS cc_start: 0.5587 (t) cc_final: 0.5267 (t) REVERT: C 51 TYR cc_start: 0.9254 (t80) cc_final: 0.8995 (t80) REVERT: C 184 GLN cc_start: 0.8890 (mt0) cc_final: 0.8453 (tp40) REVERT: C 271 ASP cc_start: 0.8737 (m-30) cc_final: 0.8506 (m-30) REVERT: D 128 TYR cc_start: 0.9005 (m-10) cc_final: 0.8769 (m-80) REVERT: D 184 GLN cc_start: 0.9101 (mt0) cc_final: 0.8518 (tp-100) REVERT: D 233 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8324 (tm-30) REVERT: D 271 ASP cc_start: 0.8777 (m-30) cc_final: 0.8442 (m-30) REVERT: E 155 GLU cc_start: 0.8852 (tp30) cc_final: 0.8485 (tm-30) REVERT: E 184 GLN cc_start: 0.9184 (mt0) cc_final: 0.8612 (mm-40) REVERT: E 187 MET cc_start: 0.8827 (mmt) cc_final: 0.8570 (mmp) REVERT: E 198 ILE cc_start: 0.8386 (mm) cc_final: 0.7920 (tp) REVERT: F 74 MET cc_start: 0.8229 (tpt) cc_final: 0.7986 (tpt) REVERT: F 129 TYR cc_start: 0.9459 (t80) cc_final: 0.9217 (t80) REVERT: F 184 GLN cc_start: 0.8988 (mt0) cc_final: 0.8581 (tp-100) REVERT: F 233 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8233 (tm-30) REVERT: F 244 MET cc_start: 0.9148 (tpt) cc_final: 0.8887 (tpp) REVERT: G 233 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 271 ASP cc_start: 0.8558 (m-30) cc_final: 0.8256 (m-30) REVERT: H 184 GLN cc_start: 0.8990 (mt0) cc_final: 0.8561 (tp40) REVERT: H 221 TRP cc_start: 0.8249 (t60) cc_final: 0.7633 (t60) REVERT: H 237 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8555 (tm-30) REVERT: H 248 ILE cc_start: 0.8714 (mm) cc_final: 0.8223 (tp) REVERT: H 271 ASP cc_start: 0.8947 (m-30) cc_final: 0.8709 (m-30) REVERT: I 184 GLN cc_start: 0.8934 (mt0) cc_final: 0.8672 (tp40) REVERT: J 184 GLN cc_start: 0.8996 (mt0) cc_final: 0.8546 (tp40) REVERT: J 192 LEU cc_start: 0.8993 (tt) cc_final: 0.8788 (tp) REVERT: J 208 LYS cc_start: 0.8949 (tppt) cc_final: 0.8417 (tmmt) REVERT: J 249 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8294 (ttmm) REVERT: J 262 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8166 (mmmm) REVERT: K 22 LEU cc_start: 0.8917 (tp) cc_final: 0.8699 (tp) REVERT: K 153 ARG cc_start: 0.9123 (ttp80) cc_final: 0.8699 (ptt180) REVERT: K 221 TRP cc_start: 0.8514 (t60) cc_final: 0.8069 (t60) REVERT: L 31 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8756 (tm-30) REVERT: L 48 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.8024 (t0) REVERT: L 51 TYR cc_start: 0.9229 (t80) cc_final: 0.8789 (t80) REVERT: L 74 MET cc_start: 0.8522 (tpt) cc_final: 0.8023 (tpt) REVERT: L 129 TYR cc_start: 0.9346 (t80) cc_final: 0.8918 (t80) REVERT: L 157 LEU cc_start: 0.9118 (tp) cc_final: 0.8855 (tp) REVERT: L 160 PHE cc_start: 0.8407 (m-80) cc_final: 0.8194 (m-80) REVERT: L 183 TYR cc_start: 0.9076 (t80) cc_final: 0.8668 (t80) REVERT: L 184 GLN cc_start: 0.8916 (mt0) cc_final: 0.8542 (tp40) REVERT: L 208 LYS cc_start: 0.8765 (tppt) cc_final: 0.8227 (tmmt) REVERT: L 244 MET cc_start: 0.9027 (tpt) cc_final: 0.8803 (tpt) REVERT: M 51 TYR cc_start: 0.9189 (t80) cc_final: 0.8852 (t80) REVERT: M 74 MET cc_start: 0.8518 (tpt) cc_final: 0.7951 (tpt) REVERT: M 135 GLU cc_start: 0.8800 (pm20) cc_final: 0.8206 (pp20) REVERT: M 184 GLN cc_start: 0.9146 (mt0) cc_final: 0.8485 (tp-100) REVERT: M 187 MET cc_start: 0.9053 (mmp) cc_final: 0.8832 (mmm) REVERT: M 216 LEU cc_start: 0.8799 (mt) cc_final: 0.8572 (mt) REVERT: M 271 ASP cc_start: 0.8916 (m-30) cc_final: 0.8508 (m-30) REVERT: N 41 CYS cc_start: 0.5259 (t) cc_final: 0.4897 (t) REVERT: N 152 LYS cc_start: 0.9121 (tppp) cc_final: 0.8845 (tppp) REVERT: N 155 GLU cc_start: 0.8738 (tp30) cc_final: 0.8493 (tm-30) REVERT: N 183 TYR cc_start: 0.9115 (t80) cc_final: 0.8715 (t80) REVERT: N 184 GLN cc_start: 0.9064 (mt0) cc_final: 0.8147 (tp40) REVERT: O 128 TYR cc_start: 0.8712 (m-10) cc_final: 0.8484 (m-80) REVERT: O 154 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8580 (mm-30) REVERT: O 184 GLN cc_start: 0.8944 (mt0) cc_final: 0.8708 (tp-100) REVERT: O 244 MET cc_start: 0.9202 (tpt) cc_final: 0.8891 (tpt) REVERT: O 248 ILE cc_start: 0.9061 (tp) cc_final: 0.8811 (tp) REVERT: P 128 TYR cc_start: 0.8975 (m-10) cc_final: 0.8634 (m-80) REVERT: P 184 GLN cc_start: 0.9045 (mt0) cc_final: 0.8757 (tp40) REVERT: P 198 ILE cc_start: 0.8440 (mm) cc_final: 0.8139 (tp) REVERT: P 221 TRP cc_start: 0.8365 (t60) cc_final: 0.7910 (t60) REVERT: Q 160 PHE cc_start: 0.8437 (m-80) cc_final: 0.8096 (m-80) REVERT: Q 184 GLN cc_start: 0.9024 (mt0) cc_final: 0.8582 (tp40) REVERT: R 74 MET cc_start: 0.8461 (tpp) cc_final: 0.8052 (tpt) REVERT: R 78 THR cc_start: 0.6787 (m) cc_final: 0.6470 (m) REVERT: R 184 GLN cc_start: 0.9230 (mt0) cc_final: 0.8814 (tp-100) REVERT: R 187 MET cc_start: 0.8739 (mmm) cc_final: 0.8382 (mmm) REVERT: R 233 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8250 (tm-30) REVERT: R 249 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8189 (ttmm) REVERT: S 103 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8238 (tpp80) REVERT: S 160 PHE cc_start: 0.8121 (m-80) cc_final: 0.7920 (m-80) REVERT: T 128 TYR cc_start: 0.8678 (m-10) cc_final: 0.8335 (m-80) REVERT: T 154 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8592 (mm-30) REVERT: T 249 LYS cc_start: 0.8501 (tttt) cc_final: 0.8269 (ttpp) outliers start: 4 outliers final: 1 residues processed: 1037 average time/residue: 0.2281 time to fit residues: 393.4255 Evaluate side-chains 708 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 706 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 212 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 475 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 351 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 516 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 406 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN G 227 ASN H 48 ASN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 48 ASN M 227 ASN N 217 GLN N 227 ASN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.104664 restraints weight = 76169.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106984 restraints weight = 47525.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108364 restraints weight = 35377.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109444 restraints weight = 29737.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109804 restraints weight = 26413.350| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42620 Z= 0.132 Angle : 0.549 8.173 57900 Z= 0.287 Chirality : 0.039 0.154 6740 Planarity : 0.004 0.057 7180 Dihedral : 3.783 31.922 5700 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.09 % Allowed : 1.49 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.12), residues: 5260 helix: 2.64 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.86 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 247 TYR 0.028 0.001 TYR J 183 PHE 0.023 0.001 PHE R 160 TRP 0.016 0.001 TRP G 221 HIS 0.003 0.001 HIS N 141 Details of bonding type rmsd covalent geometry : bond 0.00275 (42580) covalent geometry : angle 0.54670 (57820) SS BOND : bond 0.00318 ( 40) SS BOND : angle 1.37486 ( 80) hydrogen bonds : bond 0.04847 ( 3171) hydrogen bonds : angle 3.66635 ( 9513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 998 time to evaluate : 1.499 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 THR cc_start: 0.9165 (t) cc_final: 0.8946 (t) REVERT: A 128 TYR cc_start: 0.8940 (m-10) cc_final: 0.8373 (m-80) REVERT: A 156 ILE cc_start: 0.9313 (tp) cc_final: 0.9104 (tp) REVERT: A 184 GLN cc_start: 0.8930 (mt0) cc_final: 0.8358 (tp40) REVERT: A 208 LYS cc_start: 0.8783 (tppt) cc_final: 0.8146 (tmmt) REVERT: B 74 MET cc_start: 0.8256 (tpt) cc_final: 0.7956 (tpp) REVERT: B 128 TYR cc_start: 0.8906 (m-10) cc_final: 0.8642 (m-80) REVERT: B 174 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8333 (ptt180) REVERT: B 184 GLN cc_start: 0.8986 (mt0) cc_final: 0.8629 (tp40) REVERT: B 233 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 241 ARG cc_start: 0.9113 (tpp80) cc_final: 0.8754 (mmm-85) REVERT: C 31 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8832 (tm-30) REVERT: C 41 CYS cc_start: 0.5356 (t) cc_final: 0.5114 (t) REVERT: C 51 TYR cc_start: 0.9274 (t80) cc_final: 0.9024 (t80) REVERT: C 156 ILE cc_start: 0.9388 (tp) cc_final: 0.9118 (tp) REVERT: C 184 GLN cc_start: 0.8890 (mt0) cc_final: 0.8558 (tp40) REVERT: C 271 ASP cc_start: 0.8762 (m-30) cc_final: 0.8380 (m-30) REVERT: D 128 TYR cc_start: 0.9025 (m-10) cc_final: 0.8794 (m-80) REVERT: D 155 GLU cc_start: 0.8725 (tp30) cc_final: 0.8019 (tm-30) REVERT: D 184 GLN cc_start: 0.9084 (mt0) cc_final: 0.8551 (tp-100) REVERT: D 233 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8334 (tm-30) REVERT: D 241 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8660 (tpp80) REVERT: D 271 ASP cc_start: 0.8784 (m-30) cc_final: 0.8382 (m-30) REVERT: E 155 GLU cc_start: 0.8850 (tp30) cc_final: 0.8514 (tm-30) REVERT: E 184 GLN cc_start: 0.9082 (mt0) cc_final: 0.8433 (mm-40) REVERT: E 198 ILE cc_start: 0.8387 (mm) cc_final: 0.7894 (tp) REVERT: F 31 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8631 (tm-30) REVERT: F 74 MET cc_start: 0.8316 (tpt) cc_final: 0.8042 (tpt) REVERT: F 128 TYR cc_start: 0.8944 (m-10) cc_final: 0.8439 (m-80) REVERT: F 129 TYR cc_start: 0.9435 (t80) cc_final: 0.9201 (t80) REVERT: F 184 GLN cc_start: 0.8993 (mt0) cc_final: 0.8535 (tp-100) REVERT: F 233 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8226 (tm-30) REVERT: G 233 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8020 (tm-30) REVERT: G 245 MET cc_start: 0.8255 (mtm) cc_final: 0.7967 (mtp) REVERT: G 271 ASP cc_start: 0.8728 (m-30) cc_final: 0.8369 (m-30) REVERT: H 14 ARG cc_start: 0.8091 (ptt90) cc_final: 0.7684 (ppt170) REVERT: H 184 GLN cc_start: 0.8996 (mt0) cc_final: 0.8629 (tp40) REVERT: H 187 MET cc_start: 0.9059 (mmp) cc_final: 0.8717 (mmm) REVERT: H 237 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8552 (tm-30) REVERT: H 248 ILE cc_start: 0.8774 (mm) cc_final: 0.8267 (tp) REVERT: H 271 ASP cc_start: 0.8972 (m-30) cc_final: 0.8682 (m-30) REVERT: I 184 GLN cc_start: 0.9013 (mt0) cc_final: 0.8584 (tp40) REVERT: I 187 MET cc_start: 0.8779 (mmt) cc_final: 0.8409 (mmm) REVERT: J 184 GLN cc_start: 0.9010 (mt0) cc_final: 0.8464 (tp40) REVERT: J 208 LYS cc_start: 0.8969 (tppt) cc_final: 0.8422 (tmmt) REVERT: J 244 MET cc_start: 0.9059 (tpt) cc_final: 0.8787 (tpp) REVERT: J 249 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8214 (ttmm) REVERT: J 262 LYS cc_start: 0.8433 (mmmm) cc_final: 0.8193 (mmmm) REVERT: K 22 LEU cc_start: 0.8953 (tp) cc_final: 0.8723 (tp) REVERT: K 174 ARG cc_start: 0.8607 (ttp80) cc_final: 0.8242 (ptm-80) REVERT: K 221 TRP cc_start: 0.8521 (t60) cc_final: 0.8075 (t60) REVERT: K 279 THR cc_start: 0.7670 (m) cc_final: 0.7224 (p) REVERT: L 31 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8708 (tm-30) REVERT: L 41 CYS cc_start: 0.5334 (t) cc_final: 0.5045 (t) REVERT: L 51 TYR cc_start: 0.9185 (t80) cc_final: 0.8832 (t80) REVERT: L 73 GLN cc_start: 0.9185 (mp10) cc_final: 0.8606 (mt0) REVERT: L 129 TYR cc_start: 0.9355 (t80) cc_final: 0.8887 (t80) REVERT: L 157 LEU cc_start: 0.9172 (tp) cc_final: 0.8859 (tp) REVERT: L 160 PHE cc_start: 0.8432 (m-80) cc_final: 0.8211 (m-80) REVERT: L 184 GLN cc_start: 0.8915 (mt0) cc_final: 0.8550 (tp40) REVERT: L 208 LYS cc_start: 0.8782 (tppt) cc_final: 0.8207 (tmmt) REVERT: M 51 TYR cc_start: 0.9269 (t80) cc_final: 0.9030 (t80) REVERT: M 74 MET cc_start: 0.8619 (tpt) cc_final: 0.8103 (tpt) REVERT: M 184 GLN cc_start: 0.9196 (mt0) cc_final: 0.8506 (tp-100) REVERT: M 187 MET cc_start: 0.9074 (mmp) cc_final: 0.8834 (mmm) REVERT: M 216 LEU cc_start: 0.8776 (mt) cc_final: 0.8575 (mt) REVERT: M 271 ASP cc_start: 0.8889 (m-30) cc_final: 0.8484 (m-30) REVERT: N 41 CYS cc_start: 0.5286 (t) cc_final: 0.5028 (t) REVERT: N 152 LYS cc_start: 0.9100 (tppp) cc_final: 0.8858 (tppp) REVERT: N 183 TYR cc_start: 0.9153 (t80) cc_final: 0.8805 (t80) REVERT: N 184 GLN cc_start: 0.9054 (mt0) cc_final: 0.8174 (tp40) REVERT: O 128 TYR cc_start: 0.8786 (m-10) cc_final: 0.8508 (m-80) REVERT: O 154 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8570 (mm-30) REVERT: O 184 GLN cc_start: 0.9019 (mt0) cc_final: 0.8551 (tp-100) REVERT: O 187 MET cc_start: 0.8964 (mmt) cc_final: 0.8728 (mmp) REVERT: O 244 MET cc_start: 0.9163 (tpt) cc_final: 0.8824 (tpt) REVERT: O 248 ILE cc_start: 0.9022 (tp) cc_final: 0.8778 (tp) REVERT: P 74 MET cc_start: 0.8411 (tpp) cc_final: 0.7881 (tpp) REVERT: P 128 TYR cc_start: 0.8947 (m-10) cc_final: 0.8674 (m-80) REVERT: P 184 GLN cc_start: 0.9042 (mt0) cc_final: 0.8760 (tp40) REVERT: P 198 ILE cc_start: 0.8371 (mm) cc_final: 0.8083 (tp) REVERT: P 221 TRP cc_start: 0.8481 (t60) cc_final: 0.8049 (t60) REVERT: Q 184 GLN cc_start: 0.9130 (mt0) cc_final: 0.8577 (tp40) REVERT: R 74 MET cc_start: 0.8487 (tpp) cc_final: 0.8106 (tpt) REVERT: R 184 GLN cc_start: 0.9214 (mt0) cc_final: 0.8625 (tp40) REVERT: R 187 MET cc_start: 0.8788 (mmm) cc_final: 0.8440 (mmm) REVERT: R 233 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8263 (tm-30) REVERT: S 103 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8295 (tpp80) REVERT: S 152 LYS cc_start: 0.9200 (tptp) cc_final: 0.8972 (tppp) REVERT: T 128 TYR cc_start: 0.8804 (m-10) cc_final: 0.8493 (m-80) REVERT: T 154 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8585 (mm-30) REVERT: T 187 MET cc_start: 0.8998 (mmt) cc_final: 0.8651 (mmp) REVERT: T 248 ILE cc_start: 0.8983 (tp) cc_final: 0.8640 (tp) outliers start: 4 outliers final: 0 residues processed: 1001 average time/residue: 0.2250 time to fit residues: 375.6481 Evaluate side-chains 705 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 121 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 419 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 238 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 400 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 ASN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN N 48 ASN N 217 GLN N 227 ASN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095346 restraints weight = 75987.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097307 restraints weight = 48739.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098646 restraints weight = 36591.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099515 restraints weight = 30364.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.100005 restraints weight = 26922.274| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 42620 Z= 0.154 Angle : 0.574 7.444 57900 Z= 0.301 Chirality : 0.040 0.153 6740 Planarity : 0.004 0.060 7180 Dihedral : 3.811 30.200 5700 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.04 % Allowed : 1.52 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.12), residues: 5260 helix: 2.70 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.66 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 247 TYR 0.013 0.001 TYR Q 129 PHE 0.020 0.001 PHE R 160 TRP 0.023 0.001 TRP G 221 HIS 0.004 0.001 HIS I 246 Details of bonding type rmsd covalent geometry : bond 0.00336 (42580) covalent geometry : angle 0.57162 (57820) SS BOND : bond 0.00490 ( 40) SS BOND : angle 1.54848 ( 80) hydrogen bonds : bond 0.05085 ( 3171) hydrogen bonds : angle 3.75967 ( 9513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 932 time to evaluate : 1.622 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: A 122 THR cc_start: 0.9202 (t) cc_final: 0.8970 (t) REVERT: A 128 TYR cc_start: 0.8933 (m-10) cc_final: 0.8390 (m-80) REVERT: A 156 ILE cc_start: 0.9326 (tp) cc_final: 0.9058 (tp) REVERT: A 184 GLN cc_start: 0.8935 (mt0) cc_final: 0.8476 (tp40) REVERT: A 208 LYS cc_start: 0.8873 (tppt) cc_final: 0.8251 (tmmt) REVERT: B 74 MET cc_start: 0.8287 (tpt) cc_final: 0.8021 (tpp) REVERT: B 128 TYR cc_start: 0.8911 (m-10) cc_final: 0.8677 (m-80) REVERT: B 184 GLN cc_start: 0.9150 (mt0) cc_final: 0.8624 (tp40) REVERT: B 233 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8266 (tm-30) REVERT: B 241 ARG cc_start: 0.9091 (tpp80) cc_final: 0.8746 (mmm-85) REVERT: C 31 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8871 (tm-30) REVERT: C 41 CYS cc_start: 0.5354 (t) cc_final: 0.5078 (t) REVERT: C 155 GLU cc_start: 0.8769 (tp30) cc_final: 0.8517 (tm-30) REVERT: C 184 GLN cc_start: 0.8901 (mt0) cc_final: 0.8514 (tp40) REVERT: C 230 GLU cc_start: 0.8565 (tp30) cc_final: 0.8271 (tp30) REVERT: C 271 ASP cc_start: 0.8726 (m-30) cc_final: 0.8332 (m-30) REVERT: D 128 TYR cc_start: 0.9002 (m-10) cc_final: 0.8788 (m-80) REVERT: D 184 GLN cc_start: 0.9086 (mt0) cc_final: 0.8575 (tp-100) REVERT: D 233 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8387 (tm-30) REVERT: D 241 ARG cc_start: 0.9084 (tpp80) cc_final: 0.8792 (tpp80) REVERT: D 271 ASP cc_start: 0.8714 (m-30) cc_final: 0.8319 (m-30) REVERT: E 154 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7885 (mm-30) REVERT: E 184 GLN cc_start: 0.9069 (mt0) cc_final: 0.8653 (mm-40) REVERT: E 198 ILE cc_start: 0.8393 (mm) cc_final: 0.8028 (tp) REVERT: E 245 MET cc_start: 0.8055 (mtm) cc_final: 0.7818 (mtm) REVERT: F 74 MET cc_start: 0.8349 (tpt) cc_final: 0.8092 (tpt) REVERT: F 129 TYR cc_start: 0.9453 (t80) cc_final: 0.9229 (t80) REVERT: F 184 GLN cc_start: 0.8982 (mt0) cc_final: 0.8515 (tp-100) REVERT: F 233 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8284 (tm-30) REVERT: G 233 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8006 (tm-30) REVERT: G 271 ASP cc_start: 0.8745 (m-30) cc_final: 0.8402 (m-30) REVERT: H 14 ARG cc_start: 0.7977 (ptt90) cc_final: 0.7631 (ppt170) REVERT: H 184 GLN cc_start: 0.9000 (mt0) cc_final: 0.8656 (tp40) REVERT: H 187 MET cc_start: 0.9103 (mmp) cc_final: 0.8754 (mmt) REVERT: H 230 GLU cc_start: 0.8404 (tp30) cc_final: 0.8146 (tp30) REVERT: H 237 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8582 (tm-30) REVERT: H 248 ILE cc_start: 0.8775 (mm) cc_final: 0.8245 (tp) REVERT: H 271 ASP cc_start: 0.8961 (m-30) cc_final: 0.8685 (m-30) REVERT: I 184 GLN cc_start: 0.8969 (mt0) cc_final: 0.8489 (tp40) REVERT: I 187 MET cc_start: 0.8919 (mmt) cc_final: 0.8638 (mmm) REVERT: I 245 MET cc_start: 0.8209 (ttm) cc_final: 0.7976 (mtm) REVERT: J 184 GLN cc_start: 0.8985 (mt0) cc_final: 0.8485 (tp40) REVERT: J 187 MET cc_start: 0.8656 (mmt) cc_final: 0.8380 (mmp) REVERT: J 208 LYS cc_start: 0.8969 (tppt) cc_final: 0.8437 (tmmt) REVERT: J 244 MET cc_start: 0.9041 (tpt) cc_final: 0.8813 (tpp) REVERT: J 249 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8150 (ttmm) REVERT: J 262 LYS cc_start: 0.8379 (mmmm) cc_final: 0.8129 (mmmm) REVERT: K 22 LEU cc_start: 0.8994 (tp) cc_final: 0.8741 (tp) REVERT: K 174 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8196 (ptm-80) REVERT: K 221 TRP cc_start: 0.8638 (t60) cc_final: 0.8033 (t60) REVERT: K 279 THR cc_start: 0.7743 (m) cc_final: 0.7361 (p) REVERT: L 14 ARG cc_start: 0.7878 (ptt90) cc_final: 0.7309 (ppt170) REVERT: L 31 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8699 (tm-30) REVERT: L 51 TYR cc_start: 0.9260 (t80) cc_final: 0.9036 (t80) REVERT: L 129 TYR cc_start: 0.9439 (t80) cc_final: 0.8989 (t80) REVERT: L 157 LEU cc_start: 0.9178 (tp) cc_final: 0.8843 (tp) REVERT: L 184 GLN cc_start: 0.8962 (mt0) cc_final: 0.8553 (tp40) REVERT: L 208 LYS cc_start: 0.8813 (tppt) cc_final: 0.8228 (tmmt) REVERT: L 244 MET cc_start: 0.9004 (tpt) cc_final: 0.8624 (tpt) REVERT: M 51 TYR cc_start: 0.9348 (t80) cc_final: 0.9122 (t80) REVERT: M 74 MET cc_start: 0.8548 (tpt) cc_final: 0.8074 (tpt) REVERT: M 174 ARG cc_start: 0.8284 (ptm160) cc_final: 0.7972 (ptt180) REVERT: M 184 GLN cc_start: 0.9204 (mt0) cc_final: 0.8623 (tp-100) REVERT: M 187 MET cc_start: 0.9048 (mmp) cc_final: 0.8796 (mmm) REVERT: M 271 ASP cc_start: 0.8835 (m-30) cc_final: 0.8461 (m-30) REVERT: N 41 CYS cc_start: 0.5366 (t) cc_final: 0.5134 (t) REVERT: N 152 LYS cc_start: 0.9066 (tppp) cc_final: 0.8839 (tppp) REVERT: N 183 TYR cc_start: 0.9240 (t80) cc_final: 0.8857 (t80) REVERT: N 184 GLN cc_start: 0.9160 (mt0) cc_final: 0.8285 (tp40) REVERT: O 154 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8529 (mm-30) REVERT: O 184 GLN cc_start: 0.8886 (mt0) cc_final: 0.8550 (tp-100) REVERT: O 187 MET cc_start: 0.9049 (mmt) cc_final: 0.8846 (mmp) REVERT: O 244 MET cc_start: 0.9152 (tpt) cc_final: 0.8849 (tpt) REVERT: O 248 ILE cc_start: 0.9056 (tp) cc_final: 0.8790 (tp) REVERT: P 128 TYR cc_start: 0.9005 (m-10) cc_final: 0.8750 (m-80) REVERT: P 184 GLN cc_start: 0.8968 (mt0) cc_final: 0.8694 (tp40) REVERT: P 221 TRP cc_start: 0.8489 (t60) cc_final: 0.8050 (t60) REVERT: P 279 THR cc_start: 0.7370 (m) cc_final: 0.6992 (p) REVERT: Q 184 GLN cc_start: 0.8999 (mt0) cc_final: 0.8572 (tp40) REVERT: Q 230 GLU cc_start: 0.8494 (tp30) cc_final: 0.8095 (tp30) REVERT: R 74 MET cc_start: 0.8550 (tpp) cc_final: 0.8094 (tpt) REVERT: R 78 THR cc_start: 0.6978 (m) cc_final: 0.6677 (m) REVERT: R 157 LEU cc_start: 0.9178 (tp) cc_final: 0.8893 (tp) REVERT: R 160 PHE cc_start: 0.8355 (m-80) cc_final: 0.8138 (m-80) REVERT: R 184 GLN cc_start: 0.9231 (mt0) cc_final: 0.8747 (tp-100) REVERT: R 187 MET cc_start: 0.8823 (mmm) cc_final: 0.8555 (mmm) REVERT: R 233 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8324 (tm-30) REVERT: R 244 MET cc_start: 0.9194 (tpt) cc_final: 0.8890 (tpp) REVERT: R 245 MET cc_start: 0.8002 (mtm) cc_final: 0.7642 (mtt) REVERT: S 152 LYS cc_start: 0.9173 (tptp) cc_final: 0.8951 (tppp) REVERT: T 128 TYR cc_start: 0.8843 (m-10) cc_final: 0.8555 (m-80) REVERT: T 154 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8555 (mm-30) REVERT: T 187 MET cc_start: 0.8989 (mmt) cc_final: 0.8682 (mmp) REVERT: T 258 SER cc_start: 0.8608 (p) cc_final: 0.8318 (p) outliers start: 2 outliers final: 0 residues processed: 934 average time/residue: 0.2276 time to fit residues: 355.0896 Evaluate side-chains 673 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 8.9990 chunk 272 optimal weight: 0.0970 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 463 optimal weight: 3.9990 chunk 343 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 48 ASN M 227 ASN N 48 ASN N 217 GLN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096927 restraints weight = 75059.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098896 restraints weight = 47967.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100051 restraints weight = 36044.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100925 restraints weight = 30430.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100925 restraints weight = 26904.155| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42620 Z= 0.149 Angle : 0.570 7.699 57900 Z= 0.299 Chirality : 0.040 0.149 6740 Planarity : 0.005 0.162 7180 Dihedral : 3.846 28.320 5700 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.06 % Allowed : 1.43 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.12), residues: 5260 helix: 2.77 (0.08), residues: 4100 sheet: None (None), residues: 0 loop : -2.58 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 174 TYR 0.015 0.001 TYR P 81 PHE 0.026 0.001 PHE L 160 TRP 0.024 0.001 TRP G 221 HIS 0.004 0.001 HIS H 246 Details of bonding type rmsd covalent geometry : bond 0.00324 (42580) covalent geometry : angle 0.56841 (57820) SS BOND : bond 0.00361 ( 40) SS BOND : angle 1.33390 ( 80) hydrogen bonds : bond 0.05079 ( 3171) hydrogen bonds : angle 3.75627 ( 9513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 931 time to evaluate : 1.421 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: 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 14 ARG cc_start: 0.7969 (ptt90) cc_final: 0.7591 (ppt170) REVERT: A 129 TYR cc_start: 0.9268 (t80) cc_final: 0.9013 (t80) REVERT: A 184 GLN cc_start: 0.8898 (mt0) cc_final: 0.8418 (tp40) REVERT: A 208 LYS cc_start: 0.8868 (tppt) cc_final: 0.8249 (tmmt) REVERT: B 74 MET cc_start: 0.8250 (tpt) cc_final: 0.7977 (tpp) REVERT: B 128 TYR cc_start: 0.8888 (m-10) cc_final: 0.8684 (m-80) REVERT: B 184 GLN cc_start: 0.8890 (mt0) cc_final: 0.8454 (tp40) REVERT: C 31 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8950 (tm-30) REVERT: C 41 CYS cc_start: 0.5300 (t) cc_final: 0.5044 (t) REVERT: C 184 GLN cc_start: 0.8827 (mt0) cc_final: 0.8460 (tp40) REVERT: C 271 ASP cc_start: 0.8756 (m-30) cc_final: 0.8386 (m-30) REVERT: D 128 TYR cc_start: 0.8967 (m-10) cc_final: 0.8760 (m-80) REVERT: D 152 LYS cc_start: 0.9261 (tppp) cc_final: 0.9018 (tppp) REVERT: D 155 GLU cc_start: 0.8633 (tp30) cc_final: 0.8331 (tm-30) REVERT: D 184 GLN cc_start: 0.9124 (mt0) cc_final: 0.8593 (tp-100) REVERT: D 233 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8387 (tm-30) REVERT: D 241 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8837 (tpp80) REVERT: D 271 ASP cc_start: 0.8664 (m-30) cc_final: 0.8256 (m-30) REVERT: E 184 GLN cc_start: 0.9028 (mt0) cc_final: 0.8620 (mm-40) REVERT: E 198 ILE cc_start: 0.8408 (mm) cc_final: 0.7967 (tp) REVERT: F 31 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8744 (tm-30) REVERT: F 74 MET cc_start: 0.8312 (tpt) cc_final: 0.8110 (tpt) REVERT: F 128 TYR cc_start: 0.8982 (m-10) cc_final: 0.8421 (m-80) REVERT: F 129 TYR cc_start: 0.9426 (t80) cc_final: 0.9201 (t80) REVERT: F 184 GLN cc_start: 0.8906 (mt0) cc_final: 0.8581 (tp-100) REVERT: F 233 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8200 (tm-30) REVERT: G 187 MET cc_start: 0.9012 (mmm) cc_final: 0.8806 (mmm) REVERT: G 233 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8095 (tm-30) REVERT: G 271 ASP cc_start: 0.8741 (m-30) cc_final: 0.8401 (m-30) REVERT: H 14 ARG cc_start: 0.7958 (ptt90) cc_final: 0.7680 (ppt170) REVERT: H 184 GLN cc_start: 0.8941 (mt0) cc_final: 0.8653 (tp40) REVERT: H 187 MET cc_start: 0.9101 (mmp) cc_final: 0.8886 (mmm) REVERT: H 230 GLU cc_start: 0.8438 (tp30) cc_final: 0.8170 (tp30) REVERT: H 237 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8546 (tm-30) REVERT: H 248 ILE cc_start: 0.8853 (mm) cc_final: 0.8377 (tp) REVERT: H 261 VAL cc_start: 0.8511 (t) cc_final: 0.8288 (m) REVERT: H 271 ASP cc_start: 0.8966 (m-30) cc_final: 0.8677 (m-30) REVERT: I 184 GLN cc_start: 0.8934 (mt0) cc_final: 0.8473 (tp40) REVERT: I 245 MET cc_start: 0.8163 (ttm) cc_final: 0.7947 (mtm) REVERT: J 154 GLU cc_start: 0.8679 (tp30) cc_final: 0.8291 (tp30) REVERT: J 184 GLN cc_start: 0.8977 (mt0) cc_final: 0.8482 (tp40) REVERT: J 208 LYS cc_start: 0.8980 (tppt) cc_final: 0.8511 (tmmt) REVERT: J 255 ILE cc_start: 0.9242 (mm) cc_final: 0.9016 (mm) REVERT: J 262 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8152 (mmmm) REVERT: K 22 LEU cc_start: 0.9003 (tp) cc_final: 0.8731 (tp) REVERT: K 174 ARG cc_start: 0.8587 (ttp80) cc_final: 0.8243 (ptm-80) REVERT: K 221 TRP cc_start: 0.8638 (t60) cc_final: 0.8022 (t60) REVERT: K 279 THR cc_start: 0.7709 (m) cc_final: 0.7321 (p) REVERT: L 31 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8731 (tm-30) REVERT: L 74 MET cc_start: 0.8425 (tpt) cc_final: 0.7966 (tpt) REVERT: L 157 LEU cc_start: 0.9183 (tp) cc_final: 0.8896 (tp) REVERT: L 160 PHE cc_start: 0.8298 (m-80) cc_final: 0.8026 (m-80) REVERT: L 184 GLN cc_start: 0.9042 (mt0) cc_final: 0.8497 (tp40) REVERT: L 208 LYS cc_start: 0.8794 (tppt) cc_final: 0.8246 (tmmt) REVERT: L 244 MET cc_start: 0.9139 (tpt) cc_final: 0.8931 (tpt) REVERT: M 74 MET cc_start: 0.8438 (tpt) cc_final: 0.8061 (tpt) REVERT: M 184 GLN cc_start: 0.9090 (mt0) cc_final: 0.8600 (tp-100) REVERT: M 271 ASP cc_start: 0.8834 (m-30) cc_final: 0.8451 (m-30) REVERT: N 41 CYS cc_start: 0.5388 (t) cc_final: 0.5071 (t) REVERT: N 152 LYS cc_start: 0.9133 (tppp) cc_final: 0.8910 (tppp) REVERT: N 183 TYR cc_start: 0.9262 (t80) cc_final: 0.8816 (t80) REVERT: N 184 GLN cc_start: 0.9145 (mt0) cc_final: 0.8249 (tp40) REVERT: O 154 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8555 (mm-30) REVERT: O 184 GLN cc_start: 0.8951 (mt0) cc_final: 0.8537 (tp-100) REVERT: O 248 ILE cc_start: 0.9049 (tp) cc_final: 0.8815 (tp) REVERT: P 26 LEU cc_start: 0.8969 (tp) cc_final: 0.8730 (tp) REVERT: P 128 TYR cc_start: 0.9027 (m-10) cc_final: 0.8789 (m-80) REVERT: P 184 GLN cc_start: 0.8883 (mt0) cc_final: 0.8676 (tp40) REVERT: P 221 TRP cc_start: 0.8482 (t60) cc_final: 0.8078 (t60) REVERT: P 279 THR cc_start: 0.7462 (m) cc_final: 0.7108 (p) REVERT: Q 153 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8822 (ttt180) REVERT: Q 157 LEU cc_start: 0.9286 (tp) cc_final: 0.9011 (tp) REVERT: Q 184 GLN cc_start: 0.8952 (mt0) cc_final: 0.8566 (tp40) REVERT: Q 230 GLU cc_start: 0.8497 (tp30) cc_final: 0.8101 (tp30) REVERT: R 74 MET cc_start: 0.8502 (tpp) cc_final: 0.8084 (tpt) REVERT: R 157 LEU cc_start: 0.9219 (tp) cc_final: 0.8942 (tp) REVERT: R 184 GLN cc_start: 0.9190 (mt0) cc_final: 0.8745 (tp-100) REVERT: R 233 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8287 (tm-30) REVERT: R 244 MET cc_start: 0.9090 (tpt) cc_final: 0.8838 (tpp) REVERT: S 187 MET cc_start: 0.8749 (mmt) cc_final: 0.8537 (mmp) REVERT: S 249 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7952 (ttmm) REVERT: T 187 MET cc_start: 0.8975 (mmt) cc_final: 0.8727 (mmp) outliers start: 3 outliers final: 0 residues processed: 934 average time/residue: 0.2216 time to fit residues: 344.6592 Evaluate side-chains 679 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 679 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 281 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 404 optimal weight: 5.9990 chunk 457 optimal weight: 8.9990 chunk 4 optimal weight: 0.0270 chunk 300 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN N 217 GLN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN T 48 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098303 restraints weight = 74433.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100320 restraints weight = 47395.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.101626 restraints weight = 35472.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.102469 restraints weight = 29630.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102938 restraints weight = 26471.993| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42620 Z= 0.136 Angle : 0.571 8.094 57900 Z= 0.300 Chirality : 0.040 0.154 6740 Planarity : 0.004 0.058 7180 Dihedral : 3.794 26.094 5700 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 0.61 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.12), residues: 5260 helix: 2.99 (0.08), residues: 3980 sheet: None (None), residues: 0 loop : -2.41 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 247 TYR 0.025 0.001 TYR Q 183 PHE 0.023 0.001 PHE L 160 TRP 0.024 0.001 TRP G 221 HIS 0.003 0.001 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00286 (42580) covalent geometry : angle 0.57005 (57820) SS BOND : bond 0.00342 ( 40) SS BOND : angle 1.21284 ( 80) hydrogen bonds : bond 0.04884 ( 3171) hydrogen bonds : angle 3.69958 ( 9513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 933 time to evaluate : 1.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8553 (tpt) cc_final: 0.8339 (tpt) REVERT: A 122 THR cc_start: 0.9139 (t) cc_final: 0.8908 (t) REVERT: A 128 TYR cc_start: 0.8984 (m-10) cc_final: 0.8425 (m-80) REVERT: A 156 ILE cc_start: 0.9253 (tp) cc_final: 0.8970 (tp) REVERT: A 184 GLN cc_start: 0.8992 (mt0) cc_final: 0.8392 (tp-100) REVERT: A 208 LYS cc_start: 0.8959 (tppt) cc_final: 0.8268 (tmmt) REVERT: A 248 ILE cc_start: 0.9162 (tp) cc_final: 0.8937 (tp) REVERT: B 74 MET cc_start: 0.8210 (tpt) cc_final: 0.7920 (tpp) REVERT: B 128 TYR cc_start: 0.8868 (m-10) cc_final: 0.8664 (m-80) REVERT: B 184 GLN cc_start: 0.8898 (mt0) cc_final: 0.8440 (tp40) REVERT: C 41 CYS cc_start: 0.5263 (t) cc_final: 0.5007 (t) REVERT: C 74 MET cc_start: 0.8447 (tpt) cc_final: 0.8205 (tpt) REVERT: C 184 GLN cc_start: 0.8845 (mt0) cc_final: 0.8481 (tp40) REVERT: C 271 ASP cc_start: 0.8724 (m-30) cc_final: 0.8388 (m-30) REVERT: D 152 LYS cc_start: 0.9246 (tppp) cc_final: 0.9015 (tppp) REVERT: D 184 GLN cc_start: 0.9091 (mt0) cc_final: 0.8599 (tp-100) REVERT: D 233 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 241 ARG cc_start: 0.9148 (tpp80) cc_final: 0.8925 (tpp80) REVERT: D 271 ASP cc_start: 0.8632 (m-30) cc_final: 0.8246 (m-30) REVERT: E 184 GLN cc_start: 0.9085 (mt0) cc_final: 0.8582 (mm-40) REVERT: E 198 ILE cc_start: 0.8211 (mm) cc_final: 0.7922 (tp) REVERT: F 128 TYR cc_start: 0.8962 (m-10) cc_final: 0.8432 (m-80) REVERT: F 129 TYR cc_start: 0.9404 (t80) cc_final: 0.9179 (t80) REVERT: F 184 GLN cc_start: 0.8889 (mt0) cc_final: 0.8583 (tp-100) REVERT: F 233 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8268 (tm-30) REVERT: G 74 MET cc_start: 0.8337 (tpt) cc_final: 0.8060 (tpp) REVERT: G 78 THR cc_start: 0.7308 (m) cc_final: 0.7021 (m) REVERT: G 233 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8025 (tm-30) REVERT: G 271 ASP cc_start: 0.8777 (m-30) cc_final: 0.8417 (m-30) REVERT: H 26 LEU cc_start: 0.8784 (tp) cc_final: 0.8558 (tp) REVERT: H 184 GLN cc_start: 0.8904 (mt0) cc_final: 0.8646 (tp40) REVERT: H 230 GLU cc_start: 0.8426 (tp30) cc_final: 0.8141 (tp30) REVERT: H 237 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8507 (tm-30) REVERT: H 248 ILE cc_start: 0.8817 (mm) cc_final: 0.8331 (tp) REVERT: H 261 VAL cc_start: 0.8482 (t) cc_final: 0.8260 (m) REVERT: H 271 ASP cc_start: 0.8933 (m-30) cc_final: 0.8614 (m-30) REVERT: I 184 GLN cc_start: 0.8945 (mt0) cc_final: 0.8430 (tp40) REVERT: I 245 MET cc_start: 0.8142 (ttm) cc_final: 0.7918 (mtm) REVERT: J 184 GLN cc_start: 0.8944 (mt0) cc_final: 0.8473 (tp40) REVERT: J 187 MET cc_start: 0.8633 (mmt) cc_final: 0.8282 (mmp) REVERT: J 198 ILE cc_start: 0.7908 (mm) cc_final: 0.7666 (tp) REVERT: J 208 LYS cc_start: 0.9015 (tppt) cc_final: 0.8524 (tmmt) REVERT: J 249 LYS cc_start: 0.8210 (ttmm) cc_final: 0.7979 (ttmm) REVERT: J 262 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8140 (mmmm) REVERT: K 22 LEU cc_start: 0.8982 (tp) cc_final: 0.8684 (tp) REVERT: K 135 GLU cc_start: 0.8813 (pm20) cc_final: 0.8233 (pp20) REVERT: K 174 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8224 (ptm-80) REVERT: K 221 TRP cc_start: 0.8570 (t60) cc_final: 0.7966 (t60) REVERT: K 244 MET cc_start: 0.8932 (tpt) cc_final: 0.8687 (tpt) REVERT: K 279 THR cc_start: 0.7503 (m) cc_final: 0.7129 (p) REVERT: L 14 ARG cc_start: 0.7889 (ptt90) cc_final: 0.7448 (ppt170) REVERT: L 31 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8718 (tm-30) REVERT: L 157 LEU cc_start: 0.9179 (tp) cc_final: 0.8859 (tp) REVERT: L 160 PHE cc_start: 0.8295 (m-80) cc_final: 0.8092 (m-80) REVERT: L 184 GLN cc_start: 0.8967 (mt0) cc_final: 0.8508 (tp40) REVERT: L 208 LYS cc_start: 0.8760 (tppt) cc_final: 0.8183 (tmmt) REVERT: M 174 ARG cc_start: 0.8290 (ptm160) cc_final: 0.7953 (ptt180) REVERT: M 184 GLN cc_start: 0.9082 (mt0) cc_final: 0.8537 (tp-100) REVERT: M 271 ASP cc_start: 0.8809 (m-30) cc_final: 0.8428 (m-30) REVERT: N 41 CYS cc_start: 0.5300 (t) cc_final: 0.5069 (t) REVERT: N 78 THR cc_start: 0.7148 (m) cc_final: 0.6922 (m) REVERT: N 183 TYR cc_start: 0.9302 (t80) cc_final: 0.8884 (t80) REVERT: N 184 GLN cc_start: 0.9106 (mt0) cc_final: 0.8281 (tp40) REVERT: O 184 GLN cc_start: 0.8761 (mt0) cc_final: 0.8525 (tp-100) REVERT: P 74 MET cc_start: 0.8378 (tpp) cc_final: 0.8039 (tpp) REVERT: P 135 GLU cc_start: 0.8778 (pm20) cc_final: 0.8328 (pp20) REVERT: P 184 GLN cc_start: 0.8875 (mt0) cc_final: 0.8666 (tp40) REVERT: P 221 TRP cc_start: 0.8482 (t60) cc_final: 0.8080 (t60) REVERT: P 279 THR cc_start: 0.7392 (m) cc_final: 0.7033 (p) REVERT: Q 31 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8988 (tm-30) REVERT: Q 157 LEU cc_start: 0.9236 (tp) cc_final: 0.8992 (tp) REVERT: Q 160 PHE cc_start: 0.8289 (m-80) cc_final: 0.8073 (m-80) REVERT: Q 184 GLN cc_start: 0.8929 (mt0) cc_final: 0.8542 (tp40) REVERT: Q 187 MET cc_start: 0.9144 (mmp) cc_final: 0.8875 (mmm) REVERT: R 51 TYR cc_start: 0.9263 (t80) cc_final: 0.8983 (t80) REVERT: R 74 MET cc_start: 0.8536 (tpp) cc_final: 0.8234 (tpt) REVERT: R 157 LEU cc_start: 0.9228 (tp) cc_final: 0.8951 (tp) REVERT: R 184 GLN cc_start: 0.9170 (mt0) cc_final: 0.8651 (tp-100) REVERT: R 233 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8292 (tm-30) REVERT: T 14 ARG cc_start: 0.7982 (ptt90) cc_final: 0.7768 (ppt170) REVERT: T 187 MET cc_start: 0.8937 (mmt) cc_final: 0.8665 (mmp) REVERT: T 258 SER cc_start: 0.8644 (p) cc_final: 0.8444 (p) outliers start: 2 outliers final: 0 residues processed: 935 average time/residue: 0.2217 time to fit residues: 347.1336 Evaluate side-chains 680 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 342 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 422 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 470 optimal weight: 6.9990 chunk 273 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 224 HIS ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 HIS G 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 HIS J 227 ASN K 224 HIS N 217 GLN N 224 HIS ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 224 HIS Q 224 HIS S 48 ASN S 224 HIS T 48 ASN T 224 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.093784 restraints weight = 75925.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095735 restraints weight = 48001.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097059 restraints weight = 35832.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097898 restraints weight = 29726.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097898 restraints weight = 26573.593| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 42620 Z= 0.217 Angle : 0.681 8.039 57900 Z= 0.356 Chirality : 0.043 0.200 6740 Planarity : 0.005 0.058 7180 Dihedral : 3.976 28.883 5700 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.04 % Allowed : 0.65 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.12), residues: 5260 helix: 2.56 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.84 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 174 TYR 0.019 0.002 TYR M 81 PHE 0.036 0.002 PHE P 104 TRP 0.026 0.002 TRP G 221 HIS 0.003 0.001 HIS J 246 Details of bonding type rmsd covalent geometry : bond 0.00491 (42580) covalent geometry : angle 0.67895 (57820) SS BOND : bond 0.00400 ( 40) SS BOND : angle 1.44025 ( 80) hydrogen bonds : bond 0.05757 ( 3171) hydrogen bonds : angle 4.03418 ( 9513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 865 time to evaluate : 1.613 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.8987 (mt0) cc_final: 0.8568 (tp-100) REVERT: A 208 LYS cc_start: 0.9020 (tppt) cc_final: 0.8330 (tmmt) REVERT: B 128 TYR cc_start: 0.8916 (m-10) cc_final: 0.8624 (m-80) REVERT: B 155 GLU cc_start: 0.8754 (tp30) cc_final: 0.8534 (tm-30) REVERT: B 184 GLN cc_start: 0.8972 (mt0) cc_final: 0.8513 (tp40) REVERT: C 41 CYS cc_start: 0.5274 (t) cc_final: 0.5073 (t) REVERT: C 184 GLN cc_start: 0.8920 (mt0) cc_final: 0.8527 (tp40) REVERT: C 187 MET cc_start: 0.8717 (mmt) cc_final: 0.8478 (mmm) REVERT: C 271 ASP cc_start: 0.8763 (m-30) cc_final: 0.8433 (m-30) REVERT: D 152 LYS cc_start: 0.9265 (tppp) cc_final: 0.9032 (tppp) REVERT: D 184 GLN cc_start: 0.9135 (mt0) cc_final: 0.8588 (tp-100) REVERT: D 237 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 241 ARG cc_start: 0.9208 (tpp80) cc_final: 0.8900 (tpp80) REVERT: D 271 ASP cc_start: 0.8646 (m-30) cc_final: 0.8214 (m-30) REVERT: E 26 LEU cc_start: 0.9011 (tp) cc_final: 0.8696 (tp) REVERT: E 184 GLN cc_start: 0.9011 (mt0) cc_final: 0.8712 (mm-40) REVERT: E 187 MET cc_start: 0.8833 (mmt) cc_final: 0.8573 (mmp) REVERT: E 198 ILE cc_start: 0.8237 (mm) cc_final: 0.7910 (tp) REVERT: F 129 TYR cc_start: 0.9488 (t80) cc_final: 0.9204 (t80) REVERT: F 184 GLN cc_start: 0.8958 (mt0) cc_final: 0.8598 (tp-100) REVERT: F 233 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 262 LYS cc_start: 0.8369 (mmmm) cc_final: 0.8130 (mmmm) REVERT: G 74 MET cc_start: 0.8373 (tpt) cc_final: 0.8040 (tpp) REVERT: G 78 THR cc_start: 0.7531 (m) cc_final: 0.7228 (m) REVERT: G 187 MET cc_start: 0.9077 (mmm) cc_final: 0.8848 (mmm) REVERT: G 233 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8084 (tm-30) REVERT: G 271 ASP cc_start: 0.8743 (m-30) cc_final: 0.8398 (m-30) REVERT: H 26 LEU cc_start: 0.8925 (tp) cc_final: 0.8686 (tp) REVERT: H 70 LEU cc_start: 0.9392 (mm) cc_final: 0.9142 (mp) REVERT: H 184 GLN cc_start: 0.8958 (mt0) cc_final: 0.8691 (tp40) REVERT: H 187 MET cc_start: 0.9162 (mmp) cc_final: 0.8849 (mmm) REVERT: H 230 GLU cc_start: 0.8512 (tp30) cc_final: 0.8245 (tp30) REVERT: H 237 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8486 (tm-30) REVERT: H 245 MET cc_start: 0.8202 (mtm) cc_final: 0.7769 (mtt) REVERT: H 271 ASP cc_start: 0.8869 (m-30) cc_final: 0.8571 (m-30) REVERT: I 184 GLN cc_start: 0.9004 (mt0) cc_final: 0.8672 (tp-100) REVERT: I 245 MET cc_start: 0.8249 (ttm) cc_final: 0.7996 (mtm) REVERT: J 130 GLU cc_start: 0.9087 (pt0) cc_final: 0.8875 (pt0) REVERT: J 184 GLN cc_start: 0.8964 (mt0) cc_final: 0.8537 (tp40) REVERT: J 187 MET cc_start: 0.8763 (mmt) cc_final: 0.8393 (mmp) REVERT: J 208 LYS cc_start: 0.9018 (tppt) cc_final: 0.8524 (tmmt) REVERT: J 249 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8083 (ttmm) REVERT: J 262 LYS cc_start: 0.8420 (mmmm) cc_final: 0.8146 (mmmm) REVERT: K 22 LEU cc_start: 0.9048 (tp) cc_final: 0.8752 (tp) REVERT: K 279 THR cc_start: 0.7600 (m) cc_final: 0.7239 (p) REVERT: L 31 GLN cc_start: 0.9110 (tm-30) cc_final: 0.8794 (tm-30) REVERT: L 157 LEU cc_start: 0.9293 (tp) cc_final: 0.9021 (tp) REVERT: L 184 GLN cc_start: 0.9061 (mt0) cc_final: 0.8594 (tp40) REVERT: L 208 LYS cc_start: 0.8875 (tppt) cc_final: 0.8291 (tmmt) REVERT: M 174 ARG cc_start: 0.8274 (ptm160) cc_final: 0.7945 (ptt180) REVERT: M 184 GLN cc_start: 0.9100 (mt0) cc_final: 0.8516 (tp-100) REVERT: M 271 ASP cc_start: 0.8797 (m-30) cc_final: 0.8469 (m-30) REVERT: N 41 CYS cc_start: 0.5331 (t) cc_final: 0.5128 (t) REVERT: N 152 LYS cc_start: 0.9113 (tppp) cc_final: 0.8890 (tppp) REVERT: N 184 GLN cc_start: 0.9157 (mt0) cc_final: 0.8646 (mm-40) REVERT: O 160 PHE cc_start: 0.8309 (m-80) cc_final: 0.8108 (m-80) REVERT: O 184 GLN cc_start: 0.8917 (mt0) cc_final: 0.8516 (tp40) REVERT: O 187 MET cc_start: 0.9124 (mmt) cc_final: 0.8883 (mmp) REVERT: O 245 MET cc_start: 0.7963 (mtm) cc_final: 0.7646 (mtm) REVERT: O 258 SER cc_start: 0.8674 (p) cc_final: 0.8360 (p) REVERT: P 279 THR cc_start: 0.7411 (m) cc_final: 0.7086 (p) REVERT: Q 157 LEU cc_start: 0.9324 (tp) cc_final: 0.9102 (tp) REVERT: Q 184 GLN cc_start: 0.8995 (mt0) cc_final: 0.8573 (tp40) REVERT: Q 230 GLU cc_start: 0.8533 (tp30) cc_final: 0.8277 (tp30) REVERT: R 74 MET cc_start: 0.8595 (tpp) cc_final: 0.8257 (tpt) REVERT: R 157 LEU cc_start: 0.9292 (tp) cc_final: 0.9044 (tp) REVERT: R 184 GLN cc_start: 0.9231 (mt0) cc_final: 0.8687 (tp-100) REVERT: R 244 MET cc_start: 0.9134 (tpt) cc_final: 0.8854 (tpp) REVERT: S 187 MET cc_start: 0.8807 (mmt) cc_final: 0.8474 (mmp) REVERT: S 249 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8296 (ttmm) REVERT: T 14 ARG cc_start: 0.7885 (ptt90) cc_final: 0.7544 (ppt170) REVERT: T 128 TYR cc_start: 0.8921 (m-10) cc_final: 0.8708 (m-80) REVERT: T 174 ARG cc_start: 0.8818 (ptm-80) cc_final: 0.8490 (ptt180) REVERT: T 187 MET cc_start: 0.8992 (mmt) cc_final: 0.8784 (mmp) outliers start: 2 outliers final: 0 residues processed: 867 average time/residue: 0.2198 time to fit residues: 319.7924 Evaluate side-chains 631 residues out of total 4620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 479 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 470 optimal weight: 4.9990 chunk 386 optimal weight: 0.8980 chunk 415 optimal weight: 0.8980 chunk 334 optimal weight: 0.9980 chunk 427 optimal weight: 0.9990 chunk 498 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 GLN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 ASN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN N 217 GLN R 227 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099327 restraints weight = 73882.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101298 restraints weight = 47334.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.102620 restraints weight = 35502.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103291 restraints weight = 29637.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.103291 restraints weight = 26737.793| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42620 Z= 0.136 Angle : 0.592 7.630 57900 Z= 0.310 Chirality : 0.040 0.156 6740 Planarity : 0.005 0.124 7180 Dihedral : 3.863 26.749 5700 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.12), residues: 5260 helix: 2.97 (0.08), residues: 3980 sheet: None (None), residues: 0 loop : -2.46 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 174 TYR 0.023 0.001 TYR G 183 PHE 0.025 0.001 PHE P 104 TRP 0.023 0.001 TRP G 221 HIS 0.003 0.001 HIS K 246 Details of bonding type rmsd covalent geometry : bond 0.00277 (42580) covalent geometry : angle 0.59147 (57820) SS BOND : bond 0.00338 ( 40) SS BOND : angle 1.08764 ( 80) hydrogen bonds : bond 0.04909 ( 3171) hydrogen bonds : angle 3.74108 ( 9513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7302.20 seconds wall clock time: 126 minutes 56.79 seconds (7616.79 seconds total)