Starting phenix.real_space_refine on Sat Mar 7 14:30:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ytq_10921/03_2026/6ytq_10921.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ytq_10921/03_2026/6ytq_10921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ytq_10921/03_2026/6ytq_10921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ytq_10921/03_2026/6ytq_10921.map" model { file = "/net/cci-nas-00/data/ceres_data/6ytq_10921/03_2026/6ytq_10921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ytq_10921/03_2026/6ytq_10921.cif" } resolution = 4.02 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= 0.000 sd= 0.006 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 440 5.16 5 C 29480 2.51 5 N 7678 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 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: 45782 Number of models: 1 Model: "" Number of chains: 22 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 Chain: "U" 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: "V" 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: 10.03, per 1000 atoms: 0.22 Number of scatterers: 45782 At special positions: 0 Unit cell: (140.7, 140.7, 207.7, 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 440 16.00 O 8184 8.00 N 7678 7.00 C 29480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS U 41 " - pdb=" SG CYS U 131 " distance=2.03 Simple disulfide: pdb=" SG CYS U 43 " - pdb=" SG CYS U 162 " distance=2.03 Simple disulfide: pdb=" SG CYS V 41 " - pdb=" SG CYS V 131 " distance=2.03 Simple disulfide: pdb=" SG CYS V 43 " - pdb=" SG CYS V 162 " distance=2.03 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: 3.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11176 Finding SS restraints... Secondary structure from input PDB file: 264 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.573A pdb=" N ILE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.605A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.969A 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: 3.756A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.541A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE A 145 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 167 through 210 Processing helix chain 'A' and resid 216 through 253 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: 3.605A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.969A 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: 3.757A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE B 145 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 167 through 210 Processing helix chain 'B' and resid 216 through 253 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: 3.604A pdb=" N ILE C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.969A 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: 3.757A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 4.096A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE C 145 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 167 through 210 Processing helix chain 'C' and resid 216 through 253 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: 3.605A pdb=" N ILE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.969A 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: 3.757A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.689A pdb=" N PHE D 145 " --> pdb=" O TYR D 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 167 through 210 Processing helix chain 'D' and resid 216 through 253 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: 3.605A pdb=" N ILE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.968A 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: 3.757A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 4.097A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.687A pdb=" N PHE E 145 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 146 " --> pdb=" O PRO E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 146' Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 167 through 210 Processing helix chain 'E' and resid 216 through 253 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: 3.605A pdb=" N ILE F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.969A 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: 3.757A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE F 145 " --> pdb=" O TYR F 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 146 " --> pdb=" O PRO F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 146' Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 167 through 210 Processing helix chain 'F' and resid 216 through 253 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: 3.605A pdb=" N ILE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.968A 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: 3.756A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE G 145 " --> pdb=" O TYR G 142 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP G 146 " --> pdb=" O PRO G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 142 through 146' Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 167 through 210 Processing helix chain 'G' and resid 216 through 253 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: 3.605A pdb=" N ILE H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.968A 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: 3.756A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.540A pdb=" N LEU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE H 145 " --> pdb=" O TYR H 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP H 146 " --> pdb=" O PRO H 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 142 through 146' Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 167 through 210 Processing helix chain 'H' and resid 216 through 253 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: 3.605A pdb=" N ILE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.968A 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: 3.757A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU I 116 " --> pdb=" O VAL I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.687A pdb=" N PHE I 145 " --> pdb=" O TYR I 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 146 " --> pdb=" O PRO I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 146' Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 167 through 210 Processing helix chain 'I' and resid 216 through 253 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: 3.604A pdb=" N ILE J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.969A 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: 3.756A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.539A pdb=" N LEU J 116 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE J 145 " --> pdb=" O TYR J 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP J 146 " --> pdb=" O PRO J 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 142 through 146' Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 167 through 210 Processing helix chain 'J' and resid 216 through 253 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: 3.604A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.968A 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: 3.757A 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: 3.540A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 4.095A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.688A pdb=" N PHE K 145 " --> pdb=" O TYR K 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP K 146 " --> pdb=" O PRO K 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 142 through 146' Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 167 through 210 Processing helix chain 'K' and resid 216 through 253 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: 3.629A pdb=" N ILE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 removed outlier: 3.969A 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: 3.751A 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: 3.548A pdb=" N LEU L 116 " --> pdb=" O VAL L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE L 145 " --> pdb=" O TYR L 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP L 146 " --> pdb=" O PRO L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 142 through 146' Processing helix chain 'L' and resid 149 through 159 Processing helix chain 'L' and resid 167 through 210 Processing helix chain 'L' and resid 216 through 253 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: 3.628A pdb=" N ILE M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 70 removed outlier: 3.970A 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: 3.750A 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: 3.548A pdb=" N LEU M 116 " --> pdb=" O VAL M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.693A pdb=" N PHE M 145 " --> pdb=" O TYR M 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP M 146 " --> pdb=" O PRO M 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 142 through 146' Processing helix chain 'M' and resid 149 through 159 Processing helix chain 'M' and resid 167 through 210 Processing helix chain 'M' and resid 216 through 253 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: 3.629A pdb=" N ILE N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 removed outlier: 3.969A 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: 3.751A 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: 3.549A pdb=" N LEU N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE N 145 " --> pdb=" O TYR N 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP N 146 " --> pdb=" O PRO N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 142 through 146' Processing helix chain 'N' and resid 149 through 159 Processing helix chain 'N' and resid 167 through 210 Processing helix chain 'N' and resid 216 through 253 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: 3.628A pdb=" N ILE O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 70 removed outlier: 3.969A 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: 3.750A 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: 3.549A pdb=" N LEU O 116 " --> pdb=" O VAL O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 4.107A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.693A pdb=" N PHE O 145 " --> pdb=" O TYR O 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP O 146 " --> pdb=" O PRO O 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 142 through 146' Processing helix chain 'O' and resid 149 through 159 Processing helix chain 'O' and resid 167 through 210 Processing helix chain 'O' and resid 216 through 253 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: 3.629A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.969A 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: 3.750A 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: 3.548A pdb=" N LEU P 116 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 4.107A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE P 145 " --> pdb=" O TYR P 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP P 146 " --> pdb=" O PRO P 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 142 through 146' Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 167 through 210 Processing helix chain 'P' and resid 216 through 253 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: 3.628A pdb=" N ILE Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 70 removed outlier: 3.970A 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: 3.751A 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: 3.548A pdb=" N LEU Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 4.105A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 146 removed outlier: 3.693A pdb=" N PHE Q 145 " --> pdb=" O TYR Q 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP Q 146 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 142 through 146' Processing helix chain 'Q' and resid 149 through 159 Processing helix chain 'Q' and resid 167 through 210 Processing helix chain 'Q' and resid 216 through 253 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: 3.629A pdb=" N ILE R 19 " --> pdb=" O ASN R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 removed outlier: 3.969A 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: 3.752A 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: 3.548A pdb=" N LEU R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE R 145 " --> pdb=" O TYR R 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP R 146 " --> pdb=" O PRO R 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 142 through 146' Processing helix chain 'R' and resid 149 through 159 Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'R' and resid 216 through 253 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: 3.628A pdb=" N ILE S 19 " --> pdb=" O ASN S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 removed outlier: 3.969A 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: 3.751A 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: 3.548A pdb=" N LEU S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE S 145 " --> pdb=" O TYR S 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP S 146 " --> pdb=" O PRO S 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 142 through 146' Processing helix chain 'S' and resid 149 through 159 Processing helix chain 'S' and resid 167 through 210 Processing helix chain 'S' and resid 216 through 253 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: 3.629A pdb=" N ILE T 19 " --> pdb=" O ASN T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 removed outlier: 3.969A 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: 3.751A 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: 3.548A pdb=" N LEU T 116 " --> pdb=" O VAL T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE T 145 " --> pdb=" O TYR T 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP T 146 " --> pdb=" O PRO T 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 142 through 146' Processing helix chain 'T' and resid 149 through 159 Processing helix chain 'T' and resid 167 through 210 Processing helix chain 'T' and resid 216 through 253 Processing helix chain 'T' and resid 270 through 276 Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE U 19 " --> pdb=" O ASN U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE U 55 " --> pdb=" O TYR U 51 " (cutoff:3.500A) Proline residue: U 59 - end of helix Processing helix chain 'U' and resid 71 through 82 removed outlier: 3.750A pdb=" N TRP U 75 " --> pdb=" O ARG U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 112 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.548A pdb=" N LEU U 116 " --> pdb=" O VAL U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS U 131 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE U 145 " --> pdb=" O TYR U 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP U 146 " --> pdb=" O PRO U 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 142 through 146' Processing helix chain 'U' and resid 149 through 159 Processing helix chain 'U' and resid 167 through 210 Processing helix chain 'U' and resid 216 through 253 Processing helix chain 'U' and resid 270 through 276 Processing helix chain 'V' and resid 5 through 15 Processing helix chain 'V' and resid 15 through 38 removed outlier: 3.629A pdb=" N ILE V 19 " --> pdb=" O ASN V 15 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 70 removed outlier: 3.969A pdb=" N PHE V 55 " --> pdb=" O TYR V 51 " (cutoff:3.500A) Proline residue: V 59 - end of helix Processing helix chain 'V' and resid 71 through 82 removed outlier: 3.751A pdb=" N TRP V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 112 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.547A pdb=" N LEU V 116 " --> pdb=" O VAL V 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 133 removed outlier: 4.106A pdb=" N CYS V 131 " --> pdb=" O THR V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 142 through 146 removed outlier: 3.692A pdb=" N PHE V 145 " --> pdb=" O TYR V 142 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP V 146 " --> pdb=" O PRO V 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 142 through 146' Processing helix chain 'V' and resid 149 through 159 Processing helix chain 'V' and resid 167 through 210 Processing helix chain 'V' and resid 216 through 253 Processing helix chain 'V' and resid 270 through 276 3498 hydrogen bonds defined for protein. 10494 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: 8.42 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 14454 1.35 - 1.47: 11828 1.47 - 1.59: 20006 1.59 - 1.72: 0 1.72 - 1.84: 550 Bond restraints: 46838 Sorted by residual: bond pdb=" CG GLU Q 259 " pdb=" CD GLU Q 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.73e+00 bond pdb=" CG GLU T 259 " pdb=" CD GLU T 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG GLU P 259 " pdb=" CD GLU P 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.67e+00 bond pdb=" CG GLU O 259 " pdb=" CD GLU O 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.67e+00 bond pdb=" CG GLU L 259 " pdb=" CD GLU L 259 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.65e+00 ... (remaining 46833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 59076 1.14 - 2.28: 3469 2.28 - 3.42: 634 3.42 - 4.57: 326 4.57 - 5.71: 97 Bond angle restraints: 63602 Sorted by residual: angle pdb=" C SER R 258 " pdb=" N GLU R 259 " pdb=" CA GLU R 259 " ideal model delta sigma weight residual 122.29 127.32 -5.03 1.65e+00 3.67e-01 9.31e+00 angle pdb=" C SER L 258 " pdb=" N GLU L 259 " pdb=" CA GLU L 259 " ideal model delta sigma weight residual 122.29 127.31 -5.02 1.65e+00 3.67e-01 9.26e+00 angle pdb=" C SER N 258 " pdb=" N GLU N 259 " pdb=" CA GLU N 259 " ideal model delta sigma weight residual 122.29 127.31 -5.02 1.65e+00 3.67e-01 9.25e+00 angle pdb=" C SER O 258 " pdb=" N GLU O 259 " pdb=" CA GLU O 259 " ideal model delta sigma weight residual 122.29 127.29 -5.00 1.65e+00 3.67e-01 9.20e+00 angle pdb=" C SER P 258 " pdb=" N GLU P 259 " pdb=" CA GLU P 259 " ideal model delta sigma weight residual 122.29 127.29 -5.00 1.65e+00 3.67e-01 9.19e+00 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 25046 17.13 - 34.26: 2234 34.26 - 51.39: 583 51.39 - 68.52: 55 68.52 - 85.65: 66 Dihedral angle restraints: 27984 sinusoidal: 10802 harmonic: 17182 Sorted by residual: dihedral pdb=" CB CYS M 43 " pdb=" SG CYS M 43 " pdb=" SG CYS M 162 " pdb=" CB CYS M 162 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS R 43 " pdb=" SG CYS R 43 " pdb=" SG CYS R 162 " pdb=" CB CYS R 162 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS V 43 " pdb=" SG CYS V 43 " pdb=" SG CYS V 162 " pdb=" CB CYS V 162 " ideal model delta sinusoidal sigma weight residual -86.00 -171.65 85.65 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 27981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4910 0.038 - 0.075: 1950 0.075 - 0.113: 360 0.113 - 0.150: 161 0.150 - 0.188: 33 Chirality restraints: 7414 Sorted by residual: chirality pdb=" CA GLU L 259 " pdb=" N GLU L 259 " pdb=" C GLU L 259 " pdb=" CB GLU L 259 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA GLU Q 259 " pdb=" N GLU Q 259 " pdb=" C GLU Q 259 " pdb=" CB GLU Q 259 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA GLU S 259 " pdb=" N GLU S 259 " pdb=" C GLU S 259 " pdb=" CB GLU S 259 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.56e-01 ... (remaining 7411 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU O 259 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C GLU O 259 " -0.054 2.00e-02 2.50e+03 pdb=" O GLU O 259 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP O 260 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 259 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" C GLU R 259 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU R 259 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP R 260 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T 259 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C GLU T 259 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU T 259 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP T 260 " -0.018 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 19248 2.91 - 3.40: 51405 3.40 - 3.90: 70761 3.90 - 4.40: 74682 4.40 - 4.90: 126585 Nonbonded interactions: 342681 Sorted by model distance: nonbonded pdb=" O SER O 138 " pdb=" OG SER O 138 " model vdw 2.407 3.040 nonbonded pdb=" O SER S 138 " pdb=" OG SER S 138 " model vdw 2.407 3.040 nonbonded pdb=" O SER Q 138 " pdb=" OG SER Q 138 " model vdw 2.407 3.040 nonbonded pdb=" O SER P 138 " pdb=" OG SER P 138 " model vdw 2.408 3.040 nonbonded pdb=" O SER N 138 " pdb=" OG SER N 138 " model vdw 2.408 3.040 ... (remaining 342676 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' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.060 Extract box with map and model: 0.750 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 38.180 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.170 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.006 0.048 46882 Z= 0.250 Angle : 0.707 6.547 63690 Z= 0.390 Chirality : 0.043 0.188 7414 Planarity : 0.005 0.052 7898 Dihedral : 13.936 81.472 16676 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % 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: -0.58 (0.10), residues: 5786 helix: 0.50 (0.07), residues: 4422 sheet: None (None), residues: 0 loop : -3.29 (0.13), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 174 TYR 0.007 0.001 TYR N 220 PHE 0.012 0.002 PHE R 68 TRP 0.009 0.001 TRP C 221 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00551 (46838) covalent geometry : angle 0.68159 (63602) SS BOND : bond 0.00129 ( 44) SS BOND : angle 5.07532 ( 88) hydrogen bonds : bond 0.12473 ( 3498) hydrogen bonds : angle 5.29661 (10494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1260 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8303 (mt0) cc_final: 0.7813 (tt0) REVERT: A 74 MET cc_start: 0.7875 (tmm) cc_final: 0.7563 (tmm) REVERT: A 184 GLN cc_start: 0.8591 (mt0) cc_final: 0.8370 (tt0) REVERT: A 187 MET cc_start: 0.9309 (mmp) cc_final: 0.9052 (tpp) REVERT: A 228 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 245 MET cc_start: 0.8045 (ttm) cc_final: 0.7735 (ttm) REVERT: A 249 LYS cc_start: 0.8681 (tttt) cc_final: 0.8283 (ttpp) REVERT: B 12 LEU cc_start: 0.7621 (pp) cc_final: 0.7231 (mt) REVERT: B 51 TYR cc_start: 0.9031 (t80) cc_final: 0.8477 (t80) REVERT: B 74 MET cc_start: 0.7796 (tmm) cc_final: 0.7436 (tmm) REVERT: B 155 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8101 (tm-30) REVERT: B 237 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 249 LYS cc_start: 0.8794 (tttt) cc_final: 0.8573 (tttm) REVERT: C 12 LEU cc_start: 0.7820 (pp) cc_final: 0.7509 (mt) REVERT: C 32 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 74 MET cc_start: 0.7826 (tmm) cc_final: 0.7033 (tmm) REVERT: C 208 LYS cc_start: 0.8538 (tptp) cc_final: 0.8253 (tmmt) REVERT: C 211 SER cc_start: 0.9353 (t) cc_final: 0.8527 (p) REVERT: C 237 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 249 LYS cc_start: 0.8682 (tttt) cc_final: 0.8271 (ttpp) REVERT: D 7 ASN cc_start: 0.5643 (t0) cc_final: 0.5173 (p0) REVERT: D 12 LEU cc_start: 0.7769 (pp) cc_final: 0.7377 (mt) REVERT: D 74 MET cc_start: 0.7641 (tmm) cc_final: 0.7307 (tmm) REVERT: D 155 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 175 ASP cc_start: 0.8777 (t70) cc_final: 0.8356 (t0) REVERT: D 203 SER cc_start: 0.9209 (p) cc_final: 0.8969 (t) REVERT: D 273 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8211 (tptm) REVERT: E 74 MET cc_start: 0.7067 (tmm) cc_final: 0.6843 (tmm) REVERT: E 174 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7851 (tmm-80) REVERT: E 195 LEU cc_start: 0.8591 (tt) cc_final: 0.8331 (tp) REVERT: F 74 MET cc_start: 0.7557 (tmm) cc_final: 0.6888 (tmm) REVERT: F 128 TYR cc_start: 0.8976 (m-10) cc_final: 0.8712 (m-80) REVERT: F 155 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8460 (tm-30) REVERT: F 238 GLN cc_start: 0.8358 (tt0) cc_final: 0.8137 (tt0) REVERT: F 249 LYS cc_start: 0.8966 (tttt) cc_final: 0.8606 (ttpp) REVERT: F 273 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8724 (tptp) REVERT: G 12 LEU cc_start: 0.7679 (pp) cc_final: 0.7406 (mm) REVERT: G 74 MET cc_start: 0.7511 (tmm) cc_final: 0.7149 (tmm) REVERT: G 128 TYR cc_start: 0.8814 (m-10) cc_final: 0.8600 (m-80) REVERT: G 155 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 237 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8222 (tm-30) REVERT: H 74 MET cc_start: 0.7807 (tmm) cc_final: 0.7574 (tmm) REVERT: H 187 MET cc_start: 0.9286 (mmp) cc_final: 0.9022 (mmt) REVERT: H 208 LYS cc_start: 0.8580 (tptp) cc_final: 0.8357 (tmmt) REVERT: H 245 MET cc_start: 0.7769 (ttm) cc_final: 0.7542 (ttp) REVERT: H 270 GLN cc_start: 0.7784 (tp40) cc_final: 0.7509 (tp40) REVERT: H 273 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8021 (tptm) REVERT: I 116 LEU cc_start: 0.8634 (mp) cc_final: 0.8373 (tt) REVERT: I 130 GLU cc_start: 0.7523 (pp20) cc_final: 0.7273 (pp20) REVERT: I 155 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8255 (tm-30) REVERT: I 233 GLU cc_start: 0.8511 (tp30) cc_final: 0.8181 (tt0) REVERT: I 234 GLN cc_start: 0.8976 (tt0) cc_final: 0.8652 (tt0) REVERT: I 237 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8291 (tm-30) REVERT: J 51 TYR cc_start: 0.8987 (t80) cc_final: 0.8318 (t80) REVERT: J 74 MET cc_start: 0.7973 (tmm) cc_final: 0.7400 (tmm) REVERT: J 250 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8241 (tmmt) REVERT: K 74 MET cc_start: 0.7994 (tmm) cc_final: 0.7191 (tmm) REVERT: K 77 ILE cc_start: 0.9218 (mt) cc_final: 0.8984 (mt) REVERT: K 249 LYS cc_start: 0.8662 (tttt) cc_final: 0.8353 (ttpp) REVERT: L 50 TYR cc_start: 0.8634 (m-80) cc_final: 0.8216 (m-80) REVERT: L 74 MET cc_start: 0.7961 (tmm) cc_final: 0.7150 (tmm) REVERT: L 169 ASP cc_start: 0.7837 (t0) cc_final: 0.7488 (t70) REVERT: L 187 MET cc_start: 0.9468 (mmp) cc_final: 0.9129 (tpp) REVERT: L 237 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8173 (tm-30) REVERT: L 273 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8597 (tptp) REVERT: M 50 TYR cc_start: 0.8649 (m-80) cc_final: 0.8429 (m-80) REVERT: M 74 MET cc_start: 0.7724 (tmm) cc_final: 0.7098 (tmm) REVERT: M 130 GLU cc_start: 0.7785 (pp20) cc_final: 0.7446 (pp20) REVERT: M 155 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8246 (tm-30) REVERT: M 233 GLU cc_start: 0.8345 (tp30) cc_final: 0.8033 (tp30) REVERT: N 73 GLN cc_start: 0.8359 (mt0) cc_final: 0.8049 (tt0) REVERT: N 74 MET cc_start: 0.8210 (tmm) cc_final: 0.7618 (tmm) REVERT: N 249 LYS cc_start: 0.8799 (tttt) cc_final: 0.8578 (ttpp) REVERT: O 74 MET cc_start: 0.7874 (tmm) cc_final: 0.7154 (tmm) REVERT: O 130 GLU cc_start: 0.7916 (pp20) cc_final: 0.7556 (pp20) REVERT: O 208 LYS cc_start: 0.8473 (tptp) cc_final: 0.8249 (tmmt) REVERT: O 237 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8407 (tm-30) REVERT: P 5 LEU cc_start: 0.4925 (mt) cc_final: 0.4594 (tt) REVERT: P 50 TYR cc_start: 0.8505 (m-80) cc_final: 0.8256 (m-80) REVERT: P 128 TYR cc_start: 0.8909 (m-10) cc_final: 0.8522 (m-80) REVERT: P 176 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7921 (tm-30) REVERT: P 203 SER cc_start: 0.9031 (p) cc_final: 0.8822 (p) REVERT: P 237 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8404 (tm-30) REVERT: P 249 LYS cc_start: 0.8734 (tttt) cc_final: 0.8453 (tmtt) REVERT: Q 74 MET cc_start: 0.7616 (tmm) cc_final: 0.7030 (tmm) REVERT: Q 237 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8397 (tm-30) REVERT: Q 249 LYS cc_start: 0.8643 (tttt) cc_final: 0.8367 (tmtt) REVERT: Q 250 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8307 (tmmt) REVERT: Q 273 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8420 (tptp) REVERT: R 74 MET cc_start: 0.7854 (tmm) cc_final: 0.7160 (tmm) REVERT: R 233 GLU cc_start: 0.8508 (tp30) cc_final: 0.8064 (tt0) REVERT: R 237 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8064 (tm-30) REVERT: R 245 MET cc_start: 0.8193 (ttm) cc_final: 0.7706 (ttm) REVERT: R 249 LYS cc_start: 0.8841 (tttt) cc_final: 0.8489 (ttpp) REVERT: R 272 TRP cc_start: 0.8836 (m100) cc_final: 0.8478 (m100) REVERT: R 273 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8546 (tptp) REVERT: S 12 LEU cc_start: 0.7914 (pp) cc_final: 0.7530 (mt) REVERT: S 31 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8682 (tm-30) REVERT: S 73 GLN cc_start: 0.8332 (mt0) cc_final: 0.8103 (tt0) REVERT: S 203 SER cc_start: 0.9271 (p) cc_final: 0.9021 (t) REVERT: S 233 GLU cc_start: 0.8175 (tp30) cc_final: 0.7969 (tt0) REVERT: S 249 LYS cc_start: 0.8632 (tttt) cc_final: 0.8202 (tttm) REVERT: T 51 TYR cc_start: 0.8773 (t80) cc_final: 0.8214 (t80) REVERT: T 74 MET cc_start: 0.7802 (tmm) cc_final: 0.7231 (tmm) REVERT: T 249 LYS cc_start: 0.8466 (tttt) cc_final: 0.8127 (ttpp) REVERT: U 12 LEU cc_start: 0.7661 (pp) cc_final: 0.7281 (mt) REVERT: U 184 GLN cc_start: 0.8543 (mt0) cc_final: 0.8251 (mm-40) REVERT: U 201 LEU cc_start: 0.9351 (tp) cc_final: 0.8940 (tt) REVERT: U 233 GLU cc_start: 0.8076 (tp30) cc_final: 0.7803 (tp30) REVERT: U 249 LYS cc_start: 0.8728 (tttt) cc_final: 0.8376 (ttpp) REVERT: V 32 GLN cc_start: 0.8234 (tm-30) cc_final: 0.8027 (tm-30) REVERT: V 74 MET cc_start: 0.7612 (tmm) cc_final: 0.6999 (tmm) REVERT: V 130 GLU cc_start: 0.8056 (pp20) cc_final: 0.7823 (pp20) REVERT: V 155 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8129 (tm-30) REVERT: V 225 LEU cc_start: 0.8643 (mt) cc_final: 0.8253 (mt) REVERT: V 250 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8509 (tmmt) REVERT: V 273 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8419 (tptm) outliers start: 0 outliers final: 0 residues processed: 1260 average time/residue: 0.3093 time to fit residues: 612.6965 Evaluate side-chains 748 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 0.0970 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.0870 chunk 488 optimal weight: 0.7980 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 10.0000 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 48 ASN A 227 ASN B 48 ASN B 227 ASN C 48 ASN C 227 ASN D 48 ASN E 48 ASN E 181 HIS ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN G 48 ASN G 227 ASN H 48 ASN H 227 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN I 226 GLN I 227 ASN J 48 ASN J 227 ASN K 48 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN M 48 ASN N 44 GLN N 48 ASN N 227 ASN O 48 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN P 227 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN S 44 GLN S 48 ASN T 48 ASN T 227 ASN U 48 ASN U 73 GLN V 48 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107010 restraints weight = 78208.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109827 restraints weight = 44776.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111423 restraints weight = 32155.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112581 restraints weight = 26750.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.113197 restraints weight = 23926.516| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46882 Z= 0.137 Angle : 0.559 6.555 63690 Z= 0.299 Chirality : 0.040 0.204 7414 Planarity : 0.005 0.054 7898 Dihedral : 4.019 17.615 6270 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.43 % Allowed : 5.10 % Favored : 94.47 % 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: 1.34 (0.11), residues: 5786 helix: 1.89 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -3.14 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 174 TYR 0.014 0.001 TYR P 81 PHE 0.015 0.001 PHE E 232 TRP 0.007 0.001 TRP K 272 HIS 0.003 0.001 HIS V 224 Details of bonding type rmsd covalent geometry : bond 0.00280 (46838) covalent geometry : angle 0.55208 (63602) SS BOND : bond 0.00158 ( 44) SS BOND : angle 2.47516 ( 88) hydrogen bonds : bond 0.04966 ( 3498) hydrogen bonds : angle 3.98146 (10494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1076 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8053 (tmm) cc_final: 0.7584 (tmm) REVERT: A 77 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 155 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8323 (tm-30) REVERT: A 187 MET cc_start: 0.9223 (mmp) cc_final: 0.9007 (tpp) REVERT: A 249 LYS cc_start: 0.8382 (tttt) cc_final: 0.8134 (ttpp) REVERT: B 12 LEU cc_start: 0.7603 (pp) cc_final: 0.7297 (mt) REVERT: B 51 TYR cc_start: 0.9047 (t80) cc_final: 0.8754 (t80) REVERT: B 74 MET cc_start: 0.8125 (tmm) cc_final: 0.7629 (tmm) REVERT: B 251 LEU cc_start: 0.9058 (tp) cc_final: 0.8848 (tt) REVERT: C 78 THR cc_start: 0.7139 (p) cc_final: 0.6905 (t) REVERT: C 208 LYS cc_start: 0.8483 (tptp) cc_final: 0.8152 (tmmt) REVERT: C 211 SER cc_start: 0.9370 (t) cc_final: 0.8550 (p) REVERT: C 242 LEU cc_start: 0.9084 (mm) cc_final: 0.8844 (mt) REVERT: C 250 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8110 (ttmt) REVERT: D 7 ASN cc_start: 0.5054 (t0) cc_final: 0.4758 (p0) REVERT: D 74 MET cc_start: 0.7922 (tmm) cc_final: 0.7710 (tmm) REVERT: D 155 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8099 (tm-30) REVERT: D 175 ASP cc_start: 0.8808 (t70) cc_final: 0.8508 (t70) REVERT: D 201 LEU cc_start: 0.9220 (tp) cc_final: 0.8967 (tt) REVERT: D 203 SER cc_start: 0.9088 (p) cc_final: 0.8884 (t) REVERT: D 237 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8452 (tm-30) REVERT: E 74 MET cc_start: 0.7320 (tmm) cc_final: 0.6376 (tmm) REVERT: E 176 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7839 (tm-30) REVERT: E 195 LEU cc_start: 0.8517 (tt) cc_final: 0.8281 (tp) REVERT: E 249 LYS cc_start: 0.8734 (tttt) cc_final: 0.8379 (ttpp) REVERT: F 74 MET cc_start: 0.7662 (tmm) cc_final: 0.6903 (tmm) REVERT: F 155 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8492 (tm-30) REVERT: F 220 TYR cc_start: 0.8792 (t80) cc_final: 0.8519 (t80) REVERT: F 249 LYS cc_start: 0.8745 (tttt) cc_final: 0.8449 (ttpp) REVERT: G 74 MET cc_start: 0.7810 (tmm) cc_final: 0.7201 (tmm) REVERT: G 99 LEU cc_start: 0.8859 (mt) cc_final: 0.8608 (mt) REVERT: G 237 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8215 (tm-30) REVERT: H 12 LEU cc_start: 0.7703 (pp) cc_final: 0.7390 (mp) REVERT: H 73 GLN cc_start: 0.8065 (mt0) cc_final: 0.7599 (tt0) REVERT: H 99 LEU cc_start: 0.8640 (mt) cc_final: 0.7861 (pp) REVERT: H 128 TYR cc_start: 0.9082 (m-10) cc_final: 0.8811 (m-80) REVERT: H 237 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8301 (tm-30) REVERT: H 245 MET cc_start: 0.7676 (ttm) cc_final: 0.7378 (ttp) REVERT: H 250 LYS cc_start: 0.8583 (tmmt) cc_final: 0.7911 (ttmt) REVERT: H 270 GLN cc_start: 0.7759 (tp40) cc_final: 0.7374 (tp40) REVERT: I 77 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8487 (mp) REVERT: I 155 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8316 (tm-30) REVERT: I 237 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8321 (tm-30) REVERT: I 238 GLN cc_start: 0.8278 (tt0) cc_final: 0.8003 (tt0) REVERT: J 51 TYR cc_start: 0.8948 (t80) cc_final: 0.8223 (t80) REVERT: J 74 MET cc_start: 0.8185 (tmm) cc_final: 0.7660 (tmm) REVERT: J 208 LYS cc_start: 0.8581 (mmmm) cc_final: 0.8037 (tmmt) REVERT: J 250 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8089 (tmmt) REVERT: K 74 MET cc_start: 0.7949 (tmm) cc_final: 0.7400 (tmm) REVERT: K 99 LEU cc_start: 0.8800 (mt) cc_final: 0.8590 (mt) REVERT: K 130 GLU cc_start: 0.8383 (pp20) cc_final: 0.8154 (pp20) REVERT: L 50 TYR cc_start: 0.8542 (m-80) cc_final: 0.8051 (m-80) REVERT: L 53 SER cc_start: 0.8394 (t) cc_final: 0.8186 (t) REVERT: L 74 MET cc_start: 0.8079 (tmm) cc_final: 0.7207 (tmm) REVERT: L 144 MET cc_start: 0.7932 (pmm) cc_final: 0.7642 (pmm) REVERT: L 187 MET cc_start: 0.9373 (mmp) cc_final: 0.9088 (tpp) REVERT: L 249 LYS cc_start: 0.8388 (tmtt) cc_final: 0.7895 (ttpp) REVERT: L 273 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8310 (tptp) REVERT: M 50 TYR cc_start: 0.8456 (m-80) cc_final: 0.8201 (m-80) REVERT: M 74 MET cc_start: 0.7889 (tmm) cc_final: 0.7180 (tmm) REVERT: M 155 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8405 (tm-30) REVERT: M 237 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8424 (tm-30) REVERT: N 74 MET cc_start: 0.8041 (tmm) cc_final: 0.7485 (tmm) REVERT: N 78 THR cc_start: 0.7688 (p) cc_final: 0.7005 (t) REVERT: O 74 MET cc_start: 0.7956 (tmm) cc_final: 0.7500 (tmm) REVERT: O 78 THR cc_start: 0.7147 (p) cc_final: 0.6563 (t) REVERT: O 99 LEU cc_start: 0.8873 (mt) cc_final: 0.8636 (mt) REVERT: O 128 TYR cc_start: 0.9000 (m-10) cc_final: 0.8615 (m-80) REVERT: O 176 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7953 (tm-30) REVERT: O 208 LYS cc_start: 0.8411 (tptp) cc_final: 0.8204 (tmmt) REVERT: O 233 GLU cc_start: 0.8378 (tp30) cc_final: 0.8024 (tt0) REVERT: P 5 LEU cc_start: 0.5303 (mt) cc_final: 0.4885 (tt) REVERT: P 50 TYR cc_start: 0.8372 (m-80) cc_final: 0.8162 (m-80) REVERT: P 74 MET cc_start: 0.8154 (tpp) cc_final: 0.7880 (tpp) REVERT: P 116 LEU cc_start: 0.9117 (tp) cc_final: 0.8888 (tt) REVERT: P 176 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7875 (tm-30) REVERT: P 233 GLU cc_start: 0.8291 (tp30) cc_final: 0.8005 (tp30) REVERT: P 237 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8484 (tm-30) REVERT: Q 5 LEU cc_start: 0.5788 (mt) cc_final: 0.5454 (tt) REVERT: Q 116 LEU cc_start: 0.8748 (mt) cc_final: 0.8405 (tt) REVERT: Q 233 GLU cc_start: 0.8433 (tp30) cc_final: 0.8080 (tp30) REVERT: Q 237 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8442 (tm-30) REVERT: Q 249 LYS cc_start: 0.8412 (tttt) cc_final: 0.8171 (ttpp) REVERT: Q 250 LYS cc_start: 0.8350 (ttmt) cc_final: 0.8112 (tmmt) REVERT: R 51 TYR cc_start: 0.9164 (t80) cc_final: 0.8334 (t80) REVERT: R 74 MET cc_start: 0.7888 (tmm) cc_final: 0.7363 (tmm) REVERT: R 99 LEU cc_start: 0.8489 (mt) cc_final: 0.8117 (mt) REVERT: R 130 GLU cc_start: 0.7707 (pp20) cc_final: 0.7488 (pp20) REVERT: R 233 GLU cc_start: 0.8378 (tp30) cc_final: 0.8007 (tp30) REVERT: R 237 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8174 (tm-30) REVERT: R 249 LYS cc_start: 0.8629 (tttt) cc_final: 0.8308 (ttpp) REVERT: R 272 TRP cc_start: 0.8841 (m100) cc_final: 0.8490 (m100) REVERT: R 273 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8663 (tptm) REVERT: S 12 LEU cc_start: 0.7752 (pp) cc_final: 0.7550 (mt) REVERT: S 99 LEU cc_start: 0.8640 (mt) cc_final: 0.8398 (mt) REVERT: S 155 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8104 (tm-30) REVERT: S 203 SER cc_start: 0.9262 (p) cc_final: 0.8998 (t) REVERT: S 237 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8381 (tm-30) REVERT: S 249 LYS cc_start: 0.8535 (tttt) cc_final: 0.8270 (ttpp) REVERT: T 12 LEU cc_start: 0.7869 (pp) cc_final: 0.7440 (mt) REVERT: T 51 TYR cc_start: 0.8755 (t80) cc_final: 0.8118 (t80) REVERT: T 74 MET cc_start: 0.8008 (tmm) cc_final: 0.7268 (tmm) REVERT: T 99 LEU cc_start: 0.8939 (mt) cc_final: 0.8693 (mt) REVERT: T 155 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8128 (tm-30) REVERT: T 208 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8158 (tmmt) REVERT: U 12 LEU cc_start: 0.7380 (pp) cc_final: 0.7113 (mt) REVERT: U 74 MET cc_start: 0.7815 (tmm) cc_final: 0.7307 (tmm) REVERT: U 128 TYR cc_start: 0.8984 (m-10) cc_final: 0.8590 (m-80) REVERT: U 130 GLU cc_start: 0.8015 (pp20) cc_final: 0.7712 (pp20) REVERT: U 155 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8335 (tm-30) REVERT: U 176 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8130 (tm-30) REVERT: U 184 GLN cc_start: 0.8455 (mt0) cc_final: 0.8141 (mm-40) REVERT: U 249 LYS cc_start: 0.8493 (tttt) cc_final: 0.8226 (ttpp) REVERT: V 73 GLN cc_start: 0.8236 (mt0) cc_final: 0.8024 (mt0) REVERT: V 74 MET cc_start: 0.8032 (tmm) cc_final: 0.7766 (tmm) REVERT: V 155 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8407 (tm-30) REVERT: V 250 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8187 (tmmt) REVERT: V 273 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8241 (tptm) outliers start: 22 outliers final: 0 residues processed: 1093 average time/residue: 0.2693 time to fit residues: 488.8010 Evaluate side-chains 754 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 752 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 233 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 404 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 323 optimal weight: 0.0270 chunk 232 optimal weight: 0.2980 chunk 168 optimal weight: 2.9990 chunk 431 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 411 optimal weight: 6.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 73 GLN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 227 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN Q 227 ASN R 44 GLN R 227 ASN T 227 ASN U 44 GLN U 48 ASN V 44 GLN V 227 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103441 restraints weight = 79062.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105993 restraints weight = 46841.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107574 restraints weight = 33899.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108481 restraints weight = 28004.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108963 restraints weight = 24971.004| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46882 Z= 0.127 Angle : 0.538 6.188 63690 Z= 0.288 Chirality : 0.039 0.213 7414 Planarity : 0.005 0.053 7898 Dihedral : 3.919 18.468 6270 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.31 % Allowed : 4.57 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.10 (0.11), residues: 5786 helix: 2.42 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.86 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 14 TYR 0.013 0.001 TYR E 128 PHE 0.014 0.001 PHE Q 232 TRP 0.008 0.001 TRP C 221 HIS 0.003 0.000 HIS G 224 Details of bonding type rmsd covalent geometry : bond 0.00255 (46838) covalent geometry : angle 0.53092 (63602) SS BOND : bond 0.00267 ( 44) SS BOND : angle 2.33284 ( 88) hydrogen bonds : bond 0.04422 ( 3498) hydrogen bonds : angle 3.64834 (10494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 1052 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8067 (tmm) cc_final: 0.7664 (tmm) REVERT: A 77 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8811 (mp) REVERT: A 78 THR cc_start: 0.7721 (p) cc_final: 0.7363 (t) REVERT: B 12 LEU cc_start: 0.7501 (pp) cc_final: 0.7247 (mt) REVERT: B 74 MET cc_start: 0.8056 (tmm) cc_final: 0.7693 (tmm) REVERT: B 78 THR cc_start: 0.7580 (p) cc_final: 0.7148 (p) REVERT: B 116 LEU cc_start: 0.8827 (tp) cc_final: 0.8610 (tt) REVERT: B 135 GLU cc_start: 0.8253 (pp20) cc_final: 0.7851 (pp20) REVERT: B 251 LEU cc_start: 0.9068 (tp) cc_final: 0.8854 (tt) REVERT: C 12 LEU cc_start: 0.7776 (mt) cc_final: 0.7308 (pp) REVERT: C 250 LYS cc_start: 0.8520 (tmmt) cc_final: 0.8021 (ttmt) REVERT: D 7 ASN cc_start: 0.5188 (t0) cc_final: 0.4844 (p0) REVERT: D 175 ASP cc_start: 0.8734 (t70) cc_final: 0.8409 (t70) REVERT: D 227 ASN cc_start: 0.8894 (m-40) cc_final: 0.8591 (m-40) REVERT: D 228 GLU cc_start: 0.8230 (pp20) cc_final: 0.7880 (tm-30) REVERT: E 74 MET cc_start: 0.7140 (tmm) cc_final: 0.6421 (tmm) REVERT: E 99 LEU cc_start: 0.8820 (mt) cc_final: 0.8609 (mt) REVERT: E 176 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7925 (tm-30) REVERT: F 74 MET cc_start: 0.7738 (tmm) cc_final: 0.7000 (tmm) REVERT: F 128 TYR cc_start: 0.8824 (m-80) cc_final: 0.8422 (m-80) REVERT: F 135 GLU cc_start: 0.8116 (pp20) cc_final: 0.7580 (pp20) REVERT: F 220 TYR cc_start: 0.8791 (t80) cc_final: 0.8469 (t80) REVERT: F 249 LYS cc_start: 0.8615 (tttt) cc_final: 0.8259 (ttpp) REVERT: G 99 LEU cc_start: 0.8796 (mt) cc_final: 0.8547 (mt) REVERT: G 233 GLU cc_start: 0.8361 (tp30) cc_final: 0.8105 (tt0) REVERT: G 237 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8200 (tm-30) REVERT: G 273 LYS cc_start: 0.8689 (tptt) cc_final: 0.8387 (tptm) REVERT: H 12 LEU cc_start: 0.7511 (pp) cc_final: 0.7204 (mm) REVERT: H 74 MET cc_start: 0.8047 (tmm) cc_final: 0.7416 (tmm) REVERT: H 99 LEU cc_start: 0.8642 (mt) cc_final: 0.7820 (pp) REVERT: H 128 TYR cc_start: 0.9065 (m-10) cc_final: 0.8709 (m-80) REVERT: H 237 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8171 (tm-30) REVERT: H 250 LYS cc_start: 0.8443 (tmmt) cc_final: 0.7777 (ttmt) REVERT: H 270 GLN cc_start: 0.7719 (tp40) cc_final: 0.7369 (tp40) REVERT: I 77 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (mp) REVERT: I 135 GLU cc_start: 0.8230 (pp20) cc_final: 0.7619 (pp20) REVERT: I 249 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8312 (ttpp) REVERT: J 51 TYR cc_start: 0.9042 (t80) cc_final: 0.8293 (t80) REVERT: J 74 MET cc_start: 0.8180 (tmm) cc_final: 0.7620 (tmm) REVERT: J 208 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8102 (tmmt) REVERT: J 250 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7988 (tmmt) REVERT: K 74 MET cc_start: 0.7984 (tmm) cc_final: 0.7369 (tmm) REVERT: K 78 THR cc_start: 0.7128 (p) cc_final: 0.6668 (p) REVERT: L 50 TYR cc_start: 0.8571 (m-80) cc_final: 0.7929 (m-10) REVERT: L 74 MET cc_start: 0.8049 (tmm) cc_final: 0.7355 (tmm) REVERT: L 77 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8826 (mp) REVERT: L 135 GLU cc_start: 0.8293 (pp20) cc_final: 0.7605 (pp20) REVERT: L 237 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8332 (tm-30) REVERT: L 249 LYS cc_start: 0.8175 (tmtt) cc_final: 0.7647 (ttpp) REVERT: L 273 LYS cc_start: 0.8704 (mmtm) cc_final: 0.8345 (tptp) REVERT: M 50 TYR cc_start: 0.8398 (m-80) cc_final: 0.8188 (m-80) REVERT: M 74 MET cc_start: 0.7976 (tmm) cc_final: 0.7361 (tmm) REVERT: M 78 THR cc_start: 0.7050 (p) cc_final: 0.6134 (p) REVERT: N 53 SER cc_start: 0.8528 (t) cc_final: 0.8285 (t) REVERT: N 74 MET cc_start: 0.8070 (tmm) cc_final: 0.7562 (tmm) REVERT: N 78 THR cc_start: 0.7721 (p) cc_final: 0.7079 (t) REVERT: N 99 LEU cc_start: 0.8633 (mt) cc_final: 0.8418 (mt) REVERT: N 144 MET cc_start: 0.7624 (pmm) cc_final: 0.7109 (pmm) REVERT: N 249 LYS cc_start: 0.8419 (tttm) cc_final: 0.7960 (ttpp) REVERT: O 74 MET cc_start: 0.7932 (tmm) cc_final: 0.7321 (tmm) REVERT: O 99 LEU cc_start: 0.8831 (mt) cc_final: 0.8585 (mt) REVERT: O 128 TYR cc_start: 0.8913 (m-10) cc_final: 0.8503 (m-80) REVERT: O 176 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8017 (tm-30) REVERT: O 208 LYS cc_start: 0.8429 (tptp) cc_final: 0.8176 (tmmt) REVERT: O 233 GLU cc_start: 0.8406 (tp30) cc_final: 0.7990 (tt0) REVERT: O 237 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8530 (tm-30) REVERT: P 50 TYR cc_start: 0.8387 (m-80) cc_final: 0.8162 (m-80) REVERT: P 74 MET cc_start: 0.8551 (tpp) cc_final: 0.8158 (tpp) REVERT: P 116 LEU cc_start: 0.9107 (tp) cc_final: 0.8878 (tt) REVERT: P 176 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7829 (tm-30) REVERT: P 237 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8568 (tm-30) REVERT: Q 74 MET cc_start: 0.8178 (tpp) cc_final: 0.7872 (tpp) REVERT: Q 116 LEU cc_start: 0.8759 (mt) cc_final: 0.8442 (tt) REVERT: Q 153 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8628 (ttp-170) REVERT: Q 233 GLU cc_start: 0.8352 (tp30) cc_final: 0.8018 (tp30) REVERT: Q 250 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8058 (tmmt) REVERT: R 74 MET cc_start: 0.7773 (tmm) cc_final: 0.7454 (tmm) REVERT: R 78 THR cc_start: 0.7412 (p) cc_final: 0.6979 (t) REVERT: R 99 LEU cc_start: 0.8386 (mt) cc_final: 0.8001 (mt) REVERT: R 233 GLU cc_start: 0.8366 (tp30) cc_final: 0.8024 (tp30) REVERT: R 249 LYS cc_start: 0.8547 (tttt) cc_final: 0.8236 (ttpp) REVERT: R 272 TRP cc_start: 0.8841 (m100) cc_final: 0.8486 (m100) REVERT: R 273 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8587 (tptm) REVERT: S 99 LEU cc_start: 0.8545 (mt) cc_final: 0.8295 (mt) REVERT: S 203 SER cc_start: 0.9150 (p) cc_final: 0.8917 (t) REVERT: S 237 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8413 (tm-30) REVERT: S 273 LYS cc_start: 0.8797 (tptm) cc_final: 0.8586 (mmtt) REVERT: T 12 LEU cc_start: 0.7709 (pp) cc_final: 0.7339 (mt) REVERT: T 51 TYR cc_start: 0.8824 (t80) cc_final: 0.8275 (t80) REVERT: T 74 MET cc_start: 0.7992 (tmm) cc_final: 0.7458 (tpp) REVERT: T 99 LEU cc_start: 0.8839 (mt) cc_final: 0.8608 (mt) REVERT: T 130 GLU cc_start: 0.8398 (pp20) cc_final: 0.8167 (pp20) REVERT: T 208 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8110 (tmmt) REVERT: U 12 LEU cc_start: 0.7384 (pp) cc_final: 0.7100 (mt) REVERT: U 74 MET cc_start: 0.7810 (tmm) cc_final: 0.7235 (tmm) REVERT: U 78 THR cc_start: 0.7236 (p) cc_final: 0.6949 (p) REVERT: U 128 TYR cc_start: 0.8983 (m-10) cc_final: 0.8653 (m-80) REVERT: U 184 GLN cc_start: 0.8415 (mt0) cc_final: 0.8169 (mm-40) REVERT: V 12 LEU cc_start: 0.7484 (pp) cc_final: 0.7210 (mt) REVERT: V 74 MET cc_start: 0.7781 (tmm) cc_final: 0.7471 (tpp) REVERT: V 128 TYR cc_start: 0.9043 (m-10) cc_final: 0.8658 (m-80) REVERT: V 250 LYS cc_start: 0.8476 (ttmt) cc_final: 0.8091 (tmmt) outliers start: 16 outliers final: 0 residues processed: 1065 average time/residue: 0.2693 time to fit residues: 470.7263 Evaluate side-chains 746 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 743 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 113 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 454 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 524 optimal weight: 6.9990 chunk 190 optimal weight: 9.9990 chunk 566 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS C 48 ASN D 181 HIS E 227 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 HIS F 238 GLN G 181 HIS H 48 ASN H 227 ASN I 181 HIS I 227 ASN L 181 HIS M 181 HIS ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 227 ASN Q 48 ASN Q 181 HIS Q 227 ASN S 48 ASN T 227 ASN U 181 HIS U 227 ASN V 227 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097470 restraints weight = 80024.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099977 restraints weight = 46962.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.101617 restraints weight = 34541.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102450 restraints weight = 28776.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102857 restraints weight = 26177.894| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 46882 Z= 0.270 Angle : 0.722 8.340 63690 Z= 0.383 Chirality : 0.045 0.226 7414 Planarity : 0.005 0.051 7898 Dihedral : 4.116 20.110 6270 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.31 % Allowed : 5.16 % Favored : 94.53 % 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: 1.81 (0.11), residues: 5786 helix: 2.18 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.77 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 247 TYR 0.017 0.002 TYR B 51 PHE 0.018 0.002 PHE D 34 TRP 0.012 0.001 TRP V 221 HIS 0.008 0.002 HIS S 239 Details of bonding type rmsd covalent geometry : bond 0.00618 (46838) covalent geometry : angle 0.71896 (63602) SS BOND : bond 0.00225 ( 44) SS BOND : angle 2.00124 ( 88) hydrogen bonds : bond 0.06027 ( 3498) hydrogen bonds : angle 4.24573 (10494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 897 time to evaluate : 1.799 Fit side-chains revert: symmetry clash REVERT: A 20 ASN cc_start: 0.8771 (m-40) cc_final: 0.8570 (m-40) REVERT: A 74 MET cc_start: 0.8193 (tmm) cc_final: 0.7627 (tmm) REVERT: A 77 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8852 (mp) REVERT: A 237 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 249 LYS cc_start: 0.8511 (tmtt) cc_final: 0.7829 (ttpp) REVERT: B 12 LEU cc_start: 0.7567 (pp) cc_final: 0.7286 (mt) REVERT: B 74 MET cc_start: 0.7973 (tmm) cc_final: 0.7484 (tmm) REVERT: B 116 LEU cc_start: 0.8952 (tp) cc_final: 0.8520 (tt) REVERT: C 12 LEU cc_start: 0.7967 (mt) cc_final: 0.7499 (pp) REVERT: C 174 ARG cc_start: 0.8537 (tmm-80) cc_final: 0.8094 (tmm-80) REVERT: C 249 LYS cc_start: 0.8943 (tmtt) cc_final: 0.8326 (ttpp) REVERT: D 12 LEU cc_start: 0.8316 (mm) cc_final: 0.7785 (pp) REVERT: D 152 LYS cc_start: 0.9244 (tptt) cc_final: 0.9026 (tptm) REVERT: D 175 ASP cc_start: 0.8858 (t70) cc_final: 0.8524 (t70) REVERT: D 227 ASN cc_start: 0.8871 (m-40) cc_final: 0.8669 (m-40) REVERT: D 237 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8532 (tm-30) REVERT: E 74 MET cc_start: 0.7453 (tmm) cc_final: 0.6599 (tmm) REVERT: E 129 TYR cc_start: 0.9381 (t80) cc_final: 0.9168 (t80) REVERT: E 135 GLU cc_start: 0.8249 (pm20) cc_final: 0.7638 (pp20) REVERT: E 176 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8049 (tm-30) REVERT: E 249 LYS cc_start: 0.8990 (tmtt) cc_final: 0.8349 (ttpp) REVERT: E 255 ILE cc_start: 0.9353 (pt) cc_final: 0.8814 (pt) REVERT: F 12 LEU cc_start: 0.8127 (mt) cc_final: 0.7571 (pp) REVERT: F 74 MET cc_start: 0.7993 (tmm) cc_final: 0.7134 (tmm) REVERT: F 271 ASP cc_start: 0.8917 (m-30) cc_final: 0.8684 (m-30) REVERT: G 74 MET cc_start: 0.8620 (tpp) cc_final: 0.8364 (tpp) REVERT: G 99 LEU cc_start: 0.9075 (mt) cc_final: 0.8805 (mt) REVERT: G 175 ASP cc_start: 0.8651 (t70) cc_final: 0.8233 (t70) REVERT: G 187 MET cc_start: 0.9209 (mmm) cc_final: 0.8982 (mmm) REVERT: G 233 GLU cc_start: 0.8338 (tp30) cc_final: 0.8099 (tp30) REVERT: G 273 LYS cc_start: 0.8730 (tptt) cc_final: 0.8437 (tptm) REVERT: H 12 LEU cc_start: 0.7642 (pp) cc_final: 0.7390 (mp) REVERT: H 74 MET cc_start: 0.7740 (tmm) cc_final: 0.7276 (tmm) REVERT: H 99 LEU cc_start: 0.9016 (mt) cc_final: 0.8760 (mt) REVERT: H 203 SER cc_start: 0.8914 (t) cc_final: 0.8699 (p) REVERT: H 237 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8541 (tm-30) REVERT: H 249 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8014 (ttpp) REVERT: I 12 LEU cc_start: 0.8171 (mm) cc_final: 0.7691 (pp) REVERT: I 77 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8770 (mp) REVERT: I 175 ASP cc_start: 0.8731 (t70) cc_final: 0.8496 (t70) REVERT: J 32 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8053 (tm-30) REVERT: J 74 MET cc_start: 0.8106 (tmm) cc_final: 0.7618 (tmm) REVERT: J 78 THR cc_start: 0.7556 (p) cc_final: 0.7079 (p) REVERT: J 208 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8261 (tmmt) REVERT: J 249 LYS cc_start: 0.8438 (tttm) cc_final: 0.7979 (ttpp) REVERT: J 250 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8221 (tmmt) REVERT: K 74 MET cc_start: 0.8000 (tmm) cc_final: 0.7367 (tmm) REVERT: K 249 LYS cc_start: 0.8549 (tttt) cc_final: 0.8264 (ttpp) REVERT: L 12 LEU cc_start: 0.8079 (mt) cc_final: 0.7725 (pp) REVERT: L 50 TYR cc_start: 0.8640 (m-80) cc_final: 0.8260 (m-80) REVERT: L 74 MET cc_start: 0.8213 (tmm) cc_final: 0.7495 (tmm) REVERT: L 237 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8492 (tm-30) REVERT: L 249 LYS cc_start: 0.8413 (tmtt) cc_final: 0.7828 (ttpp) REVERT: L 273 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8450 (tptp) REVERT: M 12 LEU cc_start: 0.8087 (mt) cc_final: 0.7642 (pp) REVERT: M 21 SER cc_start: 0.8860 (t) cc_final: 0.8631 (t) REVERT: M 50 TYR cc_start: 0.8663 (m-80) cc_final: 0.8418 (m-80) REVERT: M 74 MET cc_start: 0.8030 (tmm) cc_final: 0.7254 (tmm) REVERT: N 12 LEU cc_start: 0.8137 (mm) cc_final: 0.7614 (pp) REVERT: N 74 MET cc_start: 0.8155 (tmm) cc_final: 0.7414 (tmm) REVERT: N 144 MET cc_start: 0.7854 (pmm) cc_final: 0.7131 (pmm) REVERT: N 175 ASP cc_start: 0.8822 (t70) cc_final: 0.8480 (t70) REVERT: N 249 LYS cc_start: 0.8617 (tttm) cc_final: 0.8252 (ttpp) REVERT: O 12 LEU cc_start: 0.8150 (mm) cc_final: 0.7670 (pp) REVERT: O 74 MET cc_start: 0.8022 (tmm) cc_final: 0.7378 (tmm) REVERT: O 78 THR cc_start: 0.7061 (p) cc_final: 0.6609 (p) REVERT: O 99 LEU cc_start: 0.9089 (mt) cc_final: 0.8864 (mt) REVERT: O 135 GLU cc_start: 0.8087 (pm20) cc_final: 0.7612 (pp20) REVERT: O 144 MET cc_start: 0.7693 (pmm) cc_final: 0.7482 (pmm) REVERT: O 208 LYS cc_start: 0.8410 (tptp) cc_final: 0.8205 (tmmt) REVERT: P 12 LEU cc_start: 0.7695 (mt) cc_final: 0.7387 (pp) REVERT: P 50 TYR cc_start: 0.8445 (m-80) cc_final: 0.8214 (m-80) REVERT: P 74 MET cc_start: 0.8529 (tpp) cc_final: 0.8023 (tpp) REVERT: P 175 ASP cc_start: 0.8465 (t70) cc_final: 0.8168 (t70) REVERT: Q 74 MET cc_start: 0.8384 (tpp) cc_final: 0.8007 (tpp) REVERT: Q 250 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8159 (tmmt) REVERT: Q 271 ASP cc_start: 0.8897 (m-30) cc_final: 0.8632 (m-30) REVERT: R 74 MET cc_start: 0.7935 (tmm) cc_final: 0.7254 (tmm) REVERT: R 99 LEU cc_start: 0.8777 (mt) cc_final: 0.8454 (mt) REVERT: R 249 LYS cc_start: 0.8694 (tttt) cc_final: 0.8335 (ttpp) REVERT: R 271 ASP cc_start: 0.8826 (m-30) cc_final: 0.8599 (m-30) REVERT: R 273 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8617 (tptm) REVERT: S 48 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7982 (t0) REVERT: S 237 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8341 (tm-30) REVERT: S 249 LYS cc_start: 0.8676 (tttm) cc_final: 0.8286 (tttm) REVERT: S 273 LYS cc_start: 0.8845 (tptm) cc_final: 0.8621 (mmtt) REVERT: T 12 LEU cc_start: 0.7781 (pp) cc_final: 0.7416 (mt) REVERT: T 74 MET cc_start: 0.7785 (tmm) cc_final: 0.7024 (tmm) REVERT: T 78 THR cc_start: 0.7781 (p) cc_final: 0.7519 (p) REVERT: T 99 LEU cc_start: 0.8967 (mt) cc_final: 0.8759 (mt) REVERT: T 130 GLU cc_start: 0.8543 (pp20) cc_final: 0.8246 (pp20) REVERT: T 208 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8118 (tmmt) REVERT: T 249 LYS cc_start: 0.8651 (tttt) cc_final: 0.8426 (tttm) REVERT: T 264 ILE cc_start: 0.8995 (mt) cc_final: 0.8721 (mm) REVERT: U 12 LEU cc_start: 0.7554 (pp) cc_final: 0.7293 (mt) REVERT: U 74 MET cc_start: 0.7955 (tmm) cc_final: 0.7171 (tmm) REVERT: U 78 THR cc_start: 0.7514 (p) cc_final: 0.7070 (t) REVERT: U 249 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8170 (ttpp) REVERT: V 12 LEU cc_start: 0.7575 (pp) cc_final: 0.7289 (mt) REVERT: V 187 MET cc_start: 0.9165 (mmm) cc_final: 0.8901 (mmm) REVERT: V 249 LYS cc_start: 0.8819 (tmtt) cc_final: 0.8217 (ttpp) REVERT: V 250 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8405 (tmmt) outliers start: 16 outliers final: 1 residues processed: 911 average time/residue: 0.2639 time to fit residues: 394.0650 Evaluate side-chains 683 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 679 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 255 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 208 optimal weight: 30.0000 chunk 286 optimal weight: 30.0000 chunk 401 optimal weight: 3.9990 chunk 571 optimal weight: 6.9990 chunk 542 optimal weight: 4.9990 chunk 347 optimal weight: 5.9990 chunk 412 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 chunk 499 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 48 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN E 44 GLN E 48 ASN E 227 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 ASN H 44 GLN I 44 GLN I 227 ASN J 44 GLN J 48 ASN J 227 ASN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 227 ASN O 48 ASN P 44 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 227 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 181 HIS S 227 ASN T 48 ASN T 227 ASN U 48 ASN V 44 GLN V 48 ASN V 227 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102055 restraints weight = 78422.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104835 restraints weight = 44335.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106555 restraints weight = 31728.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107708 restraints weight = 26078.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108199 restraints weight = 23301.276| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 46882 Z= 0.140 Angle : 0.575 6.454 63690 Z= 0.307 Chirality : 0.040 0.244 7414 Planarity : 0.005 0.052 7898 Dihedral : 3.935 20.485 6270 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.09 % 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: 2.41 (0.11), residues: 5786 helix: 2.59 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.54 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 247 TYR 0.010 0.001 TYR U 183 PHE 0.019 0.001 PHE E 55 TRP 0.009 0.001 TRP Q 221 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00290 (46838) covalent geometry : angle 0.56741 (63602) SS BOND : bond 0.00424 ( 44) SS BOND : angle 2.53223 ( 88) hydrogen bonds : bond 0.05008 ( 3498) hydrogen bonds : angle 3.72695 (10494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 933 time to evaluate : 1.651 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8308 (tmm) cc_final: 0.8015 (tmm) REVERT: A 78 THR cc_start: 0.7760 (p) cc_final: 0.7385 (t) REVERT: B 21 SER cc_start: 0.8742 (t) cc_final: 0.8533 (t) REVERT: B 116 LEU cc_start: 0.8872 (tp) cc_final: 0.8575 (tt) REVERT: C 12 LEU cc_start: 0.7832 (mt) cc_final: 0.7339 (pp) REVERT: C 233 GLU cc_start: 0.8028 (tp30) cc_final: 0.7647 (tt0) REVERT: C 249 LYS cc_start: 0.8717 (tmtt) cc_final: 0.8076 (ttpp) REVERT: C 250 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8166 (ttmt) REVERT: D 12 LEU cc_start: 0.8191 (mm) cc_final: 0.7645 (pp) REVERT: D 152 LYS cc_start: 0.9253 (tptt) cc_final: 0.9027 (tptm) REVERT: D 175 ASP cc_start: 0.8712 (t70) cc_final: 0.8381 (t70) REVERT: E 74 MET cc_start: 0.7315 (tmm) cc_final: 0.6531 (tmm) REVERT: E 99 LEU cc_start: 0.8779 (mt) cc_final: 0.8578 (mt) REVERT: E 176 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 249 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8056 (ttpp) REVERT: E 255 ILE cc_start: 0.9334 (pt) cc_final: 0.8799 (pt) REVERT: F 74 MET cc_start: 0.7920 (tmm) cc_final: 0.7072 (tmm) REVERT: F 271 ASP cc_start: 0.8907 (m-30) cc_final: 0.8695 (m-30) REVERT: G 74 MET cc_start: 0.8554 (tpp) cc_final: 0.8284 (tpp) REVERT: G 99 LEU cc_start: 0.8989 (mt) cc_final: 0.8701 (mt) REVERT: G 175 ASP cc_start: 0.8590 (t70) cc_final: 0.8130 (t70) REVERT: G 237 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8263 (tm-30) REVERT: G 273 LYS cc_start: 0.8664 (tptt) cc_final: 0.8334 (tptm) REVERT: H 74 MET cc_start: 0.8022 (tmm) cc_final: 0.7743 (tmm) REVERT: H 99 LEU cc_start: 0.8722 (mt) cc_final: 0.8418 (mt) REVERT: H 187 MET cc_start: 0.9386 (mmp) cc_final: 0.9133 (mmt) REVERT: H 203 SER cc_start: 0.8914 (t) cc_final: 0.8662 (p) REVERT: H 237 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8425 (tm-30) REVERT: H 250 LYS cc_start: 0.8683 (tmmt) cc_final: 0.8000 (ttmt) REVERT: I 242 LEU cc_start: 0.9127 (mm) cc_final: 0.8851 (mt) REVERT: I 249 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8474 (ttpp) REVERT: I 250 LYS cc_start: 0.8720 (tmmt) cc_final: 0.7996 (ttpt) REVERT: J 74 MET cc_start: 0.7994 (tmm) cc_final: 0.7695 (tmm) REVERT: J 176 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8159 (tm-30) REVERT: J 208 LYS cc_start: 0.8628 (mmmm) cc_final: 0.8301 (tmmt) REVERT: J 250 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8090 (tmmt) REVERT: K 12 LEU cc_start: 0.7982 (pp) cc_final: 0.7744 (mt) REVERT: K 32 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7704 (tm-30) REVERT: K 74 MET cc_start: 0.7906 (tmm) cc_final: 0.7245 (tmm) REVERT: K 78 THR cc_start: 0.6969 (p) cc_final: 0.6629 (p) REVERT: K 99 LEU cc_start: 0.8801 (mt) cc_final: 0.8584 (mt) REVERT: K 174 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7548 (tmm-80) REVERT: K 249 LYS cc_start: 0.8402 (tttt) cc_final: 0.8159 (ttpp) REVERT: L 12 LEU cc_start: 0.8078 (mt) cc_final: 0.7683 (pp) REVERT: L 50 TYR cc_start: 0.8523 (m-80) cc_final: 0.8243 (m-80) REVERT: L 99 LEU cc_start: 0.8859 (mt) cc_final: 0.8602 (mt) REVERT: L 135 GLU cc_start: 0.8332 (pp20) cc_final: 0.7921 (pp20) REVERT: L 233 GLU cc_start: 0.8317 (tp30) cc_final: 0.8100 (tt0) REVERT: L 237 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8248 (tm-30) REVERT: L 249 LYS cc_start: 0.8219 (tmtt) cc_final: 0.7888 (ttpp) REVERT: M 12 LEU cc_start: 0.8012 (mt) cc_final: 0.7517 (pp) REVERT: M 50 TYR cc_start: 0.8535 (m-80) cc_final: 0.8334 (m-80) REVERT: M 74 MET cc_start: 0.7951 (tmm) cc_final: 0.7597 (tmm) REVERT: M 78 THR cc_start: 0.7026 (p) cc_final: 0.5907 (p) REVERT: N 12 LEU cc_start: 0.8073 (mm) cc_final: 0.7525 (pp) REVERT: N 74 MET cc_start: 0.8191 (tmm) cc_final: 0.7949 (tmm) REVERT: N 78 THR cc_start: 0.7679 (p) cc_final: 0.7135 (t) REVERT: N 99 LEU cc_start: 0.8765 (mt) cc_final: 0.8547 (mt) REVERT: N 249 LYS cc_start: 0.8534 (tttm) cc_final: 0.8052 (ttpp) REVERT: O 12 LEU cc_start: 0.7948 (mm) cc_final: 0.7574 (pp) REVERT: O 74 MET cc_start: 0.7955 (tmm) cc_final: 0.7353 (tmm) REVERT: O 99 LEU cc_start: 0.8951 (mt) cc_final: 0.8713 (mt) REVERT: O 128 TYR cc_start: 0.8971 (m-10) cc_final: 0.8603 (m-80) REVERT: O 144 MET cc_start: 0.7585 (pmm) cc_final: 0.7384 (pmm) REVERT: O 208 LYS cc_start: 0.8377 (tptp) cc_final: 0.8157 (tmmt) REVERT: P 12 LEU cc_start: 0.7707 (mt) cc_final: 0.7402 (pp) REVERT: P 74 MET cc_start: 0.8567 (tpp) cc_final: 0.8000 (tpp) REVERT: P 77 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8789 (mp) REVERT: P 271 ASP cc_start: 0.8924 (m-30) cc_final: 0.8694 (m-30) REVERT: P 273 LYS cc_start: 0.8591 (mptt) cc_final: 0.8348 (mmtt) REVERT: Q 74 MET cc_start: 0.8386 (tpp) cc_final: 0.8148 (tpp) REVERT: Q 116 LEU cc_start: 0.8697 (mt) cc_final: 0.8454 (tt) REVERT: Q 237 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8555 (tm-30) REVERT: Q 250 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8029 (tmmt) REVERT: Q 271 ASP cc_start: 0.8899 (m-30) cc_final: 0.8650 (m-30) REVERT: R 51 TYR cc_start: 0.9158 (t80) cc_final: 0.8619 (t80) REVERT: R 74 MET cc_start: 0.7818 (tmm) cc_final: 0.7392 (tmm) REVERT: R 99 LEU cc_start: 0.8648 (mt) cc_final: 0.8291 (mt) REVERT: R 249 LYS cc_start: 0.8616 (tttt) cc_final: 0.8115 (ttpp) REVERT: R 273 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8473 (tptp) REVERT: S 99 LEU cc_start: 0.8676 (mt) cc_final: 0.8469 (mt) REVERT: S 237 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8345 (tm-30) REVERT: S 273 LYS cc_start: 0.8817 (tptm) cc_final: 0.8529 (mmtt) REVERT: T 12 LEU cc_start: 0.7635 (pp) cc_final: 0.7310 (mt) REVERT: T 74 MET cc_start: 0.7798 (tmm) cc_final: 0.7276 (tmm) REVERT: T 99 LEU cc_start: 0.8776 (mt) cc_final: 0.8506 (mt) REVERT: T 208 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8193 (tmmt) REVERT: U 12 LEU cc_start: 0.7374 (pp) cc_final: 0.7169 (mt) REVERT: U 74 MET cc_start: 0.7916 (tmm) cc_final: 0.7634 (tmm) REVERT: U 128 TYR cc_start: 0.9100 (m-10) cc_final: 0.8787 (m-80) REVERT: U 249 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8090 (ttpp) REVERT: V 12 LEU cc_start: 0.7400 (pp) cc_final: 0.7161 (mt) REVERT: V 249 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8312 (ttpp) REVERT: V 250 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8196 (tmmt) outliers start: 11 outliers final: 0 residues processed: 942 average time/residue: 0.2763 time to fit residues: 424.3304 Evaluate side-chains 693 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 692 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 457 optimal weight: 0.0870 chunk 570 optimal weight: 3.9990 chunk 485 optimal weight: 0.6980 chunk 474 optimal weight: 8.9990 chunk 353 optimal weight: 3.9990 chunk 561 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 502 optimal weight: 10.0000 chunk 392 optimal weight: 2.9990 chunk 468 optimal weight: 0.9990 chunk 445 optimal weight: 8.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN D 31 GLN D 44 GLN E 48 ASN F 44 GLN H 227 ASN L 44 GLN N 44 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 GLN S 44 GLN S 48 ASN S 227 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN U 227 ASN V 73 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102374 restraints weight = 78191.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105181 restraints weight = 44277.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.106937 restraints weight = 31661.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107931 restraints weight = 26052.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108582 restraints weight = 23420.926| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46882 Z= 0.137 Angle : 0.566 7.071 63690 Z= 0.301 Chirality : 0.040 0.251 7414 Planarity : 0.004 0.050 7898 Dihedral : 3.861 20.179 6270 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % 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 (0.11), residues: 5786 helix: 2.70 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.51 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 14 TYR 0.008 0.001 TYR M 51 PHE 0.016 0.001 PHE B 145 TRP 0.014 0.001 TRP P 221 HIS 0.003 0.001 HIS S 224 Details of bonding type rmsd covalent geometry : bond 0.00297 (46838) covalent geometry : angle 0.56241 (63602) SS BOND : bond 0.00362 ( 44) SS BOND : angle 1.73082 ( 88) hydrogen bonds : bond 0.04810 ( 3498) hydrogen bonds : angle 3.63625 (10494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 935 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.8273 (tmm) cc_final: 0.8021 (tmm) REVERT: A 78 THR cc_start: 0.7453 (p) cc_final: 0.7208 (t) REVERT: B 78 THR cc_start: 0.7369 (p) cc_final: 0.7145 (t) REVERT: B 116 LEU cc_start: 0.8854 (tp) cc_final: 0.8539 (tt) REVERT: C 12 LEU cc_start: 0.7814 (mt) cc_final: 0.7341 (pp) REVERT: C 233 GLU cc_start: 0.8034 (tp30) cc_final: 0.7525 (tt0) REVERT: C 249 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8054 (ttpp) REVERT: C 250 LYS cc_start: 0.8780 (tmmt) cc_final: 0.8139 (ttmt) REVERT: C 255 ILE cc_start: 0.9382 (pt) cc_final: 0.9100 (pt) REVERT: D 12 LEU cc_start: 0.8156 (mm) cc_final: 0.7619 (pp) REVERT: D 152 LYS cc_start: 0.9228 (tptt) cc_final: 0.9008 (tptm) REVERT: D 237 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8453 (tm-30) REVERT: E 74 MET cc_start: 0.7256 (tmm) cc_final: 0.6541 (tpp) REVERT: E 99 LEU cc_start: 0.8789 (mt) cc_final: 0.8588 (mt) REVERT: E 135 GLU cc_start: 0.8270 (pm20) cc_final: 0.7832 (pp20) REVERT: E 249 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8037 (ttpp) REVERT: E 255 ILE cc_start: 0.9301 (pt) cc_final: 0.8752 (pt) REVERT: F 74 MET cc_start: 0.7908 (tmm) cc_final: 0.7168 (tmm) REVERT: F 231 LEU cc_start: 0.8987 (mm) cc_final: 0.8658 (mm) REVERT: F 271 ASP cc_start: 0.8913 (m-30) cc_final: 0.8689 (m-30) REVERT: G 74 MET cc_start: 0.8597 (tpp) cc_final: 0.8340 (tpp) REVERT: G 99 LEU cc_start: 0.8947 (mt) cc_final: 0.8637 (mt) REVERT: G 237 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7944 (tm-30) REVERT: G 273 LYS cc_start: 0.8644 (tptt) cc_final: 0.8240 (tptm) REVERT: H 74 MET cc_start: 0.8098 (tmm) cc_final: 0.7758 (tmm) REVERT: H 77 ILE cc_start: 0.9098 (mp) cc_final: 0.8893 (mp) REVERT: H 99 LEU cc_start: 0.8774 (mt) cc_final: 0.8480 (mt) REVERT: H 135 GLU cc_start: 0.8009 (pp20) cc_final: 0.7365 (pp20) REVERT: H 203 SER cc_start: 0.8920 (t) cc_final: 0.8654 (p) REVERT: H 237 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8360 (tm-30) REVERT: H 250 LYS cc_start: 0.8749 (tmmt) cc_final: 0.8081 (ttmt) REVERT: I 130 GLU cc_start: 0.7814 (pp20) cc_final: 0.7564 (pp20) REVERT: I 250 LYS cc_start: 0.8682 (tmmt) cc_final: 0.7935 (ttpt) REVERT: J 32 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7924 (tm-30) REVERT: J 74 MET cc_start: 0.8080 (tmm) cc_final: 0.7643 (tmm) REVERT: J 176 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8127 (tm-30) REVERT: J 208 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8002 (tmmt) REVERT: K 12 LEU cc_start: 0.7984 (pp) cc_final: 0.7713 (mt) REVERT: K 32 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7676 (tm-30) REVERT: K 74 MET cc_start: 0.7738 (tmm) cc_final: 0.7198 (tmm) REVERT: K 78 THR cc_start: 0.6986 (p) cc_final: 0.6686 (p) REVERT: K 99 LEU cc_start: 0.8775 (mt) cc_final: 0.8566 (mt) REVERT: K 187 MET cc_start: 0.9403 (mmm) cc_final: 0.9050 (mmm) REVERT: K 249 LYS cc_start: 0.8385 (tttt) cc_final: 0.8090 (ttpp) REVERT: L 12 LEU cc_start: 0.8055 (mt) cc_final: 0.7670 (pp) REVERT: L 50 TYR cc_start: 0.8458 (m-80) cc_final: 0.8033 (m-80) REVERT: L 53 SER cc_start: 0.8541 (t) cc_final: 0.8329 (t) REVERT: L 99 LEU cc_start: 0.8812 (mt) cc_final: 0.8540 (mt) REVERT: L 135 GLU cc_start: 0.8302 (pp20) cc_final: 0.7854 (pp20) REVERT: L 187 MET cc_start: 0.9417 (mmp) cc_final: 0.9119 (mmt) REVERT: L 233 GLU cc_start: 0.8275 (tp30) cc_final: 0.8055 (tt0) REVERT: L 237 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8274 (tm-30) REVERT: L 249 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7695 (ttpp) REVERT: M 12 LEU cc_start: 0.7982 (mt) cc_final: 0.7505 (pp) REVERT: M 74 MET cc_start: 0.8034 (tmm) cc_final: 0.7641 (tmm) REVERT: N 12 LEU cc_start: 0.8050 (mm) cc_final: 0.7492 (pp) REVERT: N 53 SER cc_start: 0.8583 (t) cc_final: 0.8376 (t) REVERT: N 99 LEU cc_start: 0.8723 (mt) cc_final: 0.8516 (mt) REVERT: N 249 LYS cc_start: 0.8422 (tttm) cc_final: 0.8190 (ttpp) REVERT: O 12 LEU cc_start: 0.7987 (mm) cc_final: 0.7587 (pp) REVERT: O 74 MET cc_start: 0.7950 (tmm) cc_final: 0.7535 (tmm) REVERT: O 78 THR cc_start: 0.6901 (p) cc_final: 0.6592 (t) REVERT: O 99 LEU cc_start: 0.8916 (mt) cc_final: 0.8672 (mt) REVERT: O 128 TYR cc_start: 0.8975 (m-10) cc_final: 0.8633 (m-80) REVERT: O 176 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8013 (tm-30) REVERT: O 208 LYS cc_start: 0.8374 (tptp) cc_final: 0.8129 (tmmt) REVERT: O 233 GLU cc_start: 0.8413 (tp30) cc_final: 0.8035 (tt0) REVERT: O 237 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8438 (tm-30) REVERT: P 12 LEU cc_start: 0.7716 (mt) cc_final: 0.7368 (pp) REVERT: P 74 MET cc_start: 0.8494 (tpp) cc_final: 0.8040 (tpp) REVERT: P 273 LYS cc_start: 0.8583 (mptt) cc_final: 0.8363 (mmtt) REVERT: Q 74 MET cc_start: 0.8472 (tpp) cc_final: 0.8213 (tpp) REVERT: Q 116 LEU cc_start: 0.8689 (mt) cc_final: 0.8396 (tt) REVERT: Q 130 GLU cc_start: 0.8171 (pp20) cc_final: 0.7955 (pp20) REVERT: Q 135 GLU cc_start: 0.8356 (pp20) cc_final: 0.8063 (pp20) REVERT: Q 250 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8014 (tmmt) REVERT: Q 271 ASP cc_start: 0.8862 (m-30) cc_final: 0.8652 (m-30) REVERT: R 99 LEU cc_start: 0.8633 (mt) cc_final: 0.8250 (mt) REVERT: R 233 GLU cc_start: 0.8379 (tp30) cc_final: 0.8157 (tp30) REVERT: R 249 LYS cc_start: 0.8547 (tttt) cc_final: 0.8089 (ttpp) REVERT: R 271 ASP cc_start: 0.8804 (m-30) cc_final: 0.8552 (m-30) REVERT: R 273 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8430 (tptp) REVERT: S 48 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.8088 (t0) REVERT: S 74 MET cc_start: 0.8016 (tmm) cc_final: 0.7570 (tmm) REVERT: S 78 THR cc_start: 0.7689 (p) cc_final: 0.7390 (p) REVERT: S 99 LEU cc_start: 0.8674 (mt) cc_final: 0.8427 (mt) REVERT: S 187 MET cc_start: 0.9395 (mmp) cc_final: 0.9174 (mmm) REVERT: S 237 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8327 (tm-30) REVERT: S 273 LYS cc_start: 0.8779 (tptm) cc_final: 0.8515 (mmtt) REVERT: T 12 LEU cc_start: 0.7650 (pp) cc_final: 0.7311 (mt) REVERT: T 74 MET cc_start: 0.7914 (tmm) cc_final: 0.7323 (tmm) REVERT: T 99 LEU cc_start: 0.8803 (mt) cc_final: 0.8513 (mt) REVERT: T 208 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8224 (tmmt) REVERT: U 12 LEU cc_start: 0.7477 (pp) cc_final: 0.7153 (mt) REVERT: U 74 MET cc_start: 0.8023 (tmm) cc_final: 0.7659 (tmm) REVERT: U 128 TYR cc_start: 0.9124 (m-10) cc_final: 0.8869 (m-80) REVERT: U 227 ASN cc_start: 0.8781 (m-40) cc_final: 0.8555 (m-40) REVERT: U 249 LYS cc_start: 0.8382 (ttpp) cc_final: 0.8044 (ttpp) REVERT: V 99 LEU cc_start: 0.8965 (mt) cc_final: 0.8750 (mt) REVERT: V 187 MET cc_start: 0.9267 (mmm) cc_final: 0.8988 (mmm) REVERT: V 249 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8090 (ttpp) REVERT: V 250 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8151 (tmmt) outliers start: 2 outliers final: 0 residues processed: 937 average time/residue: 0.2683 time to fit residues: 414.9529 Evaluate side-chains 684 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 683 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 327 optimal weight: 2.9990 chunk 322 optimal weight: 0.0020 chunk 324 optimal weight: 2.9990 chunk 374 optimal weight: 0.0970 chunk 325 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 398 optimal weight: 4.9990 chunk 547 optimal weight: 6.9990 chunk 358 optimal weight: 0.5980 chunk 402 optimal weight: 0.0670 chunk 552 optimal weight: 3.9990 overall best weight: 0.7526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN C 48 ASN D 48 ASN E 48 ASN E 227 ASN G 227 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 ASN M 227 ASN N 48 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 GLN R 48 ASN S 48 ASN T 227 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN U 227 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104665 restraints weight = 77811.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.107538 restraints weight = 43894.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109370 restraints weight = 31186.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110393 restraints weight = 25555.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111038 restraints weight = 22852.328| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 46882 Z= 0.126 Angle : 0.556 6.621 63690 Z= 0.293 Chirality : 0.039 0.224 7414 Planarity : 0.004 0.048 7898 Dihedral : 3.791 19.330 6270 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.04 % Allowed : 1.48 % Favored : 98.48 % 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: 2.77 (0.11), residues: 5786 helix: 2.85 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.40 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 265 TYR 0.013 0.001 TYR M 51 PHE 0.013 0.001 PHE P 145 TRP 0.011 0.001 TRP D 118 HIS 0.003 0.001 HIS J 224 Details of bonding type rmsd covalent geometry : bond 0.00261 (46838) covalent geometry : angle 0.55466 (63602) SS BOND : bond 0.00204 ( 44) SS BOND : angle 1.30065 ( 88) hydrogen bonds : bond 0.04390 ( 3498) hydrogen bonds : angle 3.50171 (10494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 908 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 99 LEU cc_start: 0.8581 (mt) cc_final: 0.8337 (mt) REVERT: B 78 THR cc_start: 0.7508 (p) cc_final: 0.7283 (t) REVERT: B 116 LEU cc_start: 0.8847 (tp) cc_final: 0.8571 (tt) REVERT: C 12 LEU cc_start: 0.7866 (mt) cc_final: 0.7380 (pp) REVERT: C 250 LYS cc_start: 0.8693 (tmmt) cc_final: 0.8091 (ttmt) REVERT: D 12 LEU cc_start: 0.8217 (mm) cc_final: 0.7587 (pp) REVERT: D 53 SER cc_start: 0.8657 (t) cc_final: 0.8420 (t) REVERT: D 187 MET cc_start: 0.9415 (mmp) cc_final: 0.9211 (mmm) REVERT: D 201 LEU cc_start: 0.9193 (tp) cc_final: 0.8986 (tp) REVERT: D 228 GLU cc_start: 0.8168 (pp20) cc_final: 0.7780 (tm-30) REVERT: D 237 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8455 (tm-30) REVERT: E 12 LEU cc_start: 0.7523 (pp) cc_final: 0.7220 (mm) REVERT: E 74 MET cc_start: 0.7233 (tmm) cc_final: 0.6520 (tmm) REVERT: E 99 LEU cc_start: 0.8735 (mt) cc_final: 0.8490 (mt) REVERT: E 135 GLU cc_start: 0.8264 (pm20) cc_final: 0.7947 (pp20) REVERT: F 195 LEU cc_start: 0.8766 (tt) cc_final: 0.8335 (tp) REVERT: F 231 LEU cc_start: 0.8963 (mm) cc_final: 0.8606 (mm) REVERT: F 271 ASP cc_start: 0.8894 (m-30) cc_final: 0.8678 (m-30) REVERT: G 74 MET cc_start: 0.8622 (tpp) cc_final: 0.8353 (tpp) REVERT: G 99 LEU cc_start: 0.8910 (mt) cc_final: 0.8582 (mt) REVERT: G 233 GLU cc_start: 0.8033 (tt0) cc_final: 0.7814 (tp30) REVERT: G 273 LYS cc_start: 0.8636 (tptt) cc_final: 0.8209 (tptm) REVERT: H 73 GLN cc_start: 0.8146 (mt0) cc_final: 0.7453 (mp10) REVERT: H 74 MET cc_start: 0.7994 (tmm) cc_final: 0.7690 (tmm) REVERT: H 99 LEU cc_start: 0.8754 (mt) cc_final: 0.8436 (mt) REVERT: H 237 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8381 (tm-30) REVERT: H 250 LYS cc_start: 0.8680 (tmmt) cc_final: 0.7941 (ttmt) REVERT: H 270 GLN cc_start: 0.8000 (tp40) cc_final: 0.7398 (tp40) REVERT: I 250 LYS cc_start: 0.8565 (tmmt) cc_final: 0.7848 (ttpt) REVERT: J 32 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7910 (tm-30) REVERT: J 74 MET cc_start: 0.8027 (tmm) cc_final: 0.7517 (tmm) REVERT: J 176 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8128 (tm-30) REVERT: J 208 LYS cc_start: 0.8581 (mmmm) cc_final: 0.7928 (tmmt) REVERT: K 12 LEU cc_start: 0.7933 (pp) cc_final: 0.7680 (mt) REVERT: K 187 MET cc_start: 0.9385 (mmm) cc_final: 0.9087 (mmm) REVERT: L 50 TYR cc_start: 0.8498 (m-80) cc_final: 0.8050 (m-80) REVERT: L 99 LEU cc_start: 0.8759 (mt) cc_final: 0.8468 (mt) REVERT: L 135 GLU cc_start: 0.8370 (pp20) cc_final: 0.7912 (pp20) REVERT: L 233 GLU cc_start: 0.8274 (tp30) cc_final: 0.8039 (tt0) REVERT: L 237 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8240 (tm-30) REVERT: L 249 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7837 (ttpp) REVERT: M 12 LEU cc_start: 0.7992 (mt) cc_final: 0.7512 (pp) REVERT: M 74 MET cc_start: 0.8038 (tmm) cc_final: 0.7778 (tmm) REVERT: M 78 THR cc_start: 0.7036 (p) cc_final: 0.6486 (t) REVERT: N 53 SER cc_start: 0.8505 (t) cc_final: 0.8262 (t) REVERT: N 99 LEU cc_start: 0.8697 (mt) cc_final: 0.8455 (mt) REVERT: N 135 GLU cc_start: 0.8276 (pp20) cc_final: 0.7767 (pp20) REVERT: N 249 LYS cc_start: 0.8385 (tttm) cc_final: 0.8124 (ttpp) REVERT: O 12 LEU cc_start: 0.7911 (mm) cc_final: 0.7513 (pp) REVERT: O 99 LEU cc_start: 0.8851 (mt) cc_final: 0.8604 (mt) REVERT: O 128 TYR cc_start: 0.8941 (m-10) cc_final: 0.8572 (m-80) REVERT: O 208 LYS cc_start: 0.8344 (tptp) cc_final: 0.8072 (tmmt) REVERT: P 12 LEU cc_start: 0.7683 (mt) cc_final: 0.7340 (pp) REVERT: P 74 MET cc_start: 0.8522 (tpp) cc_final: 0.8176 (tpp) REVERT: Q 116 LEU cc_start: 0.8634 (mt) cc_final: 0.8386 (tt) REVERT: Q 271 ASP cc_start: 0.8921 (m-30) cc_final: 0.8677 (m-30) REVERT: R 5 LEU cc_start: 0.5440 (mt) cc_final: 0.5215 (mp) REVERT: R 99 LEU cc_start: 0.8504 (mt) cc_final: 0.8115 (mt) REVERT: R 233 GLU cc_start: 0.8489 (tp30) cc_final: 0.8141 (tp30) REVERT: R 249 LYS cc_start: 0.8518 (tttt) cc_final: 0.8075 (ttpp) REVERT: R 271 ASP cc_start: 0.8814 (m-30) cc_final: 0.8607 (m-30) REVERT: R 273 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8388 (tptp) REVERT: S 74 MET cc_start: 0.7995 (tmm) cc_final: 0.7453 (tmm) REVERT: S 78 THR cc_start: 0.7728 (p) cc_final: 0.7389 (p) REVERT: S 99 LEU cc_start: 0.8564 (mt) cc_final: 0.8350 (mt) REVERT: S 187 MET cc_start: 0.9382 (mmp) cc_final: 0.9146 (mmm) REVERT: S 237 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8343 (tm-30) REVERT: S 273 LYS cc_start: 0.8714 (tptm) cc_final: 0.8499 (mmtt) REVERT: T 12 LEU cc_start: 0.7613 (pp) cc_final: 0.7277 (mt) REVERT: T 74 MET cc_start: 0.7974 (tmm) cc_final: 0.7352 (tmm) REVERT: T 99 LEU cc_start: 0.8698 (mt) cc_final: 0.8424 (mt) REVERT: T 130 GLU cc_start: 0.8428 (pp20) cc_final: 0.8214 (pp20) REVERT: T 208 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8172 (tmmt) REVERT: U 12 LEU cc_start: 0.7397 (pp) cc_final: 0.7139 (mt) REVERT: U 74 MET cc_start: 0.7953 (tmm) cc_final: 0.7548 (tmm) REVERT: U 128 TYR cc_start: 0.9049 (m-10) cc_final: 0.8806 (m-80) REVERT: U 135 GLU cc_start: 0.7614 (pp20) cc_final: 0.7091 (pp20) REVERT: V 99 LEU cc_start: 0.8901 (mt) cc_final: 0.8674 (mt) REVERT: V 187 MET cc_start: 0.9248 (mmm) cc_final: 0.9047 (mmm) REVERT: V 249 LYS cc_start: 0.8644 (tmtt) cc_final: 0.8012 (ttpp) REVERT: V 250 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8039 (tmmt) outliers start: 2 outliers final: 0 residues processed: 910 average time/residue: 0.2736 time to fit residues: 411.7934 Evaluate side-chains 692 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 692 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 103 optimal weight: 0.0170 chunk 431 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 294 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 321 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 358 optimal weight: 2.9990 chunk 399 optimal weight: 0.9980 chunk 403 optimal weight: 1.9990 chunk 373 optimal weight: 0.9990 overall best weight: 0.6822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 227 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN E 48 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN G 48 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 227 ASN O 48 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN U 227 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 ASN V 227 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.130464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105880 restraints weight = 77636.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108706 restraints weight = 44020.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110548 restraints weight = 31443.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111547 restraints weight = 25760.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112267 restraints weight = 23061.275| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 46882 Z= 0.127 Angle : 0.561 7.937 63690 Z= 0.295 Chirality : 0.039 0.223 7414 Planarity : 0.004 0.049 7898 Dihedral : 3.736 18.811 6270 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: 2.85 (0.11), residues: 5786 helix: 2.89 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.30 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 265 TYR 0.012 0.001 TYR M 51 PHE 0.014 0.001 PHE Q 232 TRP 0.011 0.001 TRP P 221 HIS 0.002 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00262 (46838) covalent geometry : angle 0.55967 (63602) SS BOND : bond 0.00473 ( 44) SS BOND : angle 1.10614 ( 88) hydrogen bonds : bond 0.04174 ( 3498) hydrogen bonds : angle 3.46354 (10494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 906 time to evaluate : 1.746 Fit side-chains REVERT: A 74 MET cc_start: 0.8145 (tmm) cc_final: 0.7667 (tmm) REVERT: A 99 LEU cc_start: 0.8563 (mt) cc_final: 0.8292 (mt) REVERT: B 78 THR cc_start: 0.7527 (p) cc_final: 0.7320 (t) REVERT: B 116 LEU cc_start: 0.8857 (tp) cc_final: 0.8585 (tt) REVERT: C 12 LEU cc_start: 0.7931 (mt) cc_final: 0.7433 (pp) REVERT: C 130 GLU cc_start: 0.8156 (pp20) cc_final: 0.7935 (pp20) REVERT: C 135 GLU cc_start: 0.8091 (pp20) cc_final: 0.7361 (pp20) REVERT: C 250 LYS cc_start: 0.8600 (tmmt) cc_final: 0.8027 (ttmt) REVERT: D 12 LEU cc_start: 0.8225 (mm) cc_final: 0.7584 (pp) REVERT: D 53 SER cc_start: 0.8571 (t) cc_final: 0.8362 (t) REVERT: D 175 ASP cc_start: 0.8552 (t0) cc_final: 0.8267 (t0) REVERT: D 187 MET cc_start: 0.9404 (mmp) cc_final: 0.9187 (mmm) REVERT: D 237 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8535 (tm-30) REVERT: E 12 LEU cc_start: 0.7558 (pp) cc_final: 0.7214 (mm) REVERT: E 74 MET cc_start: 0.7154 (tmm) cc_final: 0.6473 (tmm) REVERT: E 99 LEU cc_start: 0.8724 (mt) cc_final: 0.8464 (mt) REVERT: E 238 GLN cc_start: 0.8900 (tp40) cc_final: 0.8080 (tt0) REVERT: F 12 LEU cc_start: 0.8033 (mm) cc_final: 0.7496 (pp) REVERT: F 128 TYR cc_start: 0.8911 (m-80) cc_final: 0.8509 (m-80) REVERT: F 195 LEU cc_start: 0.8761 (tt) cc_final: 0.8306 (tp) REVERT: F 231 LEU cc_start: 0.8971 (mm) cc_final: 0.8575 (mm) REVERT: G 74 MET cc_start: 0.8739 (tpp) cc_final: 0.8433 (tpp) REVERT: G 99 LEU cc_start: 0.8903 (mt) cc_final: 0.8563 (mt) REVERT: G 273 LYS cc_start: 0.8574 (tptt) cc_final: 0.8104 (tptm) REVERT: H 74 MET cc_start: 0.8000 (tmm) cc_final: 0.7708 (tmm) REVERT: H 99 LEU cc_start: 0.8747 (mt) cc_final: 0.8412 (mt) REVERT: H 237 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8357 (tm-30) REVERT: H 250 LYS cc_start: 0.8643 (tmmt) cc_final: 0.7847 (ttmt) REVERT: I 250 LYS cc_start: 0.8455 (tmmt) cc_final: 0.7751 (ttpt) REVERT: J 12 LEU cc_start: 0.8183 (mt) cc_final: 0.7718 (pp) REVERT: J 32 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7908 (tm-30) REVERT: J 74 MET cc_start: 0.8030 (tmm) cc_final: 0.7418 (tmm) REVERT: J 208 LYS cc_start: 0.8542 (mmmm) cc_final: 0.7900 (tmmt) REVERT: K 12 LEU cc_start: 0.7971 (pp) cc_final: 0.7703 (mt) REVERT: K 99 LEU cc_start: 0.8781 (mt) cc_final: 0.8577 (mt) REVERT: K 128 TYR cc_start: 0.9006 (m-10) cc_final: 0.8704 (m-80) REVERT: K 187 MET cc_start: 0.9362 (mmm) cc_final: 0.9079 (mmm) REVERT: L 50 TYR cc_start: 0.8491 (m-80) cc_final: 0.8068 (m-80) REVERT: L 53 SER cc_start: 0.8513 (t) cc_final: 0.8284 (t) REVERT: L 80 GLU cc_start: 0.6416 (pp20) cc_final: 0.6091 (tt0) REVERT: L 99 LEU cc_start: 0.8740 (mt) cc_final: 0.8448 (mt) REVERT: L 135 GLU cc_start: 0.8402 (pp20) cc_final: 0.7934 (pp20) REVERT: L 237 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8301 (tm-30) REVERT: M 12 LEU cc_start: 0.7996 (mt) cc_final: 0.7508 (pp) REVERT: M 74 MET cc_start: 0.8080 (tmm) cc_final: 0.7840 (tmm) REVERT: M 78 THR cc_start: 0.7069 (p) cc_final: 0.6499 (t) REVERT: N 12 LEU cc_start: 0.8029 (mm) cc_final: 0.7519 (pp) REVERT: N 53 SER cc_start: 0.8359 (t) cc_final: 0.8137 (t) REVERT: N 99 LEU cc_start: 0.8683 (mt) cc_final: 0.8407 (mt) REVERT: N 135 GLU cc_start: 0.8288 (pp20) cc_final: 0.7779 (pp20) REVERT: N 249 LYS cc_start: 0.8400 (tttm) cc_final: 0.8152 (ttpp) REVERT: O 12 LEU cc_start: 0.7939 (mm) cc_final: 0.7526 (pp) REVERT: O 99 LEU cc_start: 0.8862 (mt) cc_final: 0.8608 (mt) REVERT: O 128 TYR cc_start: 0.8921 (m-10) cc_final: 0.8617 (m-80) REVERT: O 135 GLU cc_start: 0.8185 (pm20) cc_final: 0.7903 (pp20) REVERT: O 144 MET cc_start: 0.7556 (pmm) cc_final: 0.7339 (pmm) REVERT: O 195 LEU cc_start: 0.8808 (tt) cc_final: 0.8608 (tp) REVERT: O 208 LYS cc_start: 0.8350 (tptp) cc_final: 0.8057 (tmmt) REVERT: O 237 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8548 (tm-30) REVERT: P 12 LEU cc_start: 0.7662 (mt) cc_final: 0.7281 (pp) REVERT: P 74 MET cc_start: 0.8475 (tpp) cc_final: 0.7999 (tpp) REVERT: Q 74 MET cc_start: 0.8299 (tpp) cc_final: 0.7994 (tpp) REVERT: Q 116 LEU cc_start: 0.8631 (mt) cc_final: 0.8376 (tt) REVERT: Q 135 GLU cc_start: 0.8318 (pp20) cc_final: 0.7961 (pp20) REVERT: R 5 LEU cc_start: 0.5442 (mt) cc_final: 0.5205 (mp) REVERT: R 21 SER cc_start: 0.8753 (t) cc_final: 0.8540 (t) REVERT: R 99 LEU cc_start: 0.8503 (mt) cc_final: 0.8084 (mt) REVERT: R 233 GLU cc_start: 0.8491 (tp30) cc_final: 0.8165 (tp30) REVERT: R 249 LYS cc_start: 0.8510 (tttt) cc_final: 0.8267 (ttpp) REVERT: R 273 LYS cc_start: 0.8933 (mmtm) cc_final: 0.8417 (tptm) REVERT: S 51 TYR cc_start: 0.9183 (t80) cc_final: 0.8721 (t80) REVERT: S 187 MET cc_start: 0.9377 (mmp) cc_final: 0.9129 (mmm) REVERT: S 237 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8359 (tm-30) REVERT: T 12 LEU cc_start: 0.7613 (pp) cc_final: 0.7265 (mt) REVERT: T 99 LEU cc_start: 0.8723 (mt) cc_final: 0.8453 (mt) REVERT: T 130 GLU cc_start: 0.8402 (pp20) cc_final: 0.8193 (pp20) REVERT: T 208 LYS cc_start: 0.8608 (mmmm) cc_final: 0.8133 (tmmt) REVERT: T 249 LYS cc_start: 0.8254 (tttm) cc_final: 0.7922 (ttpp) REVERT: U 74 MET cc_start: 0.7956 (tmm) cc_final: 0.7715 (tmm) REVERT: U 128 TYR cc_start: 0.9035 (m-10) cc_final: 0.8809 (m-80) REVERT: U 135 GLU cc_start: 0.7567 (pp20) cc_final: 0.7046 (pp20) REVERT: U 249 LYS cc_start: 0.8125 (tttm) cc_final: 0.7896 (ttpp) REVERT: V 249 LYS cc_start: 0.8559 (tmtt) cc_final: 0.7990 (ttpp) REVERT: V 250 LYS cc_start: 0.8484 (ttmt) cc_final: 0.7976 (tmmt) outliers start: 0 outliers final: 0 residues processed: 906 average time/residue: 0.2618 time to fit residues: 392.6770 Evaluate side-chains 677 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 677 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 466 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 520 optimal weight: 20.0000 chunk 546 optimal weight: 9.9990 chunk 374 optimal weight: 4.9990 chunk 481 optimal weight: 7.9990 chunk 493 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 397 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS C 48 ASN D 48 ASN H 48 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN O 181 HIS ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 ASN S 48 ASN U 48 ASN ** V 44 GLN ** 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 = 0.3598 r_free = 0.3598 target = 0.123406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098888 restraints weight = 78962.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.101427 restraints weight = 47073.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103027 restraints weight = 34782.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103879 restraints weight = 29189.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104270 restraints weight = 26505.340| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 46882 Z= 0.234 Angle : 0.694 8.296 63690 Z= 0.368 Chirality : 0.044 0.197 7414 Planarity : 0.005 0.047 7898 Dihedral : 3.912 20.632 6270 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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: 2.48 (0.11), residues: 5786 helix: 2.63 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.46 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG T 164 TYR 0.009 0.001 TYR A 142 PHE 0.023 0.002 PHE Q 104 TRP 0.017 0.001 TRP P 221 HIS 0.006 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00543 (46838) covalent geometry : angle 0.69199 (63602) SS BOND : bond 0.00193 ( 44) SS BOND : angle 1.67298 ( 88) hydrogen bonds : bond 0.05580 ( 3498) hydrogen bonds : angle 3.95350 (10494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 853 time to evaluate : 1.761 Fit side-chains REVERT: A 74 MET cc_start: 0.8164 (tmm) cc_final: 0.7797 (tmm) REVERT: A 99 LEU cc_start: 0.8903 (mt) cc_final: 0.8697 (mt) REVERT: B 21 SER cc_start: 0.8720 (t) cc_final: 0.8516 (t) REVERT: B 78 THR cc_start: 0.7712 (p) cc_final: 0.7365 (t) REVERT: B 116 LEU cc_start: 0.8910 (tp) cc_final: 0.8507 (tt) REVERT: B 146 ASP cc_start: 0.8008 (p0) cc_final: 0.7663 (m-30) REVERT: C 12 LEU cc_start: 0.7894 (mt) cc_final: 0.7441 (pp) REVERT: C 249 LYS cc_start: 0.8802 (tmtt) cc_final: 0.8160 (ttpp) REVERT: D 12 LEU cc_start: 0.8341 (mm) cc_final: 0.7777 (pp) REVERT: E 74 MET cc_start: 0.7371 (tmm) cc_final: 0.6628 (tmm) REVERT: F 12 LEU cc_start: 0.8160 (mm) cc_final: 0.7637 (pp) REVERT: F 128 TYR cc_start: 0.8989 (m-80) cc_final: 0.8562 (m-80) REVERT: F 231 LEU cc_start: 0.9042 (mm) cc_final: 0.8694 (mm) REVERT: F 271 ASP cc_start: 0.8913 (m-30) cc_final: 0.8678 (m-30) REVERT: G 99 LEU cc_start: 0.9069 (mt) cc_final: 0.8798 (mt) REVERT: G 273 LYS cc_start: 0.8653 (tptt) cc_final: 0.8400 (tptm) REVERT: H 99 LEU cc_start: 0.8848 (mt) cc_final: 0.8530 (mt) REVERT: H 237 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8496 (tm-30) REVERT: H 250 LYS cc_start: 0.8831 (tmmt) cc_final: 0.8241 (ttmt) REVERT: I 12 LEU cc_start: 0.8247 (mm) cc_final: 0.7749 (pp) REVERT: I 116 LEU cc_start: 0.8888 (tp) cc_final: 0.8580 (tt) REVERT: I 250 LYS cc_start: 0.8677 (tmmt) cc_final: 0.7980 (ttpt) REVERT: J 12 LEU cc_start: 0.8379 (mt) cc_final: 0.7902 (pp) REVERT: J 32 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7834 (tm-30) REVERT: J 74 MET cc_start: 0.7964 (tmm) cc_final: 0.7629 (tmm) REVERT: J 176 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8146 (tm-30) REVERT: J 187 MET cc_start: 0.9437 (mmp) cc_final: 0.9174 (mmp) REVERT: J 208 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8050 (tmmt) REVERT: J 249 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7709 (ttpp) REVERT: K 78 THR cc_start: 0.7004 (p) cc_final: 0.6409 (p) REVERT: K 249 LYS cc_start: 0.8522 (tttt) cc_final: 0.8282 (ttpp) REVERT: L 12 LEU cc_start: 0.8259 (mm) cc_final: 0.7868 (pp) REVERT: L 50 TYR cc_start: 0.8518 (m-80) cc_final: 0.8127 (m-80) REVERT: L 99 LEU cc_start: 0.8865 (mt) cc_final: 0.8578 (mt) REVERT: L 233 GLU cc_start: 0.8306 (tp30) cc_final: 0.8058 (tt0) REVERT: L 237 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8341 (tm-30) REVERT: L 249 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7772 (ttpp) REVERT: M 12 LEU cc_start: 0.8102 (mt) cc_final: 0.7587 (pp) REVERT: M 74 MET cc_start: 0.7988 (tmm) cc_final: 0.7495 (tmm) REVERT: M 78 THR cc_start: 0.7188 (p) cc_final: 0.5918 (p) REVERT: N 12 LEU cc_start: 0.8166 (mm) cc_final: 0.7689 (pp) REVERT: N 249 LYS cc_start: 0.8474 (tttm) cc_final: 0.8061 (ttpp) REVERT: O 12 LEU cc_start: 0.8092 (mm) cc_final: 0.7693 (pp) REVERT: O 128 TYR cc_start: 0.8995 (m-10) cc_final: 0.8608 (m-80) REVERT: P 12 LEU cc_start: 0.7799 (mt) cc_final: 0.7494 (pp) REVERT: P 74 MET cc_start: 0.8557 (tpp) cc_final: 0.8067 (tpp) REVERT: P 175 ASP cc_start: 0.8581 (t70) cc_final: 0.8270 (t70) REVERT: P 271 ASP cc_start: 0.8919 (m-30) cc_final: 0.8712 (m-30) REVERT: Q 146 ASP cc_start: 0.7794 (p0) cc_final: 0.7424 (m-30) REVERT: Q 271 ASP cc_start: 0.8911 (m-30) cc_final: 0.8684 (m-30) REVERT: R 5 LEU cc_start: 0.5725 (mt) cc_final: 0.5501 (mp) REVERT: R 99 LEU cc_start: 0.8832 (mt) cc_final: 0.8509 (mt) REVERT: R 233 GLU cc_start: 0.8455 (tp30) cc_final: 0.8158 (tp30) REVERT: R 249 LYS cc_start: 0.8680 (tttt) cc_final: 0.8235 (ttpp) REVERT: R 273 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8453 (tptp) REVERT: S 237 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8364 (tm-30) REVERT: T 12 LEU cc_start: 0.7818 (pp) cc_final: 0.7416 (mt) REVERT: T 74 MET cc_start: 0.8734 (tpp) cc_final: 0.8500 (tpp) REVERT: T 78 THR cc_start: 0.7815 (p) cc_final: 0.7447 (p) REVERT: T 99 LEU cc_start: 0.9004 (mt) cc_final: 0.8768 (mt) REVERT: T 135 GLU cc_start: 0.8258 (pm20) cc_final: 0.7862 (pp20) REVERT: T 208 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8259 (tmmt) REVERT: T 249 LYS cc_start: 0.8475 (tttm) cc_final: 0.8128 (ttpp) REVERT: U 128 TYR cc_start: 0.9156 (m-10) cc_final: 0.8798 (m-80) REVERT: U 249 LYS cc_start: 0.8249 (tttm) cc_final: 0.7878 (ttpp) REVERT: V 249 LYS cc_start: 0.8793 (tmtt) cc_final: 0.8200 (ttpp) REVERT: V 250 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8316 (tmmt) outliers start: 0 outliers final: 0 residues processed: 853 average time/residue: 0.2432 time to fit residues: 343.2117 Evaluate side-chains 667 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 667 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 100 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 448 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 455 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 550 optimal weight: 6.9990 chunk 226 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN E 48 ASN ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 227 ASN M 227 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 227 ASN ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN T 227 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 227 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.102555 restraints weight = 77849.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105408 restraints weight = 43575.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.107227 restraints weight = 30936.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108149 restraints weight = 25367.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.108872 restraints weight = 22864.312| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 46882 Z= 0.136 Angle : 0.611 7.773 63690 Z= 0.320 Chirality : 0.040 0.236 7414 Planarity : 0.005 0.051 7898 Dihedral : 3.862 19.618 6270 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.72 (0.11), residues: 5786 helix: 2.80 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.39 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 14 TYR 0.014 0.001 TYR M 51 PHE 0.020 0.001 PHE Q 104 TRP 0.011 0.001 TRP P 221 HIS 0.004 0.001 HIS B 224 Details of bonding type rmsd covalent geometry : bond 0.00284 (46838) covalent geometry : angle 0.60658 (63602) SS BOND : bond 0.00431 ( 44) SS BOND : angle 2.10317 ( 88) hydrogen bonds : bond 0.04760 ( 3498) hydrogen bonds : angle 3.61137 (10494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 886 time to evaluate : 1.252 Fit side-chains REVERT: A 74 MET cc_start: 0.8117 (tmm) cc_final: 0.7818 (tmm) REVERT: A 99 LEU cc_start: 0.8598 (mt) cc_final: 0.8356 (mt) REVERT: B 78 THR cc_start: 0.7551 (p) cc_final: 0.7130 (t) REVERT: B 116 LEU cc_start: 0.8857 (tp) cc_final: 0.8564 (tt) REVERT: B 155 GLU cc_start: 0.8368 (pp20) cc_final: 0.8147 (pp20) REVERT: C 12 LEU cc_start: 0.7941 (mt) cc_final: 0.7442 (pp) REVERT: D 12 LEU cc_start: 0.8253 (mm) cc_final: 0.7705 (pp) REVERT: D 53 SER cc_start: 0.8684 (t) cc_final: 0.8470 (t) REVERT: D 227 ASN cc_start: 0.8761 (m-40) cc_final: 0.8411 (m110) REVERT: E 74 MET cc_start: 0.7246 (tmm) cc_final: 0.6504 (tmm) REVERT: E 99 LEU cc_start: 0.8755 (mt) cc_final: 0.8540 (mt) REVERT: E 135 GLU cc_start: 0.7930 (pp20) cc_final: 0.7620 (pp20) REVERT: E 238 GLN cc_start: 0.8817 (tp40) cc_final: 0.8247 (tt0) REVERT: F 12 LEU cc_start: 0.8104 (mm) cc_final: 0.7539 (pp) REVERT: F 128 TYR cc_start: 0.8951 (m-80) cc_final: 0.8520 (m-80) REVERT: F 195 LEU cc_start: 0.8793 (tt) cc_final: 0.8325 (tp) REVERT: F 231 LEU cc_start: 0.8955 (mm) cc_final: 0.8605 (mm) REVERT: G 74 MET cc_start: 0.8634 (tpp) cc_final: 0.8341 (tpp) REVERT: G 99 LEU cc_start: 0.8985 (mt) cc_final: 0.8674 (mt) REVERT: G 273 LYS cc_start: 0.8590 (tptt) cc_final: 0.8126 (tptm) REVERT: H 74 MET cc_start: 0.7645 (tmm) cc_final: 0.6994 (tmm) REVERT: H 99 LEU cc_start: 0.8788 (mt) cc_final: 0.8460 (mt) REVERT: H 135 GLU cc_start: 0.8016 (pp20) cc_final: 0.7711 (pp20) REVERT: H 187 MET cc_start: 0.9377 (mmp) cc_final: 0.9173 (mmp) REVERT: H 237 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8388 (tm-30) REVERT: H 250 LYS cc_start: 0.8709 (tmmt) cc_final: 0.7987 (ttmt) REVERT: I 116 LEU cc_start: 0.8846 (tp) cc_final: 0.8551 (tt) REVERT: I 250 LYS cc_start: 0.8581 (tmmt) cc_final: 0.7864 (ttpt) REVERT: J 12 LEU cc_start: 0.8326 (mt) cc_final: 0.7833 (pp) REVERT: J 32 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7850 (tm-30) REVERT: J 74 MET cc_start: 0.8032 (tmm) cc_final: 0.7476 (tmm) REVERT: J 130 GLU cc_start: 0.8466 (pp20) cc_final: 0.8165 (pp20) REVERT: J 176 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8148 (tm-30) REVERT: J 208 LYS cc_start: 0.8553 (mmmm) cc_final: 0.7940 (tmmt) REVERT: K 78 THR cc_start: 0.6924 (p) cc_final: 0.6513 (p) REVERT: K 128 TYR cc_start: 0.9022 (m-10) cc_final: 0.8704 (m-80) REVERT: K 187 MET cc_start: 0.9404 (mmm) cc_final: 0.9058 (mmm) REVERT: K 249 LYS cc_start: 0.8388 (tttt) cc_final: 0.8059 (ttpp) REVERT: L 50 TYR cc_start: 0.8458 (m-80) cc_final: 0.8067 (m-80) REVERT: L 53 SER cc_start: 0.8564 (t) cc_final: 0.8357 (t) REVERT: L 99 LEU cc_start: 0.8760 (mt) cc_final: 0.8430 (mt) REVERT: L 135 GLU cc_start: 0.8577 (pp20) cc_final: 0.8192 (pp20) REVERT: L 233 GLU cc_start: 0.8336 (tp30) cc_final: 0.8104 (tt0) REVERT: L 237 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8256 (tm-30) REVERT: L 249 LYS cc_start: 0.8228 (tmtt) cc_final: 0.7939 (ttpp) REVERT: M 12 LEU cc_start: 0.8039 (mt) cc_final: 0.7562 (pp) REVERT: M 74 MET cc_start: 0.7870 (tmm) cc_final: 0.7622 (tmm) REVERT: M 78 THR cc_start: 0.7188 (p) cc_final: 0.6534 (t) REVERT: M 135 GLU cc_start: 0.8239 (pm20) cc_final: 0.7716 (pp20) REVERT: M 233 GLU cc_start: 0.8155 (tp30) cc_final: 0.7875 (tp30) REVERT: M 255 ILE cc_start: 0.9035 (tt) cc_final: 0.8779 (tt) REVERT: N 12 LEU cc_start: 0.8043 (mm) cc_final: 0.7598 (pp) REVERT: N 53 SER cc_start: 0.8594 (t) cc_final: 0.8371 (t) REVERT: N 99 LEU cc_start: 0.8858 (mt) cc_final: 0.8657 (mt) REVERT: N 135 GLU cc_start: 0.8277 (pp20) cc_final: 0.7831 (pp20) REVERT: N 249 LYS cc_start: 0.8477 (tttm) cc_final: 0.8236 (ttpp) REVERT: O 12 LEU cc_start: 0.7895 (mm) cc_final: 0.7497 (pp) REVERT: O 74 MET cc_start: 0.7847 (tmm) cc_final: 0.7288 (tmm) REVERT: O 78 THR cc_start: 0.7212 (p) cc_final: 0.6319 (p) REVERT: O 128 TYR cc_start: 0.8947 (m-10) cc_final: 0.8580 (m-80) REVERT: O 135 GLU cc_start: 0.8278 (pm20) cc_final: 0.7969 (pp20) REVERT: P 12 LEU cc_start: 0.7688 (mt) cc_final: 0.7374 (pp) REVERT: R 5 LEU cc_start: 0.5426 (mt) cc_final: 0.5211 (mp) REVERT: R 99 LEU cc_start: 0.8640 (mt) cc_final: 0.8249 (mt) REVERT: R 233 GLU cc_start: 0.8412 (tp30) cc_final: 0.8131 (tp30) REVERT: R 237 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8184 (tm-30) REVERT: R 249 LYS cc_start: 0.8552 (tttt) cc_final: 0.8046 (ttpp) REVERT: R 273 LYS cc_start: 0.8955 (mmtm) cc_final: 0.8336 (tptp) REVERT: S 187 MET cc_start: 0.9370 (mmp) cc_final: 0.9142 (mmm) REVERT: S 237 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8360 (tm-30) REVERT: T 12 LEU cc_start: 0.7665 (pp) cc_final: 0.7299 (mt) REVERT: T 99 LEU cc_start: 0.8866 (mt) cc_final: 0.8626 (mt) REVERT: T 130 GLU cc_start: 0.8480 (pp20) cc_final: 0.8171 (pp20) REVERT: T 187 MET cc_start: 0.9385 (mmp) cc_final: 0.9183 (mmp) REVERT: T 208 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8247 (tmmt) REVERT: T 249 LYS cc_start: 0.8424 (tttm) cc_final: 0.8044 (ttpp) REVERT: U 12 LEU cc_start: 0.7932 (mt) cc_final: 0.7426 (pp) REVERT: U 128 TYR cc_start: 0.9112 (m-10) cc_final: 0.8811 (m-80) REVERT: U 249 LYS cc_start: 0.8163 (tttm) cc_final: 0.7800 (ttpp) REVERT: V 249 LYS cc_start: 0.8710 (tmtt) cc_final: 0.8111 (ttpp) REVERT: V 250 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8144 (tmmt) outliers start: 0 outliers final: 0 residues processed: 886 average time/residue: 0.2217 time to fit residues: 324.8732 Evaluate side-chains 681 residues out of total 5082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 496 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 519 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 220 optimal weight: 0.6980 chunk 468 optimal weight: 0.2980 chunk 161 optimal weight: 0.0770 chunk 71 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 404 optimal weight: 3.9990 overall best weight: 0.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN D 48 ASN E 48 ASN E 227 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS O 48 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 227 ASN ** S 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN ** U 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 ASN U 227 ASN ** V 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105518 restraints weight = 76995.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108407 restraints weight = 43310.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.110192 restraints weight = 30809.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111365 restraints weight = 25161.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111932 restraints weight = 22416.718| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46882 Z= 0.132 Angle : 0.601 7.591 63690 Z= 0.314 Chirality : 0.040 0.203 7414 Planarity : 0.004 0.048 7898 Dihedral : 3.804 18.628 6270 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 2.81 (0.11), residues: 5786 helix: 2.84 (0.08), residues: 4554 sheet: None (None), residues: 0 loop : -2.25 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 14 TYR 0.025 0.001 TYR F 183 PHE 0.015 0.001 PHE J 232 TRP 0.019 0.001 TRP P 221 HIS 0.003 0.001 HIS L 224 Details of bonding type rmsd covalent geometry : bond 0.00272 (46838) covalent geometry : angle 0.59618 (63602) SS BOND : bond 0.00292 ( 44) SS BOND : angle 2.04192 ( 88) hydrogen bonds : bond 0.04204 ( 3498) hydrogen bonds : angle 3.47629 (10494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8303.24 seconds wall clock time: 144 minutes 39.46 seconds (8679.46 seconds total)