Starting phenix.real_space_refine on Mon Oct 26 18:38:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yg9_72916/10_2026/9yg9_72916.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yg9_72916/10_2026/9yg9_72916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yg9_72916/10_2026/9yg9_72916.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yg9_72916/10_2026/9yg9_72916.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yg9_72916/10_2026/9yg9_72916.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yg9_72916/10_2026/9yg9_72916.map" } resolution = 3.1 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= 0.004 sd= 0.032 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 30 5.16 5 C 13710 2.51 5 N 3732 2.21 5 O 4230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21702 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1157 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "G" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "M" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "B" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1157 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "N" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "C" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1157 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "I" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "O" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "D" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1157 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "J" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "P" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "E" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1157 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "K" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "Q" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "F" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1157 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "L" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Chain: "R" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1230 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 12, 'TRANS': 150} Time building chain proxies: 4.45, per 1000 atoms: 0.21 Number of scatterers: 21702 At special positions: 0 Unit cell: (119.9, 122.1, 139.7, 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 30 16.00 O 4230 8.00 N 3732 7.00 C 13710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.82 Conformation dependent library (CDL) restraints added in 648.2 milliseconds 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 43 sheets defined 13.6% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 85 through 97 removed outlier: 4.085A pdb=" N ASP A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'G' and resid 76 through 88 Processing helix chain 'M' and resid 76 through 87 Processing helix chain 'B' and resid 9 through 21 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.549A pdb=" N GLN B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.682A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 88 Processing helix chain 'N' and resid 76 through 87 Processing helix chain 'C' and resid 9 through 21 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.563A pdb=" N GLN C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 93 " --> pdb=" O TYR C 89 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.680A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 88 Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'D' and resid 9 through 21 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.554A pdb=" N GLN D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA D 93 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 109 removed outlier: 3.670A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 88 Processing helix chain 'P' and resid 76 through 87 Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 85 through 97 removed outlier: 4.240A pdb=" N ASP E 92 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA E 93 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS E 95 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 109 removed outlier: 3.681A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 88 Processing helix chain 'Q' and resid 76 through 87 Processing helix chain 'F' and resid 9 through 21 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 85 through 97 removed outlier: 3.703A pdb=" N GLN F 91 " --> pdb=" O HIS F 87 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS F 95 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 109 removed outlier: 3.682A pdb=" N LEU F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 88 Processing helix chain 'R' and resid 76 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 3 through 6 current: chain 'A' and resid 42 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 42 through 52 current: chain 'A' and resid 66 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 66 through 82 current: chain 'A' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 133 through 149 current: chain 'B' and resid 42 through 52 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 42 through 52 current: chain 'B' and resid 66 through 82 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 82 current: chain 'B' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 133 through 149 current: chain 'C' and resid 42 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 42 through 52 current: chain 'C' and resid 66 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 66 through 82 current: chain 'C' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 133 through 149 current: chain 'D' and resid 42 through 52 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 42 through 52 current: chain 'D' and resid 66 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 82 current: chain 'D' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 133 through 149 current: chain 'E' and resid 42 through 52 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 42 through 52 current: chain 'E' and resid 66 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 66 through 82 current: chain 'E' and resid 133 through 149 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 133 through 149 current: chain 'F' and resid 42 through 52 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 42 through 52 current: chain 'F' and resid 66 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 82 current: chain 'F' and resid 133 through 149 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'G' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 24 through 27 current: chain 'G' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 65 through 71 current: chain 'G' and resid 125 through 134 removed outlier: 6.574A pdb=" N THR G 150 " --> pdb=" O SER G 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 41 through 45 removed outlier: 4.300A pdb=" N ASP G 42 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 109 through 110 Processing sheet with id=AA6, first strand: chain 'M' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 24 through 27 current: chain 'M' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 65 through 70 current: chain 'M' and resid 125 through 134 removed outlier: 6.687A pdb=" N THR M 150 " --> pdb=" O SER M 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 41 through 45 removed outlier: 4.441A pdb=" N LEU M 60 " --> pdb=" O ASP M 42 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE M 44 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS M 58 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 109 through 110 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AB1, first strand: chain 'H' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 24 through 27 current: chain 'H' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 65 through 71 current: chain 'H' and resid 125 through 134 removed outlier: 6.575A pdb=" N THR H 150 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 41 through 45 removed outlier: 4.324A pdb=" N ASP H 42 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AB4, first strand: chain 'N' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 24 through 27 current: chain 'N' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 65 through 70 current: chain 'N' and resid 125 through 134 removed outlier: 6.675A pdb=" N THR N 150 " --> pdb=" O SER N 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 41 through 45 removed outlier: 4.432A pdb=" N LEU N 60 " --> pdb=" O ASP N 42 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE N 44 " --> pdb=" O LYS N 58 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS N 58 " --> pdb=" O ILE N 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 109 through 110 Processing sheet with id=AB7, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB8, first strand: chain 'I' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 24 through 27 current: chain 'I' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 65 through 71 current: chain 'I' and resid 125 through 134 removed outlier: 6.591A pdb=" N THR I 150 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 41 through 45 removed outlier: 4.335A pdb=" N ASP I 42 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 109 through 110 Processing sheet with id=AC2, first strand: chain 'O' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 24 through 27 current: chain 'O' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 65 through 70 current: chain 'O' and resid 125 through 134 removed outlier: 6.681A pdb=" N THR O 150 " --> pdb=" O SER O 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.431A pdb=" N LEU O 60 " --> pdb=" O ASP O 42 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ILE O 44 " --> pdb=" O LYS O 58 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS O 58 " --> pdb=" O ILE O 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 109 through 110 Processing sheet with id=AC5, first strand: chain 'D' and resid 124 through 126 Processing sheet with id=AC6, first strand: chain 'J' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 24 through 27 current: chain 'J' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 65 through 71 current: chain 'J' and resid 125 through 134 removed outlier: 6.571A pdb=" N THR J 150 " --> pdb=" O SER J 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 41 through 45 removed outlier: 4.298A pdb=" N ASP J 42 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 109 through 110 Processing sheet with id=AC9, first strand: chain 'P' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 24 through 27 current: chain 'P' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 65 through 70 current: chain 'P' and resid 125 through 134 removed outlier: 6.688A pdb=" N THR P 150 " --> pdb=" O SER P 133 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 41 through 45 removed outlier: 4.440A pdb=" N LEU P 60 " --> pdb=" O ASP P 42 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE P 44 " --> pdb=" O LYS P 58 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LYS P 58 " --> pdb=" O ILE P 44 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 109 through 110 Processing sheet with id=AD3, first strand: chain 'E' and resid 124 through 126 Processing sheet with id=AD4, first strand: chain 'K' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 24 through 27 current: chain 'K' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 65 through 71 current: chain 'K' and resid 125 through 134 removed outlier: 6.574A pdb=" N THR K 150 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 41 through 45 removed outlier: 4.322A pdb=" N ASP K 42 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 109 through 110 Processing sheet with id=AD7, first strand: chain 'Q' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 24 through 27 current: chain 'Q' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 65 through 70 current: chain 'Q' and resid 125 through 134 removed outlier: 6.675A pdb=" N THR Q 150 " --> pdb=" O SER Q 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 41 through 45 removed outlier: 4.433A pdb=" N LEU Q 60 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE Q 44 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LYS Q 58 " --> pdb=" O ILE Q 44 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 109 through 110 Processing sheet with id=AE1, first strand: chain 'F' and resid 124 through 126 Processing sheet with id=AE2, first strand: chain 'L' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 24 through 27 current: chain 'L' and resid 65 through 71 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 65 through 71 current: chain 'L' and resid 125 through 134 removed outlier: 6.592A pdb=" N THR L 150 " --> pdb=" O SER L 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 41 through 45 removed outlier: 4.335A pdb=" N ASP L 42 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 24 through 27 current: chain 'R' and resid 65 through 70 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 65 through 70 current: chain 'R' and resid 125 through 134 removed outlier: 6.680A pdb=" N THR R 150 " --> pdb=" O SER R 133 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 41 through 45 removed outlier: 4.432A pdb=" N LEU R 60 " --> pdb=" O ASP R 42 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE R 44 " --> pdb=" O LYS R 58 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYS R 58 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 109 through 110 379 hydrogen bonds defined for protein. 1029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.17 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4356 1.33 - 1.45: 5207 1.45 - 1.57: 12583 1.57 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 22182 Sorted by residual: bond pdb=" CA ALA B 86 " pdb=" CB ALA B 86 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.59e-02 3.96e+03 8.75e+00 bond pdb=" C PRO B 84 " pdb=" O PRO B 84 " ideal model delta sigma weight residual 1.233 1.207 0.026 1.06e-02 8.90e+03 5.97e+00 bond pdb=" C GLY B 83 " pdb=" N PRO B 84 " ideal model delta sigma weight residual 1.334 1.358 -0.024 1.11e-02 8.12e+03 4.75e+00 bond pdb=" N GLU B 85 " pdb=" CA GLU B 85 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.45e-02 4.76e+03 4.53e+00 bond pdb=" C GLU B 85 " pdb=" N ALA B 86 " ideal model delta sigma weight residual 1.335 1.312 0.023 1.36e-02 5.41e+03 2.85e+00 ... (remaining 22177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 28752 1.11 - 2.21: 1188 2.21 - 3.32: 223 3.32 - 4.42: 41 4.42 - 5.53: 12 Bond angle restraints: 30216 Sorted by residual: angle pdb=" CA GLU B 85 " pdb=" C GLU B 85 " pdb=" O GLU B 85 " ideal model delta sigma weight residual 122.14 118.45 3.69 1.24e+00 6.50e-01 8.87e+00 angle pdb=" CA GLY O 157 " pdb=" C GLY O 157 " pdb=" N LYS O 158 " ideal model delta sigma weight residual 114.61 118.28 -3.67 1.26e+00 6.30e-01 8.50e+00 angle pdb=" CA GLY R 157 " pdb=" C GLY R 157 " pdb=" N LYS R 158 " ideal model delta sigma weight residual 114.61 118.27 -3.66 1.26e+00 6.30e-01 8.42e+00 angle pdb=" CA GLY P 157 " pdb=" C GLY P 157 " pdb=" N LYS P 158 " ideal model delta sigma weight residual 114.61 118.19 -3.58 1.26e+00 6.30e-01 8.07e+00 angle pdb=" CA GLY M 157 " pdb=" C GLY M 157 " pdb=" N LYS M 158 " ideal model delta sigma weight residual 114.61 118.16 -3.55 1.26e+00 6.30e-01 7.92e+00 ... (remaining 30211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 12565 17.54 - 35.07: 496 35.07 - 52.61: 103 52.61 - 70.14: 46 70.14 - 87.68: 8 Dihedral angle restraints: 13218 sinusoidal: 5118 harmonic: 8100 Sorted by residual: dihedral pdb=" CA ALA G 140 " pdb=" C ALA G 140 " pdb=" N SER G 141 " pdb=" CA SER G 141 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ALA K 140 " pdb=" C ALA K 140 " pdb=" N SER K 141 " pdb=" CA SER K 141 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA PHE O 117 " pdb=" C PHE O 117 " pdb=" N VAL O 118 " pdb=" CA VAL O 118 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 13215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1975 0.027 - 0.054: 938 0.054 - 0.080: 225 0.080 - 0.107: 200 0.107 - 0.134: 118 Chirality restraints: 3456 Sorted by residual: chirality pdb=" CA ILE L 151 " pdb=" N ILE L 151 " pdb=" C ILE L 151 " pdb=" CB ILE L 151 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ILE C 40 " pdb=" N ILE C 40 " pdb=" C ILE C 40 " pdb=" CB ILE C 40 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE F 40 " pdb=" N ILE F 40 " pdb=" C ILE F 40 " pdb=" CB ILE F 40 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 3453 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 117 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO E 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 118 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 117 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO D 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 118 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 117 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.49e+00 pdb=" N PRO A 118 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 118 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 118 " -0.017 5.00e-02 4.00e+02 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2731 2.76 - 3.30: 19782 3.30 - 3.83: 32542 3.83 - 4.37: 40557 4.37 - 4.90: 73701 Nonbonded interactions: 169313 Sorted by model distance: nonbonded pdb=" OD2 ASP N 102 " pdb=" OG1 THR N 124 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP Q 102 " pdb=" OG1 THR Q 124 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP M 102 " pdb=" OG1 THR M 124 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP P 102 " pdb=" OG1 THR P 124 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP I 102 " pdb=" OG1 THR I 124 " model vdw 2.243 3.040 ... (remaining 169308 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.800 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 : 0.003 0.047 22182 Z= 0.159 Angle : 0.540 5.531 30216 Z= 0.295 Chirality : 0.042 0.134 3456 Planarity : 0.004 0.031 3948 Dihedral : 11.202 87.678 7998 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.44 (0.15), residues: 2820 helix: 0.14 (0.27), residues: 360 sheet: -0.10 (0.14), residues: 1194 loop : -0.46 (0.15), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 107 TYR 0.008 0.001 TYR R 131 PHE 0.016 0.002 PHE G 117 TRP 0.006 0.001 TRP E 81 HIS 0.004 0.001 HIS E 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (22182) covalent geometry : angle 0.54019 / 0.29 (30216) hydrogen bonds : bond 0.18920 / 13.33 ( 379) hydrogen bonds : angle 6.18398 / 4.28 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 272 time to evaluate : 0.761 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 274 average time/residue: 0.1829 time to fit residues: 72.8649 Evaluate side-chains 182 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.043729 restraints weight = 66587.983| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.92 r_work: 0.2497 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22182 Z= 0.139 Angle : 0.496 6.572 30216 Z= 0.254 Chirality : 0.041 0.155 3456 Planarity : 0.003 0.033 3948 Dihedral : 4.303 17.953 3024 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.64 % Allowed : 5.29 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.36 (0.14), residues: 2820 helix: 1.00 (0.27), residues: 378 sheet: -0.01 (0.15), residues: 1098 loop : -0.72 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 61 TYR 0.010 0.001 TYR E 89 PHE 0.010 0.001 PHE O 117 TRP 0.007 0.001 TRP F 81 HIS 0.002 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22182) covalent geometry : angle 0.49611 / 0.25 (30216) hydrogen bonds : bond 0.04071 / 2.76 ( 379) hydrogen bonds : angle 4.75204 / 3.29 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.885 Fit side-chains REVERT: A 129 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8122 (tm-30) REVERT: M 148 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8752 (tp40) REVERT: B 126 GLN cc_start: 0.8430 (pp30) cc_final: 0.8062 (pp30) REVERT: B 127 ASP cc_start: 0.9066 (t70) cc_final: 0.8814 (t70) REVERT: B 129 GLN cc_start: 0.7873 (mp10) cc_final: 0.7443 (mp10) REVERT: H 65 GLN cc_start: 0.8788 (tt0) cc_final: 0.8516 (tt0) REVERT: H 158 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7883 (ptmm) REVERT: C 126 GLN cc_start: 0.8291 (pp30) cc_final: 0.7986 (pp30) REVERT: C 127 ASP cc_start: 0.9166 (t0) cc_final: 0.8777 (t0) REVERT: C 129 GLN cc_start: 0.8335 (mp10) cc_final: 0.7842 (mp10) REVERT: I 65 GLN cc_start: 0.8941 (tt0) cc_final: 0.8696 (tt0) REVERT: O 29 GLU cc_start: 0.8008 (mp0) cc_final: 0.7782 (mp0) REVERT: O 104 ILE cc_start: 0.9144 (mm) cc_final: 0.8765 (mm) REVERT: D 126 GLN cc_start: 0.8491 (pp30) cc_final: 0.8085 (tm-30) REVERT: P 148 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8752 (tp40) REVERT: E 126 GLN cc_start: 0.8410 (pp30) cc_final: 0.8056 (pp30) REVERT: E 127 ASP cc_start: 0.9120 (t70) cc_final: 0.8898 (t70) REVERT: E 129 GLN cc_start: 0.7772 (mp10) cc_final: 0.7301 (mp10) REVERT: K 158 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7885 (ptmm) REVERT: F 127 ASP cc_start: 0.9143 (t0) cc_final: 0.8838 (t0) REVERT: F 129 GLN cc_start: 0.8222 (mp10) cc_final: 0.7849 (mp10) REVERT: L 65 GLN cc_start: 0.8928 (tt0) cc_final: 0.8683 (tt0) REVERT: R 29 GLU cc_start: 0.8003 (mp0) cc_final: 0.7774 (mp0) REVERT: R 104 ILE cc_start: 0.9146 (mm) cc_final: 0.8771 (mm) outliers start: 15 outliers final: 6 residues processed: 204 average time/residue: 0.1659 time to fit residues: 51.0662 Evaluate side-chains 188 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain L residue 3 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [52, 177, 105, 194, 80, 96, 137, 140, 85, 143, 142] chunk 52 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN G 65 GLN J 65 GLN ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.043540 restraints weight = 66775.683| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.93 r_work: 0.2494 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22182 Z= 0.112 Angle : 0.433 4.740 30216 Z= 0.223 Chirality : 0.040 0.144 3456 Planarity : 0.003 0.033 3948 Dihedral : 3.883 15.971 3024 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.81 % Allowed : 5.29 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.18 (0.15), residues: 2820 helix: 1.48 (0.27), residues: 378 sheet: 0.13 (0.15), residues: 1098 loop : -0.75 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 61 TYR 0.006 0.001 TYR N 131 PHE 0.010 0.001 PHE R 117 TRP 0.008 0.001 TRP O 96 HIS 0.001 0.000 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (22182) covalent geometry : angle 0.43295 / 0.22 (30216) hydrogen bonds : bond 0.03651 / 2.54 ( 379) hydrogen bonds : angle 4.23923 / 2.92 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.832 Fit side-chains REVERT: A 126 GLN cc_start: 0.8604 (tm130) cc_final: 0.8171 (tm-30) REVERT: A 127 ASP cc_start: 0.9240 (t70) cc_final: 0.8418 (t70) REVERT: M 95 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8044 (mtmt) REVERT: M 148 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8752 (tp40) REVERT: B 126 GLN cc_start: 0.8338 (pp30) cc_final: 0.7856 (tm-30) REVERT: B 127 ASP cc_start: 0.9101 (t70) cc_final: 0.8788 (t70) REVERT: B 129 GLN cc_start: 0.7772 (mp10) cc_final: 0.7125 (pm20) REVERT: H 158 LYS cc_start: 0.8241 (ptpp) cc_final: 0.8034 (ptmm) REVERT: N 55 LYS cc_start: 0.8406 (ptpp) cc_final: 0.7955 (ptpp) REVERT: N 113 GLU cc_start: 0.9181 (mp0) cc_final: 0.8903 (mp0) REVERT: C 126 GLN cc_start: 0.8234 (pp30) cc_final: 0.7896 (pp30) REVERT: C 127 ASP cc_start: 0.9084 (t0) cc_final: 0.8764 (t0) REVERT: C 129 GLN cc_start: 0.8015 (mp10) cc_final: 0.7331 (mp10) REVERT: I 65 GLN cc_start: 0.8886 (tt0) cc_final: 0.8650 (tt0) REVERT: I 148 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8348 (mm-40) REVERT: O 29 GLU cc_start: 0.8011 (mp0) cc_final: 0.7800 (mp0) REVERT: O 104 ILE cc_start: 0.9188 (mm) cc_final: 0.8797 (mm) REVERT: D 126 GLN cc_start: 0.8333 (pp30) cc_final: 0.7947 (pp30) REVERT: D 127 ASP cc_start: 0.8934 (t70) cc_final: 0.8680 (t70) REVERT: D 129 GLN cc_start: 0.7844 (mp10) cc_final: 0.7566 (mp10) REVERT: P 95 LYS cc_start: 0.8341 (mttt) cc_final: 0.8029 (mtmt) REVERT: P 148 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8745 (tp40) REVERT: E 126 GLN cc_start: 0.8341 (pp30) cc_final: 0.8096 (tm-30) REVERT: E 129 GLN cc_start: 0.7727 (mp10) cc_final: 0.7144 (mp10) REVERT: K 158 LYS cc_start: 0.8238 (ptpp) cc_final: 0.8024 (ptmm) REVERT: Q 55 LYS cc_start: 0.8412 (ptpp) cc_final: 0.7958 (ptpp) REVERT: F 126 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7904 (tm-30) REVERT: F 127 ASP cc_start: 0.9167 (t0) cc_final: 0.8706 (t0) REVERT: F 129 GLN cc_start: 0.8218 (mp10) cc_final: 0.7652 (mp10) REVERT: L 65 GLN cc_start: 0.8942 (tt0) cc_final: 0.8698 (tt0) REVERT: L 148 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8346 (mm-40) REVERT: R 29 GLU cc_start: 0.8004 (mp0) cc_final: 0.7801 (mp0) REVERT: R 104 ILE cc_start: 0.9195 (mm) cc_final: 0.8806 (mm) outliers start: 19 outliers final: 6 residues processed: 211 average time/residue: 0.1711 time to fit residues: 54.1574 Evaluate side-chains 196 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [214, 30, 194, 153, 151, 16, 103, 24, 99, 144, 271] chunk 214 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 271 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 65 GLN J 65 GLN ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.054926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.040532 restraints weight = 68108.667| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 3.94 r_work: 0.2407 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 22182 Z= 0.289 Angle : 0.555 5.274 30216 Z= 0.278 Chirality : 0.043 0.146 3456 Planarity : 0.003 0.032 3948 Dihedral : 4.245 16.708 3024 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.64 % Allowed : 6.22 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.41 (0.15), residues: 2820 helix: 1.62 (0.27), residues: 378 sheet: -0.07 (0.15), residues: 1194 loop : -1.01 (0.15), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 123 TYR 0.012 0.001 TYR L 11 PHE 0.016 0.002 PHE O 117 TRP 0.010 0.001 TRP I 96 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.29 (22182) covalent geometry : angle 0.55510 / 0.28 (30216) hydrogen bonds : bond 0.04603 / 3.16 ( 379) hydrogen bonds : angle 4.65555 / 3.20 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.696 Fit side-chains REVERT: A 126 GLN cc_start: 0.8665 (tm130) cc_final: 0.8280 (pp30) REVERT: A 127 ASP cc_start: 0.9247 (t70) cc_final: 0.8876 (t0) REVERT: A 129 GLN cc_start: 0.8219 (mp10) cc_final: 0.7762 (mp10) REVERT: M 95 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8094 (mtmt) REVERT: B 126 GLN cc_start: 0.8414 (pp30) cc_final: 0.7938 (pp30) REVERT: B 127 ASP cc_start: 0.9159 (t70) cc_final: 0.8828 (t70) REVERT: B 129 GLN cc_start: 0.7813 (mp10) cc_final: 0.7037 (mp10) REVERT: H 158 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (ptmm) REVERT: N 48 CYS cc_start: 0.8005 (t) cc_final: 0.7530 (t) REVERT: N 113 GLU cc_start: 0.9208 (mp0) cc_final: 0.8918 (mp0) REVERT: C 126 GLN cc_start: 0.8258 (pp30) cc_final: 0.7731 (pp30) REVERT: C 127 ASP cc_start: 0.9097 (t0) cc_final: 0.8676 (t0) REVERT: C 129 GLN cc_start: 0.8125 (mp10) cc_final: 0.7236 (mp10) REVERT: O 113 GLU cc_start: 0.9106 (mp0) cc_final: 0.8853 (mp0) REVERT: D 126 GLN cc_start: 0.8348 (pp30) cc_final: 0.7918 (pp30) REVERT: D 127 ASP cc_start: 0.8891 (t70) cc_final: 0.8626 (t70) REVERT: D 129 GLN cc_start: 0.7771 (mp10) cc_final: 0.7276 (mp10) REVERT: E 126 GLN cc_start: 0.8430 (pp30) cc_final: 0.7772 (pp30) REVERT: E 127 ASP cc_start: 0.8949 (t70) cc_final: 0.8675 (t70) REVERT: E 129 GLN cc_start: 0.7942 (mp10) cc_final: 0.7419 (mp10) REVERT: Q 48 CYS cc_start: 0.7733 (t) cc_final: 0.7280 (t) REVERT: F 126 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7761 (tm-30) REVERT: F 127 ASP cc_start: 0.9111 (t0) cc_final: 0.8598 (t0) REVERT: F 129 GLN cc_start: 0.8267 (mp10) cc_final: 0.7615 (mp10) REVERT: R 113 GLU cc_start: 0.9094 (mp0) cc_final: 0.8842 (mp0) outliers start: 15 outliers final: 8 residues processed: 200 average time/residue: 0.1804 time to fit residues: 53.3642 Evaluate side-chains 186 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain M residue 95 LYS Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [80, 117, 158, 157, 2, 160, 122, 273, 73, 179, 17] chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.056723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.042503 restraints weight = 66569.562| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 3.88 r_work: 0.2466 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22182 Z= 0.106 Angle : 0.433 4.218 30216 Z= 0.222 Chirality : 0.040 0.139 3456 Planarity : 0.003 0.032 3948 Dihedral : 3.744 14.567 3024 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.51 % Allowed : 6.65 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.34 (0.15), residues: 2820 helix: 1.92 (0.27), residues: 378 sheet: -0.05 (0.15), residues: 1140 loop : -0.99 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 54 TYR 0.007 0.001 TYR L 131 PHE 0.006 0.001 PHE I 34 TRP 0.007 0.001 TRP F 81 HIS 0.001 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22182) covalent geometry : angle 0.43276 / 0.22 (30216) hydrogen bonds : bond 0.03070 / 2.12 ( 379) hydrogen bonds : angle 3.93404 / 2.70 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8652 (tm130) cc_final: 0.8384 (pp30) REVERT: A 127 ASP cc_start: 0.9196 (t70) cc_final: 0.8953 (t70) REVERT: M 95 LYS cc_start: 0.8369 (mttt) cc_final: 0.8065 (mttt) REVERT: M 148 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8753 (tp40) REVERT: B 126 GLN cc_start: 0.8498 (pp30) cc_final: 0.7915 (pp30) REVERT: B 127 ASP cc_start: 0.9197 (t70) cc_final: 0.8832 (t70) REVERT: B 129 GLN cc_start: 0.7865 (mp10) cc_final: 0.6977 (mp10) REVERT: H 158 LYS cc_start: 0.8228 (ptpp) cc_final: 0.8017 (ptmm) REVERT: N 48 CYS cc_start: 0.7722 (t) cc_final: 0.7227 (t) REVERT: N 113 GLU cc_start: 0.9201 (mp0) cc_final: 0.8885 (mp0) REVERT: C 126 GLN cc_start: 0.8308 (pp30) cc_final: 0.7680 (pp30) REVERT: C 127 ASP cc_start: 0.9166 (t0) cc_final: 0.8829 (t0) REVERT: C 129 GLN cc_start: 0.8112 (mp10) cc_final: 0.7148 (mp10) REVERT: I 29 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8248 (mt-10) REVERT: O 113 GLU cc_start: 0.9091 (mp0) cc_final: 0.8849 (mp0) REVERT: D 126 GLN cc_start: 0.8418 (pp30) cc_final: 0.8043 (pp30) REVERT: D 127 ASP cc_start: 0.8923 (t70) cc_final: 0.8687 (t70) REVERT: D 129 GLN cc_start: 0.7754 (mp10) cc_final: 0.7205 (mp10) REVERT: P 54 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7533 (mtm-85) REVERT: P 148 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8752 (tp40) REVERT: E 126 GLN cc_start: 0.8509 (pp30) cc_final: 0.8052 (pp30) REVERT: E 127 ASP cc_start: 0.8918 (t70) cc_final: 0.8697 (t70) REVERT: E 129 GLN cc_start: 0.7876 (mp10) cc_final: 0.7382 (mp10) REVERT: Q 48 CYS cc_start: 0.7726 (t) cc_final: 0.7228 (t) REVERT: F 126 GLN cc_start: 0.8306 (tm130) cc_final: 0.7930 (tm-30) REVERT: F 127 ASP cc_start: 0.9199 (t0) cc_final: 0.8843 (t0) REVERT: F 129 GLN cc_start: 0.8313 (mp10) cc_final: 0.7766 (mp10) REVERT: L 29 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8247 (mt-10) REVERT: R 113 GLU cc_start: 0.9084 (mp0) cc_final: 0.8841 (mp0) outliers start: 12 outliers final: 7 residues processed: 204 average time/residue: 0.1714 time to fit residues: 52.5254 Evaluate side-chains 195 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [181, 34, 244, 3, 171, 18, 166, 266, 25, 271, 57] chunk 181 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.043026 restraints weight = 66544.056| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.90 r_work: 0.2485 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22182 Z= 0.083 Angle : 0.423 4.761 30216 Z= 0.216 Chirality : 0.039 0.139 3456 Planarity : 0.003 0.032 3948 Dihedral : 3.445 13.288 3024 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.64 % Allowed : 7.37 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.17 (0.15), residues: 2820 helix: 2.10 (0.27), residues: 378 sheet: 0.03 (0.14), residues: 1224 loop : -0.92 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 54 TYR 0.005 0.001 TYR L 131 PHE 0.006 0.001 PHE O 117 TRP 0.008 0.001 TRP P 96 HIS 0.001 0.000 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.08 (22182) covalent geometry : angle 0.42313 / 0.22 (30216) hydrogen bonds : bond 0.02622 / 1.82 ( 379) hydrogen bonds : angle 3.69036 / 2.52 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8647 (tm130) cc_final: 0.8361 (pp30) REVERT: A 127 ASP cc_start: 0.9232 (t70) cc_final: 0.8964 (t70) REVERT: M 148 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8752 (tp40) REVERT: B 126 GLN cc_start: 0.8525 (pp30) cc_final: 0.7934 (pp30) REVERT: B 127 ASP cc_start: 0.9210 (t70) cc_final: 0.8833 (t70) REVERT: B 129 GLN cc_start: 0.7873 (mp10) cc_final: 0.6926 (mp10) REVERT: H 129 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8635 (mt-10) REVERT: H 158 LYS cc_start: 0.8272 (ptpp) cc_final: 0.8048 (ptmm) REVERT: N 48 CYS cc_start: 0.7574 (t) cc_final: 0.7048 (t) REVERT: N 95 LYS cc_start: 0.8396 (mttt) cc_final: 0.8134 (mtmt) REVERT: N 113 GLU cc_start: 0.9188 (mp0) cc_final: 0.8885 (mp0) REVERT: C 126 GLN cc_start: 0.8332 (pp30) cc_final: 0.7955 (pp30) REVERT: C 127 ASP cc_start: 0.9149 (t0) cc_final: 0.8864 (t0) REVERT: I 29 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8285 (mt-10) REVERT: O 113 GLU cc_start: 0.9100 (mp0) cc_final: 0.8859 (mp0) REVERT: D 126 GLN cc_start: 0.8449 (pp30) cc_final: 0.8038 (pp30) REVERT: D 127 ASP cc_start: 0.8938 (t70) cc_final: 0.8640 (t70) REVERT: P 54 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7527 (mtm-85) REVERT: P 148 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8752 (tp40) REVERT: E 126 GLN cc_start: 0.8563 (pp30) cc_final: 0.7984 (pp30) REVERT: E 127 ASP cc_start: 0.8980 (t70) cc_final: 0.8696 (t70) REVERT: E 129 GLN cc_start: 0.7933 (mp10) cc_final: 0.7332 (mp10) REVERT: K 129 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8631 (mt-10) REVERT: Q 48 CYS cc_start: 0.7583 (t) cc_final: 0.7053 (t) REVERT: Q 95 LYS cc_start: 0.8403 (mttt) cc_final: 0.8129 (mtmt) REVERT: F 126 GLN cc_start: 0.8327 (tm130) cc_final: 0.7898 (tm-30) REVERT: F 127 ASP cc_start: 0.9188 (t0) cc_final: 0.8817 (t0) REVERT: F 129 GLN cc_start: 0.8314 (mp10) cc_final: 0.7734 (mp10) REVERT: L 29 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8300 (mt-10) REVERT: R 113 GLU cc_start: 0.9105 (mp0) cc_final: 0.8858 (mp0) outliers start: 15 outliers final: 12 residues processed: 208 average time/residue: 0.1646 time to fit residues: 51.6726 Evaluate side-chains 198 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain L residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [234, 226, 11, 29, 237, 38, 183, 54, 204, 14, 23] chunk 234 optimal weight: 8.9990 chunk 226 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.041652 restraints weight = 67462.559| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 3.90 r_work: 0.2442 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22182 Z= 0.171 Angle : 0.465 4.880 30216 Z= 0.235 Chirality : 0.040 0.140 3456 Planarity : 0.003 0.031 3948 Dihedral : 3.607 14.075 3024 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.68 % Allowed : 8.01 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.16 (0.15), residues: 2820 helix: 2.17 (0.27), residues: 378 sheet: 0.08 (0.15), residues: 1140 loop : -0.92 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 54 TYR 0.007 0.001 TYR L 11 PHE 0.010 0.001 PHE P 117 TRP 0.007 0.001 TRP C 81 HIS 0.002 0.001 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (22182) covalent geometry : angle 0.46478 / 0.23 (30216) hydrogen bonds : bond 0.03317 / 2.29 ( 379) hydrogen bonds : angle 3.94910 / 2.71 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8584 (tm130) cc_final: 0.8256 (pp30) REVERT: A 127 ASP cc_start: 0.9244 (t70) cc_final: 0.8966 (t70) REVERT: M 48 CYS cc_start: 0.8142 (t) cc_final: 0.7569 (t) REVERT: M 55 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8377 (ptpp) REVERT: M 148 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8747 (tp40) REVERT: B 126 GLN cc_start: 0.8538 (pp30) cc_final: 0.8018 (pp30) REVERT: B 127 ASP cc_start: 0.9220 (t70) cc_final: 0.8871 (t70) REVERT: B 129 GLN cc_start: 0.7899 (mp10) cc_final: 0.7024 (mp10) REVERT: H 158 LYS cc_start: 0.8179 (ptpp) cc_final: 0.7972 (ptmm) REVERT: N 48 CYS cc_start: 0.7763 (t) cc_final: 0.7342 (t) REVERT: N 113 GLU cc_start: 0.9201 (mp0) cc_final: 0.8925 (mp0) REVERT: C 126 GLN cc_start: 0.8341 (pp30) cc_final: 0.7948 (pp30) REVERT: C 127 ASP cc_start: 0.9154 (t0) cc_final: 0.8861 (t0) REVERT: I 29 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8254 (mt-10) REVERT: O 48 CYS cc_start: 0.7953 (t) cc_final: 0.7573 (t) REVERT: O 113 GLU cc_start: 0.9097 (mp0) cc_final: 0.8842 (mp0) REVERT: D 126 GLN cc_start: 0.8463 (pp30) cc_final: 0.7799 (pp30) REVERT: D 127 ASP cc_start: 0.8971 (t70) cc_final: 0.8649 (t0) REVERT: D 129 GLN cc_start: 0.7850 (mp10) cc_final: 0.7246 (mp10) REVERT: P 48 CYS cc_start: 0.8164 (t) cc_final: 0.7651 (t) REVERT: P 54 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7655 (mtm-85) REVERT: P 148 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8747 (tp40) REVERT: E 126 GLN cc_start: 0.8574 (pp30) cc_final: 0.8005 (pp30) REVERT: E 127 ASP cc_start: 0.8968 (t70) cc_final: 0.8695 (t70) REVERT: E 129 GLN cc_start: 0.7950 (mp10) cc_final: 0.7310 (mp10) REVERT: Q 48 CYS cc_start: 0.7803 (t) cc_final: 0.7376 (t) REVERT: F 126 GLN cc_start: 0.8346 (tm130) cc_final: 0.7891 (tm-30) REVERT: F 127 ASP cc_start: 0.9187 (t0) cc_final: 0.8814 (t0) REVERT: F 129 GLN cc_start: 0.8365 (mp10) cc_final: 0.7761 (mp10) REVERT: L 29 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8257 (mt-10) REVERT: R 48 CYS cc_start: 0.7941 (t) cc_final: 0.7560 (t) REVERT: R 113 GLU cc_start: 0.9090 (mp0) cc_final: 0.8833 (mp0) outliers start: 16 outliers final: 13 residues processed: 201 average time/residue: 0.1628 time to fit residues: 49.4835 Evaluate side-chains 199 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 65 GLN Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [28, 66, 205, 57, 23, 118, 170, 89, 147, 26, 36] chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.056004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.041673 restraints weight = 67170.178| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 3.92 r_work: 0.2450 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22182 Z= 0.139 Angle : 0.456 5.619 30216 Z= 0.232 Chirality : 0.040 0.139 3456 Planarity : 0.003 0.032 3948 Dihedral : 3.534 14.076 3024 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.77 % Allowed : 7.67 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.14 (0.15), residues: 2820 helix: 2.24 (0.27), residues: 378 sheet: 0.08 (0.15), residues: 1140 loop : -0.91 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 54 TYR 0.011 0.001 TYR P 56 PHE 0.007 0.001 PHE L 117 TRP 0.007 0.001 TRP C 81 HIS 0.001 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (22182) covalent geometry : angle 0.45587 / 0.23 (30216) hydrogen bonds : bond 0.02987 / 2.07 ( 379) hydrogen bonds : angle 3.82268 / 2.62 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8227 (pp30) REVERT: A 127 ASP cc_start: 0.9234 (t70) cc_final: 0.8944 (t70) REVERT: M 48 CYS cc_start: 0.8150 (t) cc_final: 0.7674 (t) REVERT: M 148 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8756 (tp40) REVERT: B 126 GLN cc_start: 0.8556 (pp30) cc_final: 0.8156 (pp30) REVERT: B 127 ASP cc_start: 0.9213 (t70) cc_final: 0.8886 (t70) REVERT: B 129 GLN cc_start: 0.7902 (mp10) cc_final: 0.7083 (mp10) REVERT: H 129 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8635 (mt-10) REVERT: H 158 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7956 (ptmm) REVERT: N 48 CYS cc_start: 0.7669 (t) cc_final: 0.7188 (t) REVERT: N 113 GLU cc_start: 0.9217 (mp0) cc_final: 0.8956 (mp0) REVERT: C 126 GLN cc_start: 0.8367 (pp30) cc_final: 0.8025 (pp30) REVERT: C 127 ASP cc_start: 0.9164 (t0) cc_final: 0.8876 (t0) REVERT: I 29 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8273 (mt-10) REVERT: O 48 CYS cc_start: 0.7935 (t) cc_final: 0.7557 (t) REVERT: O 113 GLU cc_start: 0.9084 (mp0) cc_final: 0.8826 (mp0) REVERT: D 126 GLN cc_start: 0.8459 (pp30) cc_final: 0.7794 (pp30) REVERT: D 127 ASP cc_start: 0.9014 (t70) cc_final: 0.8714 (t0) REVERT: D 129 GLN cc_start: 0.7861 (mp10) cc_final: 0.7271 (mp10) REVERT: P 48 CYS cc_start: 0.8125 (t) cc_final: 0.7617 (t) REVERT: P 54 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7701 (mtm-85) REVERT: P 148 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8755 (tp40) REVERT: E 126 GLN cc_start: 0.8584 (pp30) cc_final: 0.8017 (pp30) REVERT: E 127 ASP cc_start: 0.8963 (t70) cc_final: 0.8683 (t70) REVERT: E 129 GLN cc_start: 0.7939 (mp10) cc_final: 0.7289 (mp10) REVERT: K 129 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8627 (mt-10) REVERT: Q 48 CYS cc_start: 0.7827 (t) cc_final: 0.7388 (t) REVERT: Q 54 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7678 (mtt90) REVERT: F 126 GLN cc_start: 0.8306 (tm130) cc_final: 0.7816 (tm-30) REVERT: F 127 ASP cc_start: 0.9184 (t0) cc_final: 0.8808 (t0) REVERT: F 129 GLN cc_start: 0.8445 (mp10) cc_final: 0.7858 (mp10) REVERT: L 29 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8273 (mt-10) REVERT: R 48 CYS cc_start: 0.7919 (t) cc_final: 0.7542 (t) REVERT: R 113 GLU cc_start: 0.9079 (mp0) cc_final: 0.8822 (mp0) outliers start: 18 outliers final: 12 residues processed: 206 average time/residue: 0.1705 time to fit residues: 52.7438 Evaluate side-chains 199 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [241, 76, 96, 68, 243, 261, 110, 58, 276, 212, 122] chunk 241 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.039725 restraints weight = 68175.422| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 4.01 r_work: 0.2398 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 22182 Z= 0.306 Angle : 0.573 6.071 30216 Z= 0.287 Chirality : 0.043 0.141 3456 Planarity : 0.003 0.031 3948 Dihedral : 4.022 15.407 3024 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.85 % Allowed : 8.10 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.30 (0.15), residues: 2820 helix: 2.10 (0.28), residues: 378 sheet: -0.01 (0.15), residues: 1206 loop : -1.08 (0.15), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 54 TYR 0.012 0.001 TYR P 56 PHE 0.016 0.002 PHE J 128 TRP 0.009 0.001 TRP C 81 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00721 / 0.31 (22182) covalent geometry : angle 0.57257 / 0.29 (30216) hydrogen bonds : bond 0.04383 / 3.01 ( 379) hydrogen bonds : angle 4.47747 / 3.08 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8225 (pp30) REVERT: A 127 ASP cc_start: 0.9205 (t70) cc_final: 0.8917 (t70) REVERT: M 48 CYS cc_start: 0.8116 (t) cc_final: 0.7613 (t) REVERT: B 126 GLN cc_start: 0.8504 (pp30) cc_final: 0.8059 (pp30) REVERT: B 127 ASP cc_start: 0.9228 (t70) cc_final: 0.8925 (t70) REVERT: B 129 GLN cc_start: 0.7858 (mp10) cc_final: 0.7019 (mp10) REVERT: N 48 CYS cc_start: 0.7694 (t) cc_final: 0.7251 (t) REVERT: N 113 GLU cc_start: 0.9233 (mp0) cc_final: 0.8992 (mp0) REVERT: C 126 GLN cc_start: 0.8410 (pp30) cc_final: 0.8081 (pp30) REVERT: C 127 ASP cc_start: 0.9110 (t0) cc_final: 0.8802 (t0) REVERT: I 29 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8316 (mt-10) REVERT: I 129 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8721 (mt-10) REVERT: O 48 CYS cc_start: 0.8009 (t) cc_final: 0.7652 (t) REVERT: O 113 GLU cc_start: 0.9149 (mp0) cc_final: 0.8898 (mp0) REVERT: D 126 GLN cc_start: 0.8485 (pp30) cc_final: 0.7809 (pp30) REVERT: D 127 ASP cc_start: 0.9013 (t70) cc_final: 0.8721 (t0) REVERT: D 129 GLN cc_start: 0.7917 (mp10) cc_final: 0.7247 (mp10) REVERT: P 48 CYS cc_start: 0.8118 (t) cc_final: 0.7632 (t) REVERT: E 126 GLN cc_start: 0.8582 (pp30) cc_final: 0.8084 (pp30) REVERT: E 127 ASP cc_start: 0.8973 (t70) cc_final: 0.8759 (t70) REVERT: E 129 GLN cc_start: 0.7949 (mp10) cc_final: 0.7335 (mp10) REVERT: Q 48 CYS cc_start: 0.7691 (t) cc_final: 0.7247 (t) REVERT: F 126 GLN cc_start: 0.8296 (tm130) cc_final: 0.7791 (tm-30) REVERT: F 127 ASP cc_start: 0.9154 (t0) cc_final: 0.8668 (t0) REVERT: F 129 GLN cc_start: 0.8396 (mp10) cc_final: 0.7745 (mp10) REVERT: L 29 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8332 (mt-10) REVERT: L 129 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8726 (mt-10) REVERT: R 48 CYS cc_start: 0.8039 (t) cc_final: 0.7699 (t) REVERT: R 113 GLU cc_start: 0.9144 (mp0) cc_final: 0.8891 (mp0) outliers start: 20 outliers final: 16 residues processed: 201 average time/residue: 0.1693 time to fit residues: 50.9087 Evaluate side-chains 198 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [81, 181, 95, 65, 73, 137, 135, 51, 42, 107, 83] chunk 81 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.055237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.040830 restraints weight = 67582.865| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 3.93 r_work: 0.2428 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22182 Z= 0.183 Angle : 0.495 6.246 30216 Z= 0.253 Chirality : 0.040 0.138 3456 Planarity : 0.003 0.031 3948 Dihedral : 3.791 14.964 3024 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.77 % Allowed : 8.35 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.34 (0.15), residues: 2820 helix: 2.21 (0.28), residues: 378 sheet: -0.08 (0.15), residues: 1140 loop : -1.06 (0.15), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 54 TYR 0.009 0.001 TYR P 56 PHE 0.009 0.001 PHE G 128 TRP 0.008 0.001 TRP C 81 HIS 0.002 0.000 HIS E 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (22182) covalent geometry : angle 0.49523 / 0.25 (30216) hydrogen bonds : bond 0.03470 / 2.40 ( 379) hydrogen bonds : angle 4.11725 / 2.83 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5640 Ramachandran restraints generated. 2820 Oldfield, 0 Emsley, 2820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7897 (pp30) REVERT: A 127 ASP cc_start: 0.9193 (t70) cc_final: 0.8786 (t0) REVERT: A 129 GLN cc_start: 0.8387 (mp10) cc_final: 0.7676 (mp10) REVERT: M 48 CYS cc_start: 0.8023 (t) cc_final: 0.7529 (t) REVERT: M 148 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8764 (tp40) REVERT: B 126 GLN cc_start: 0.8552 (pp30) cc_final: 0.8141 (pp30) REVERT: B 127 ASP cc_start: 0.9215 (t70) cc_final: 0.8900 (t70) REVERT: B 129 GLN cc_start: 0.7930 (mp10) cc_final: 0.7107 (mp10) REVERT: N 48 CYS cc_start: 0.7652 (t) cc_final: 0.7201 (t) REVERT: N 113 GLU cc_start: 0.9231 (mp0) cc_final: 0.8983 (mp0) REVERT: N 129 GLU cc_start: 0.8811 (tt0) cc_final: 0.8558 (tt0) REVERT: C 126 GLN cc_start: 0.8401 (pp30) cc_final: 0.8065 (pp30) REVERT: C 127 ASP cc_start: 0.9153 (t0) cc_final: 0.8863 (t0) REVERT: I 29 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8246 (mt-10) REVERT: I 129 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8655 (mt-10) REVERT: O 48 CYS cc_start: 0.8125 (t) cc_final: 0.7741 (t) REVERT: O 113 GLU cc_start: 0.9178 (mp0) cc_final: 0.8921 (mp0) REVERT: D 126 GLN cc_start: 0.8481 (pp30) cc_final: 0.7821 (pp30) REVERT: D 127 ASP cc_start: 0.9022 (t70) cc_final: 0.8734 (t0) REVERT: D 129 GLN cc_start: 0.7824 (mp10) cc_final: 0.7133 (mp10) REVERT: P 48 CYS cc_start: 0.8003 (t) cc_final: 0.7496 (t) REVERT: P 148 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8765 (tp40) REVERT: E 126 GLN cc_start: 0.8556 (pp30) cc_final: 0.8082 (pp30) REVERT: E 127 ASP cc_start: 0.8968 (t70) cc_final: 0.8768 (t70) REVERT: E 129 GLN cc_start: 0.7835 (mp10) cc_final: 0.7255 (mp10) REVERT: Q 48 CYS cc_start: 0.7650 (t) cc_final: 0.7197 (t) REVERT: Q 54 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7686 (mtm-85) REVERT: F 126 GLN cc_start: 0.8278 (tm130) cc_final: 0.7764 (tm-30) REVERT: F 127 ASP cc_start: 0.9150 (t0) cc_final: 0.8672 (t0) REVERT: F 129 GLN cc_start: 0.8391 (mp10) cc_final: 0.7740 (mp10) REVERT: L 29 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8246 (mt-10) REVERT: L 129 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8663 (mt-10) REVERT: R 48 CYS cc_start: 0.8190 (t) cc_final: 0.7832 (t) REVERT: R 113 GLU cc_start: 0.9174 (mp0) cc_final: 0.8917 (mp0) outliers start: 18 outliers final: 17 residues processed: 197 average time/residue: 0.1715 time to fit residues: 51.2326 Evaluate side-chains 200 residues out of total 2346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 GLN Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain G residue 65 GLN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain M residue 158 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain J residue 88 LYS Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain K residue 88 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: [73, 162, 121, 110, 179, 266, 100, 45, 138, 213, 173] chunk 73 optimal weight: 4.9990 chunk 162 optimal weight: 0.0870 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 138 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.056018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.042035 restraints weight = 67169.505| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 3.86 r_work: 0.2465 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22182 Z= 0.110 Angle : 0.461 6.620 30216 Z= 0.237 Chirality : 0.039 0.137 3456 Planarity : 0.003 0.031 3948 Dihedral : 3.500 13.970 3024 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.47 % Allowed : 8.65 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.19 (0.15), residues: 2820 helix: 2.37 (0.28), residues: 378 sheet: -0.02 (0.15), residues: 1224 loop : -0.98 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 54 TYR 0.007 0.001 TYR R 56 PHE 0.009 0.001 PHE Q 117 TRP 0.006 0.001 TRP B 81 HIS 0.001 0.000 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (22182) covalent geometry : angle 0.46090 / 0.24 (30216) hydrogen bonds : bond 0.02812 / 1.95 ( 379) hydrogen bonds : angle 3.79911 / 2.60 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.33 seconds wall clock time: 63 minutes 3.44 seconds (3783.44 seconds total)