Starting phenix.real_space_refine on Thu Jun 19 18:52:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c9i_7436/06_2025/6c9i_7436.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c9i_7436/06_2025/6c9i_7436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c9i_7436/06_2025/6c9i_7436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c9i_7436/06_2025/6c9i_7436.map" model { file = "/net/cci-nas-00/data/ceres_data/6c9i_7436/06_2025/6c9i_7436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c9i_7436/06_2025/6c9i_7436.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 15021 2.51 5 N 4050 2.21 5 O 4533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23700 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Chain: "C" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "D" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "I" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "J" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Chain: "K" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "L" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "P" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "Q" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "R" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1084 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "T" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "V" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "W" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "X" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Time building chain proxies: 15.71, per 1000 atoms: 0.66 Number of scatterers: 23700 At special positions: 0 Unit cell: (129.69, 135.585, 131, 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 96 16.00 O 4533 8.00 N 4050 7.00 C 15021 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: 6.73 Conformation dependent library (CDL) restraints added in 3.2 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 60.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.682A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.545A pdb=" N LEU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 163 Processing helix chain 'B' and resid 24 through 45 Processing helix chain 'B' and resid 49 through 72 Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.680A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 137 removed outlier: 3.546A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 49 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 4.038A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 137 removed outlier: 3.539A pdb=" N LEU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 80 through 96 removed outlier: 4.103A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 73 through 91 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'G' and resid 17 through 31 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 73 through 91 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 36 through 39 Processing helix chain 'H' and resid 73 through 90 Processing helix chain 'I' and resid 24 through 45 Processing helix chain 'I' and resid 49 through 72 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.685A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 163 Processing helix chain 'J' and resid 24 through 45 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.547A pdb=" N MET J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 96 removed outlier: 3.679A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 163 Processing helix chain 'K' and resid 24 through 45 Processing helix chain 'K' and resid 49 through 72 Processing helix chain 'K' and resid 80 through 96 removed outlier: 4.041A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 137 removed outlier: 3.547A pdb=" N LEU K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 163 Processing helix chain 'L' and resid 24 through 45 Processing helix chain 'L' and resid 49 through 72 Processing helix chain 'L' and resid 80 through 96 removed outlier: 3.678A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 137 removed outlier: 3.540A pdb=" N LEU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 163 Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 36 through 39 Processing helix chain 'M' and resid 73 through 91 Processing helix chain 'N' and resid 17 through 31 Processing helix chain 'N' and resid 36 through 39 Processing helix chain 'N' and resid 73 through 91 Processing helix chain 'O' and resid 17 through 31 Processing helix chain 'O' and resid 36 through 39 Processing helix chain 'O' and resid 73 through 91 Processing helix chain 'P' and resid 17 through 31 Processing helix chain 'P' and resid 36 through 39 Processing helix chain 'P' and resid 73 through 90 Processing helix chain 'Q' and resid 24 through 45 Processing helix chain 'Q' and resid 49 through 72 Processing helix chain 'Q' and resid 80 through 96 removed outlier: 3.683A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 163 Processing helix chain 'R' and resid 24 through 45 Processing helix chain 'R' and resid 49 through 72 removed outlier: 3.549A pdb=" N MET R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 96 removed outlier: 3.681A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 163 Processing helix chain 'S' and resid 24 through 45 Processing helix chain 'S' and resid 49 through 72 removed outlier: 3.513A pdb=" N TYR S 64 " --> pdb=" O GLN S 60 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET S 67 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 96 removed outlier: 4.051A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 137 removed outlier: 3.546A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 163 Processing helix chain 'T' and resid 24 through 45 Processing helix chain 'T' and resid 49 through 72 Processing helix chain 'T' and resid 80 through 96 removed outlier: 4.043A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 137 removed outlier: 3.548A pdb=" N LEU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 163 Processing helix chain 'U' and resid 17 through 31 Processing helix chain 'U' and resid 36 through 39 Processing helix chain 'U' and resid 73 through 91 Processing helix chain 'V' and resid 17 through 31 Processing helix chain 'V' and resid 36 through 39 Processing helix chain 'V' and resid 73 through 91 Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 36 through 39 Processing helix chain 'W' and resid 73 through 90 Processing helix chain 'X' and resid 17 through 31 Processing helix chain 'X' and resid 36 through 39 Processing helix chain 'X' and resid 73 through 90 Processing sheet with id=AA1, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.496A pdb=" N ALA M 49 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.495A pdb=" N ALA E 49 " --> pdb=" O PHE U 44 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 6.036A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA U 49 " --> pdb=" O PHE M 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 49 through 52 removed outlier: 4.501A pdb=" N ALA G 49 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 52 removed outlier: 4.498A pdb=" N ALA F 49 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.131A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA P 49 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'V' and resid 49 through 52 removed outlier: 4.501A pdb=" N ALA V 49 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.505A pdb=" N ALA H 49 " --> pdb=" O PHE W 44 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 6.035A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA W 49 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AB6, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.508A pdb=" N ALA O 49 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.506A pdb=" N ALA N 49 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.039A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA X 49 " --> pdb=" O PHE O 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 Processing sheet with id=AC6, first strand: chain 'X' and resid 13 through 14 1768 hydrogen bonds defined for protein. 5124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.74 Time building geometry restraints manager: 7.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4408 1.30 - 1.43: 5522 1.43 - 1.56: 13812 1.56 - 1.68: 44 1.68 - 1.81: 150 Bond restraints: 23936 Sorted by residual: bond pdb=" CB HIS R 46 " pdb=" CG HIS R 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.25e+01 bond pdb=" CB HIS D 46 " pdb=" CG HIS D 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.21e+01 bond pdb=" CB HIS T 46 " pdb=" CG HIS T 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" CB HIS Q 46 " pdb=" CG HIS Q 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.17e+01 bond pdb=" CB HIS C 46 " pdb=" CG HIS C 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.16e+01 ... (remaining 23931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 22541 1.33 - 2.66: 7204 2.66 - 4.00: 1849 4.00 - 5.33: 500 5.33 - 6.66: 129 Bond angle restraints: 32223 Sorted by residual: angle pdb=" N ILE D 84 " pdb=" CA ILE D 84 " pdb=" C ILE D 84 " ideal model delta sigma weight residual 111.00 104.34 6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" C LEU Q 105 " pdb=" N PRO Q 106 " pdb=" CA PRO Q 106 " ideal model delta sigma weight residual 119.78 125.75 -5.97 1.03e+00 9.43e-01 3.36e+01 angle pdb=" C LEU J 105 " pdb=" N PRO J 106 " pdb=" CA PRO J 106 " ideal model delta sigma weight residual 119.78 125.73 -5.95 1.03e+00 9.43e-01 3.34e+01 angle pdb=" C LEU B 105 " pdb=" N PRO B 106 " pdb=" CA PRO B 106 " ideal model delta sigma weight residual 119.78 125.70 -5.92 1.03e+00 9.43e-01 3.31e+01 angle pdb=" C LEU A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta sigma weight residual 119.78 125.69 -5.91 1.03e+00 9.43e-01 3.29e+01 ... (remaining 32218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 13943 13.62 - 27.24: 532 27.24 - 40.86: 73 40.86 - 54.48: 49 54.48 - 68.10: 32 Dihedral angle restraints: 14629 sinusoidal: 5824 harmonic: 8805 Sorted by residual: dihedral pdb=" C SER T 25 " pdb=" N SER T 25 " pdb=" CA SER T 25 " pdb=" CB SER T 25 " ideal model delta harmonic sigma weight residual -122.60 -130.37 7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" CA LYS S 65 " pdb=" CB LYS S 65 " pdb=" CG LYS S 65 " pdb=" CD LYS S 65 " ideal model delta sinusoidal sigma weight residual 60.00 112.77 -52.77 3 1.50e+01 4.44e-03 9.15e+00 dihedral pdb=" C SER K 25 " pdb=" N SER K 25 " pdb=" CA SER K 25 " pdb=" CB SER K 25 " ideal model delta harmonic sigma weight residual -122.60 -130.14 7.54 0 2.50e+00 1.60e-01 9.10e+00 ... (remaining 14626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1687 0.074 - 0.149: 1383 0.149 - 0.223: 612 0.223 - 0.297: 154 0.297 - 0.371: 16 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA SER K 25 " pdb=" N SER K 25 " pdb=" C SER K 25 " pdb=" CB SER K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA SER T 25 " pdb=" N SER T 25 " pdb=" C SER T 25 " pdb=" CB SER T 25 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA SER C 25 " pdb=" N SER C 25 " pdb=" C SER C 25 " pdb=" CB SER C 25 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 3849 not shown) Planarity restraints: 4091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 50 " -0.046 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR O 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR O 50 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR O 50 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR O 50 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR O 50 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR O 50 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR O 50 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 50 " -0.045 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" CG TYR P 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR P 50 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR P 50 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR P 50 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR P 50 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR P 50 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 50 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 50 " -0.045 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR H 50 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR H 50 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR H 50 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR H 50 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR H 50 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR H 50 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 50 " -0.036 2.00e-02 2.50e+03 ... (remaining 4088 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 10696 2.91 - 3.41: 23862 3.41 - 3.91: 39885 3.91 - 4.40: 49391 4.40 - 4.90: 75800 Nonbonded interactions: 199634 Sorted by model distance: nonbonded pdb=" N ASN O 11 " pdb=" OD1 ASN O 11 " model vdw 2.417 3.120 nonbonded pdb=" N ASN W 11 " pdb=" OD1 ASN W 11 " model vdw 2.426 3.120 nonbonded pdb=" N ASN G 11 " pdb=" OD1 ASN G 11 " model vdw 2.428 3.120 nonbonded pdb=" N ASN N 11 " pdb=" OD1 ASN N 11 " model vdw 2.432 3.120 nonbonded pdb=" N ASN V 11 " pdb=" OD1 ASN V 11 " model vdw 2.432 3.120 ... (remaining 199629 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'B' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'C' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'D' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'I' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'J' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'K' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'L' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'Q' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'R' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'S' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'T' and (resid 23 through 99 or resid 103 through 163)) } ncs_group { reference = (chain 'E' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'F' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'G' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'H' selection = (chain 'M' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'N' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'O' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'P' selection = (chain 'U' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'V' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'W' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'X' } 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: 3.510 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.600 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.029 0.157 23936 Z= 1.505 Angle : 1.477 6.660 32223 Z= 0.991 Chirality : 0.115 0.371 3852 Planarity : 0.008 0.048 4091 Dihedral : 9.221 68.100 8959 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.14), residues: 3015 helix: 1.70 (0.11), residues: 1776 sheet: 2.83 (0.22), residues: 396 loop : 0.78 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.009 TRP R 86 HIS 0.004 0.002 HIS X 63 PHE 0.020 0.003 PHE J 103 TYR 0.046 0.009 TYR O 50 ARG 0.008 0.001 ARG U 43 Details of bonding type rmsd hydrogen bonds : bond 0.15043 ( 1768) hydrogen bonds : angle 6.04845 ( 5124) covalent geometry : bond 0.02940 (23936) covalent geometry : angle 1.47677 (32223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 2.399 Fit side-chains revert: symmetry clash REVERT: I 45 LYS cc_start: 0.8688 (pttt) cc_final: 0.8463 (pttt) REVERT: J 114 LYS cc_start: 0.8226 (mmtt) cc_final: 0.8022 (mmtm) REVERT: O 83 SER cc_start: 0.8733 (t) cc_final: 0.8499 (p) REVERT: P 83 SER cc_start: 0.8661 (t) cc_final: 0.8421 (p) REVERT: T 110 LEU cc_start: 0.8630 (tp) cc_final: 0.8318 (tp) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.4609 time to fit residues: 306.8501 Evaluate side-chains 325 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.098545 restraints weight = 25923.207| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.90 r_work: 0.2764 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23936 Z= 0.136 Angle : 0.474 5.307 32223 Z= 0.258 Chirality : 0.040 0.129 3852 Planarity : 0.003 0.033 4091 Dihedral : 3.519 13.801 3339 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.32 % Allowed : 4.08 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.14), residues: 3015 helix: 3.42 (0.11), residues: 1764 sheet: 2.34 (0.20), residues: 396 loop : 0.18 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP R 86 HIS 0.001 0.000 HIS U 3 PHE 0.007 0.001 PHE E 44 TYR 0.013 0.002 TYR X 61 ARG 0.004 0.001 ARG M 77 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 1768) hydrogen bonds : angle 3.96463 ( 5124) covalent geometry : bond 0.00297 (23936) covalent geometry : angle 0.47351 (32223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 368 time to evaluate : 2.626 Fit side-chains REVERT: C 36 GLU cc_start: 0.8683 (tt0) cc_final: 0.8431 (tt0) REVERT: D 36 GLU cc_start: 0.8710 (tt0) cc_final: 0.8431 (tt0) REVERT: E 39 ASP cc_start: 0.8655 (m-30) cc_final: 0.8445 (m-30) REVERT: E 51 ARG cc_start: 0.8353 (mmt-90) cc_final: 0.8052 (mmt-90) REVERT: F 39 ASP cc_start: 0.8531 (m-30) cc_final: 0.8330 (m-30) REVERT: F 51 ARG cc_start: 0.8151 (mmp80) cc_final: 0.7771 (mmp80) REVERT: G 39 ASP cc_start: 0.8530 (m-30) cc_final: 0.8300 (m-30) REVERT: H 51 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.8059 (mmt-90) REVERT: I 29 GLU cc_start: 0.8166 (tt0) cc_final: 0.7670 (mt-10) REVERT: I 36 GLU cc_start: 0.8749 (tt0) cc_final: 0.8540 (tt0) REVERT: J 29 GLU cc_start: 0.8100 (tt0) cc_final: 0.7655 (mt-10) REVERT: K 135 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8184 (mm-30) REVERT: M 39 ASP cc_start: 0.8618 (m-30) cc_final: 0.8393 (m-30) REVERT: M 51 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.8093 (mmt-90) REVERT: N 51 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.8037 (mmt-90) REVERT: O 39 ASP cc_start: 0.8555 (m-30) cc_final: 0.8355 (m-30) REVERT: P 51 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.8030 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8203 (tt0) cc_final: 0.7726 (mt-10) REVERT: Q 36 GLU cc_start: 0.8682 (tt0) cc_final: 0.8462 (tt0) REVERT: R 36 GLU cc_start: 0.8730 (tt0) cc_final: 0.8399 (tt0) REVERT: R 135 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8343 (mm-30) REVERT: S 135 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8106 (mm-30) REVERT: T 82 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7250 (pm20) REVERT: U 39 ASP cc_start: 0.8601 (m-30) cc_final: 0.8369 (m-30) REVERT: U 51 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.7373 (mmm160) REVERT: U 110 GLU cc_start: 0.8698 (tt0) cc_final: 0.8482 (tt0) REVERT: V 20 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7510 (tp30) REVERT: V 39 ASP cc_start: 0.8533 (m-30) cc_final: 0.8328 (m-30) REVERT: V 51 ARG cc_start: 0.8248 (mmt180) cc_final: 0.7795 (mmp80) REVERT: W 23 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7558 (mm-30) REVERT: W 39 ASP cc_start: 0.8631 (m-30) cc_final: 0.8357 (m-30) REVERT: W 51 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.8000 (mmt-90) REVERT: X 51 ARG cc_start: 0.8369 (mmt-90) cc_final: 0.8096 (mmt-90) outliers start: 8 outliers final: 4 residues processed: 369 average time/residue: 0.3845 time to fit residues: 215.2167 Evaluate side-chains 299 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 294 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain T residue 82 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 141 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 259 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.095020 restraints weight = 25850.120| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.92 r_work: 0.2698 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23936 Z= 0.165 Angle : 0.454 5.358 32223 Z= 0.243 Chirality : 0.039 0.130 3852 Planarity : 0.003 0.031 4091 Dihedral : 3.404 14.585 3339 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.01 % Allowed : 5.86 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.14), residues: 3015 helix: 3.40 (0.11), residues: 1761 sheet: 2.09 (0.19), residues: 396 loop : 0.05 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP R 86 HIS 0.001 0.000 HIS J 46 PHE 0.006 0.001 PHE D 40 TYR 0.011 0.002 TYR X 61 ARG 0.003 0.000 ARG M 77 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 1768) hydrogen bonds : angle 3.87035 ( 5124) covalent geometry : bond 0.00393 (23936) covalent geometry : angle 0.45419 (32223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 313 time to evaluate : 2.440 Fit side-chains REVERT: B 82 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7315 (mt-10) REVERT: D 29 GLU cc_start: 0.8178 (tt0) cc_final: 0.7719 (mt-10) REVERT: E 39 ASP cc_start: 0.8665 (m-30) cc_final: 0.8438 (m-30) REVERT: E 51 ARG cc_start: 0.8347 (mmt-90) cc_final: 0.8129 (mmt-90) REVERT: F 51 ARG cc_start: 0.8180 (mmp80) cc_final: 0.7934 (mmp80) REVERT: G 39 ASP cc_start: 0.8607 (m-30) cc_final: 0.8385 (m-30) REVERT: G 51 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7911 (mmt-90) REVERT: I 29 GLU cc_start: 0.8256 (tt0) cc_final: 0.7785 (mt-10) REVERT: I 82 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7343 (mt-10) REVERT: J 29 GLU cc_start: 0.8175 (tt0) cc_final: 0.7810 (mt-10) REVERT: J 77 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7855 (tp30) REVERT: K 77 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7846 (tp30) REVERT: K 135 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8219 (mm-30) REVERT: M 39 ASP cc_start: 0.8599 (m-30) cc_final: 0.8336 (m-30) REVERT: M 51 ARG cc_start: 0.8373 (mmt-90) cc_final: 0.8169 (mmt-90) REVERT: N 39 ASP cc_start: 0.8664 (m-30) cc_final: 0.8455 (m-30) REVERT: N 51 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.8108 (mmt-90) REVERT: O 39 ASP cc_start: 0.8536 (m-30) cc_final: 0.8307 (m-30) REVERT: P 51 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.8034 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8236 (tt0) cc_final: 0.7733 (mt-10) REVERT: R 77 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7861 (tp30) REVERT: R 135 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8422 (mm-30) REVERT: S 135 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8187 (mm-30) REVERT: T 82 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: U 39 ASP cc_start: 0.8605 (m-30) cc_final: 0.8350 (m-30) REVERT: V 20 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7518 (tp30) REVERT: V 51 ARG cc_start: 0.8357 (mmt180) cc_final: 0.8107 (mmt-90) REVERT: W 23 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7587 (mm-30) REVERT: W 39 ASP cc_start: 0.8640 (m-30) cc_final: 0.8362 (m-30) REVERT: W 51 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.8049 (mmt-90) REVERT: X 51 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.8134 (mmt-90) outliers start: 25 outliers final: 12 residues processed: 321 average time/residue: 0.3969 time to fit residues: 190.4158 Evaluate side-chains 311 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 298 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 133 optimal weight: 6.9990 chunk 2 optimal weight: 0.0570 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 276 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.098100 restraints weight = 25976.733| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.91 r_work: 0.2746 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23936 Z= 0.109 Angle : 0.384 5.173 32223 Z= 0.209 Chirality : 0.037 0.124 3852 Planarity : 0.003 0.029 4091 Dihedral : 3.209 14.295 3339 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.05 % Allowed : 6.51 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.14), residues: 3015 helix: 3.56 (0.11), residues: 1776 sheet: 2.30 (0.18), residues: 396 loop : 0.22 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 86 HIS 0.001 0.000 HIS T 46 PHE 0.005 0.001 PHE R 154 TYR 0.011 0.001 TYR H 61 ARG 0.003 0.000 ARG O 51 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1768) hydrogen bonds : angle 3.59467 ( 5124) covalent geometry : bond 0.00241 (23936) covalent geometry : angle 0.38396 (32223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 2.497 Fit side-chains REVERT: D 29 GLU cc_start: 0.8117 (tt0) cc_final: 0.7675 (mt-10) REVERT: E 39 ASP cc_start: 0.8558 (m-30) cc_final: 0.8318 (m-30) REVERT: E 51 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8047 (mmt-90) REVERT: F 23 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7423 (mt-10) REVERT: G 39 ASP cc_start: 0.8550 (m-30) cc_final: 0.8300 (m-30) REVERT: G 51 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7686 (mmt-90) REVERT: I 29 GLU cc_start: 0.8222 (tt0) cc_final: 0.7795 (mt-10) REVERT: J 29 GLU cc_start: 0.8157 (tt0) cc_final: 0.7808 (mt-10) REVERT: J 77 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7858 (tp30) REVERT: K 77 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7800 (tp30) REVERT: K 135 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8083 (mm-30) REVERT: M 23 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7493 (mt-10) REVERT: M 39 ASP cc_start: 0.8496 (m-30) cc_final: 0.8245 (m-30) REVERT: M 51 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.8081 (mmt-90) REVERT: N 23 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7471 (mt-10) REVERT: N 51 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.8018 (mmt-90) REVERT: O 39 ASP cc_start: 0.8458 (m-30) cc_final: 0.8233 (m-30) REVERT: O 51 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.7998 (mmt-90) REVERT: P 51 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.8093 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8202 (tt0) cc_final: 0.7696 (mt-10) REVERT: R 77 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7837 (tp30) REVERT: S 135 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8092 (mm-30) REVERT: T 82 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: U 23 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7307 (mt-10) REVERT: U 39 ASP cc_start: 0.8530 (m-30) cc_final: 0.8270 (m-30) REVERT: U 51 ARG cc_start: 0.8380 (mmt-90) cc_final: 0.8142 (mmt-90) REVERT: V 20 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7425 (tp30) REVERT: V 51 ARG cc_start: 0.8267 (mmt180) cc_final: 0.7989 (mmt-90) REVERT: W 23 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7524 (mm-30) REVERT: W 39 ASP cc_start: 0.8594 (m-30) cc_final: 0.8315 (m-30) REVERT: X 51 ARG cc_start: 0.8298 (mmt-90) cc_final: 0.8012 (mmp80) outliers start: 26 outliers final: 16 residues processed: 307 average time/residue: 0.4162 time to fit residues: 192.5093 Evaluate side-chains 313 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 296 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain N residue 90 GLU Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 266 optimal weight: 8.9990 chunk 164 optimal weight: 0.0970 chunk 188 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.130675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100519 restraints weight = 26002.858| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.90 r_work: 0.2786 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23936 Z= 0.096 Angle : 0.357 5.155 32223 Z= 0.196 Chirality : 0.037 0.122 3852 Planarity : 0.002 0.029 4091 Dihedral : 3.042 14.119 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.00 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.14), residues: 3015 helix: 3.58 (0.11), residues: 1812 sheet: 2.56 (0.18), residues: 396 loop : 0.49 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP S 86 HIS 0.001 0.000 HIS I 46 PHE 0.007 0.001 PHE C 40 TYR 0.010 0.001 TYR V 61 ARG 0.002 0.000 ARG W 51 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 1768) hydrogen bonds : angle 3.43565 ( 5124) covalent geometry : bond 0.00204 (23936) covalent geometry : angle 0.35711 (32223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 300 time to evaluate : 2.716 Fit side-chains REVERT: D 29 GLU cc_start: 0.8159 (tt0) cc_final: 0.7737 (mt-10) REVERT: E 39 ASP cc_start: 0.8494 (m-30) cc_final: 0.8262 (m-30) REVERT: F 51 ARG cc_start: 0.8080 (mpt180) cc_final: 0.7052 (mmm160) REVERT: G 39 ASP cc_start: 0.8437 (m-30) cc_final: 0.8159 (m-30) REVERT: I 29 GLU cc_start: 0.8202 (tt0) cc_final: 0.7769 (mt-10) REVERT: J 29 GLU cc_start: 0.8157 (tt0) cc_final: 0.7801 (mt-10) REVERT: K 135 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8131 (tp30) REVERT: L 94 TYR cc_start: 0.8420 (m-80) cc_final: 0.8094 (m-80) REVERT: M 23 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7512 (mt-10) REVERT: M 39 ASP cc_start: 0.8417 (m-30) cc_final: 0.8191 (m-30) REVERT: N 23 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7503 (mm-30) REVERT: N 51 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7962 (mmt-90) REVERT: O 51 ARG cc_start: 0.8235 (mmt-90) cc_final: 0.7979 (mmt-90) REVERT: P 51 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.8025 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8171 (tt0) cc_final: 0.7710 (mt-10) REVERT: S 135 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8146 (mm-30) REVERT: T 82 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: U 51 ARG cc_start: 0.8387 (mmt-90) cc_final: 0.8008 (mmt-90) REVERT: V 20 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7443 (tp30) REVERT: V 23 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7544 (mm-30) REVERT: V 51 ARG cc_start: 0.8213 (mmt180) cc_final: 0.7278 (mmm160) REVERT: W 39 ASP cc_start: 0.8534 (m-30) cc_final: 0.8260 (m-30) REVERT: W 51 ARG cc_start: 0.8318 (mmt-90) cc_final: 0.8014 (mmt-90) REVERT: X 51 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.8019 (mmt-90) outliers start: 16 outliers final: 11 residues processed: 305 average time/residue: 0.4369 time to fit residues: 202.7364 Evaluate side-chains 299 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 103 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 48 optimal weight: 0.0870 chunk 252 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.095830 restraints weight = 26075.064| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.89 r_work: 0.2726 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23936 Z= 0.137 Angle : 0.400 5.277 32223 Z= 0.214 Chirality : 0.038 0.124 3852 Planarity : 0.003 0.028 4091 Dihedral : 3.183 14.752 3339 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.73 % Allowed : 8.04 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.14), residues: 3015 helix: 3.50 (0.11), residues: 1788 sheet: 2.54 (0.18), residues: 396 loop : 0.41 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 86 HIS 0.001 0.000 HIS J 46 PHE 0.007 0.001 PHE C 40 TYR 0.013 0.001 TYR D 64 ARG 0.002 0.000 ARG U 43 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 1768) hydrogen bonds : angle 3.57803 ( 5124) covalent geometry : bond 0.00322 (23936) covalent geometry : angle 0.39986 (32223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 2.600 Fit side-chains REVERT: C 141 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: D 29 GLU cc_start: 0.8181 (tt0) cc_final: 0.7816 (mt-10) REVERT: E 39 ASP cc_start: 0.8509 (m-30) cc_final: 0.8278 (m-30) REVERT: G 39 ASP cc_start: 0.8529 (m-30) cc_final: 0.8263 (m-30) REVERT: I 29 GLU cc_start: 0.8222 (tt0) cc_final: 0.7760 (mt-10) REVERT: I 82 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7307 (mt-10) REVERT: J 29 GLU cc_start: 0.8172 (tt0) cc_final: 0.7749 (mt-10) REVERT: K 135 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8138 (mm-30) REVERT: L 94 TYR cc_start: 0.8486 (m-80) cc_final: 0.8106 (m-80) REVERT: M 39 ASP cc_start: 0.8512 (m-30) cc_final: 0.8283 (m-30) REVERT: M 51 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.8114 (mmt-90) REVERT: N 23 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7460 (mm-30) REVERT: O 51 ARG cc_start: 0.8265 (mmt-90) cc_final: 0.8026 (mmt-90) REVERT: P 23 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7489 (mm-30) REVERT: Q 29 GLU cc_start: 0.8234 (tt0) cc_final: 0.7758 (mt-10) REVERT: S 135 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8121 (mm-30) REVERT: T 82 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7257 (pm20) REVERT: U 23 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7432 (mm-30) REVERT: U 51 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.8018 (mmt-90) REVERT: V 20 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7427 (tp30) REVERT: V 23 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7536 (mm-30) REVERT: V 51 ARG cc_start: 0.8218 (mmt180) cc_final: 0.7951 (mmt-90) REVERT: W 23 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7608 (mm-30) REVERT: W 39 ASP cc_start: 0.8599 (m-30) cc_final: 0.8314 (m-30) REVERT: W 51 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.7941 (mmt-90) REVERT: X 23 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7337 (mm-30) REVERT: X 51 ARG cc_start: 0.8213 (mmt-90) cc_final: 0.8013 (mmt-90) outliers start: 18 outliers final: 15 residues processed: 289 average time/residue: 0.4089 time to fit residues: 176.7491 Evaluate side-chains 294 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 277 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 187 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.125438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.094992 restraints weight = 26296.770| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.89 r_work: 0.2737 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23936 Z= 0.147 Angle : 0.407 5.286 32223 Z= 0.218 Chirality : 0.038 0.126 3852 Planarity : 0.003 0.028 4091 Dihedral : 3.248 14.843 3339 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.33 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.14), residues: 3015 helix: 3.44 (0.11), residues: 1785 sheet: 2.54 (0.19), residues: 396 loop : 0.33 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 86 HIS 0.002 0.000 HIS J 46 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.001 TYR N 61 ARG 0.003 0.000 ARG X 43 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 1768) hydrogen bonds : angle 3.59887 ( 5124) covalent geometry : bond 0.00352 (23936) covalent geometry : angle 0.40679 (32223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 2.424 Fit side-chains REVERT: C 141 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: E 39 ASP cc_start: 0.8539 (m-30) cc_final: 0.8315 (m-30) REVERT: G 39 ASP cc_start: 0.8572 (m-30) cc_final: 0.8322 (m-30) REVERT: I 29 GLU cc_start: 0.8226 (tt0) cc_final: 0.7789 (mt-10) REVERT: I 82 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7310 (mt-10) REVERT: J 29 GLU cc_start: 0.8191 (tt0) cc_final: 0.7811 (mt-10) REVERT: K 135 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8154 (mm-30) REVERT: L 94 TYR cc_start: 0.8511 (m-80) cc_final: 0.8129 (m-80) REVERT: M 39 ASP cc_start: 0.8514 (m-30) cc_final: 0.8273 (m-30) REVERT: M 51 ARG cc_start: 0.8374 (mmt-90) cc_final: 0.7999 (mmt-90) REVERT: N 23 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7495 (mm-30) REVERT: O 51 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.8033 (mmt-90) REVERT: P 23 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7510 (mm-30) REVERT: P 51 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.8218 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8263 (tt0) cc_final: 0.7785 (mt-10) REVERT: S 135 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8139 (mm-30) REVERT: T 82 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: U 23 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7458 (mm-30) REVERT: U 51 ARG cc_start: 0.8368 (mmt-90) cc_final: 0.8022 (mmt-90) REVERT: V 20 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7490 (tp30) REVERT: V 23 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7580 (mm-30) REVERT: V 51 ARG cc_start: 0.8276 (mmt180) cc_final: 0.8031 (mmt-90) REVERT: W 23 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7625 (mm-30) REVERT: W 39 ASP cc_start: 0.8623 (m-30) cc_final: 0.8341 (m-30) REVERT: W 51 ARG cc_start: 0.8342 (mmt-90) cc_final: 0.7923 (mmt-90) outliers start: 16 outliers final: 13 residues processed: 282 average time/residue: 0.4053 time to fit residues: 169.4799 Evaluate side-chains 285 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 227 optimal weight: 3.9990 chunk 249 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.124309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.093881 restraints weight = 26373.680| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.89 r_work: 0.2696 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23936 Z= 0.168 Angle : 0.426 5.324 32223 Z= 0.227 Chirality : 0.039 0.128 3852 Planarity : 0.003 0.028 4091 Dihedral : 3.337 14.894 3339 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 8.57 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.14), residues: 3015 helix: 3.47 (0.11), residues: 1758 sheet: 2.49 (0.19), residues: 396 loop : 0.09 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 86 HIS 0.002 0.001 HIS J 46 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.001 TYR N 61 ARG 0.003 0.000 ARG N 51 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 1768) hydrogen bonds : angle 3.66696 ( 5124) covalent geometry : bond 0.00408 (23936) covalent geometry : angle 0.42626 (32223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 2.700 Fit side-chains REVERT: C 141 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: E 39 ASP cc_start: 0.8552 (m-30) cc_final: 0.8330 (m-30) REVERT: F 23 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 39 ASP cc_start: 0.8589 (m-30) cc_final: 0.8354 (m-30) REVERT: I 29 GLU cc_start: 0.8229 (tt0) cc_final: 0.7762 (mt-10) REVERT: I 82 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7291 (mt-10) REVERT: J 29 GLU cc_start: 0.8187 (tt0) cc_final: 0.7778 (mt-10) REVERT: K 135 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8213 (mm-30) REVERT: M 23 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7577 (mm-30) REVERT: M 39 ASP cc_start: 0.8536 (m-30) cc_final: 0.8303 (m-30) REVERT: M 51 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.7944 (mmt-90) REVERT: N 23 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7461 (mt-10) REVERT: O 23 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7606 (mm-30) REVERT: O 51 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.7994 (mmt-90) REVERT: P 23 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7503 (mm-30) REVERT: P 51 ARG cc_start: 0.8405 (mmt-90) cc_final: 0.8110 (mmt-90) REVERT: S 135 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8119 (mm-30) REVERT: T 82 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: U 23 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7436 (mm-30) REVERT: U 51 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.8060 (mmt-90) REVERT: V 20 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7452 (tp30) REVERT: V 23 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7547 (mm-30) REVERT: V 51 ARG cc_start: 0.8307 (mmt180) cc_final: 0.8053 (mmt-90) REVERT: W 23 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7507 (mm-30) REVERT: W 39 ASP cc_start: 0.8630 (m-30) cc_final: 0.8352 (m-30) REVERT: W 51 ARG cc_start: 0.8333 (mmt-90) cc_final: 0.7969 (mmt180) outliers start: 20 outliers final: 17 residues processed: 292 average time/residue: 0.4142 time to fit residues: 180.4312 Evaluate side-chains 301 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 282 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 118 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 0.5980 chunk 251 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 199 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 263 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.128505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.098288 restraints weight = 25982.244| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.88 r_work: 0.2769 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23936 Z= 0.098 Angle : 0.359 5.108 32223 Z= 0.197 Chirality : 0.037 0.121 3852 Planarity : 0.002 0.028 4091 Dihedral : 3.099 14.034 3339 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.97 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.14), residues: 3015 helix: 3.65 (0.11), residues: 1794 sheet: 2.59 (0.19), residues: 396 loop : 0.33 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP J 86 HIS 0.001 0.000 HIS I 46 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.001 TYR V 61 ARG 0.003 0.000 ARG X 51 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1768) hydrogen bonds : angle 3.42708 ( 5124) covalent geometry : bond 0.00210 (23936) covalent geometry : angle 0.35873 (32223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 309 time to evaluate : 2.654 Fit side-chains REVERT: D 29 GLU cc_start: 0.8124 (tt0) cc_final: 0.7772 (mt-10) REVERT: E 39 ASP cc_start: 0.8458 (m-30) cc_final: 0.8231 (m-30) REVERT: G 23 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7273 (mt-10) REVERT: G 39 ASP cc_start: 0.8475 (m-30) cc_final: 0.8211 (m-30) REVERT: I 29 GLU cc_start: 0.8196 (tt0) cc_final: 0.7746 (mt-10) REVERT: J 29 GLU cc_start: 0.8137 (tt0) cc_final: 0.7763 (mt-10) REVERT: K 135 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8050 (mm-30) REVERT: L 94 TYR cc_start: 0.8490 (m-80) cc_final: 0.8116 (m-80) REVERT: M 39 ASP cc_start: 0.8411 (m-30) cc_final: 0.8171 (m-30) REVERT: M 51 ARG cc_start: 0.8307 (mmt-90) cc_final: 0.7838 (mmt-90) REVERT: N 23 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7436 (mm-30) REVERT: O 51 ARG cc_start: 0.8242 (mmt-90) cc_final: 0.8038 (mmt-90) REVERT: P 23 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7498 (mm-30) REVERT: P 51 ARG cc_start: 0.8413 (mmt-90) cc_final: 0.8108 (mmt-90) REVERT: S 135 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8053 (mm-30) REVERT: T 82 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: U 23 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7470 (mm-30) REVERT: U 51 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.8040 (mmt-90) REVERT: V 20 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7283 (tp30) REVERT: V 51 ARG cc_start: 0.8221 (mmt180) cc_final: 0.7997 (mmt-90) REVERT: W 39 ASP cc_start: 0.8546 (m-30) cc_final: 0.8265 (m-30) REVERT: W 51 ARG cc_start: 0.8269 (mmt-90) cc_final: 0.7944 (mmt180) REVERT: X 23 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7608 (mt-10) outliers start: 16 outliers final: 12 residues processed: 314 average time/residue: 0.3937 time to fit residues: 186.7892 Evaluate side-chains 315 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 302 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 161 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 198 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 292 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.127634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.097127 restraints weight = 26178.965| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.90 r_work: 0.2746 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23936 Z= 0.111 Angle : 0.371 5.161 32223 Z= 0.201 Chirality : 0.037 0.122 3852 Planarity : 0.002 0.028 4091 Dihedral : 3.110 14.293 3339 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.57 % Allowed : 9.18 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.14), residues: 3015 helix: 3.61 (0.11), residues: 1794 sheet: 2.59 (0.19), residues: 396 loop : 0.32 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 86 HIS 0.001 0.000 HIS J 46 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.001 TYR H 61 ARG 0.003 0.000 ARG X 51 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 1768) hydrogen bonds : angle 3.46673 ( 5124) covalent geometry : bond 0.00253 (23936) covalent geometry : angle 0.37112 (32223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 295 time to evaluate : 2.573 Fit side-chains REVERT: E 39 ASP cc_start: 0.8480 (m-30) cc_final: 0.8255 (m-30) REVERT: F 23 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7707 (mm-30) REVERT: G 23 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7327 (mt-10) REVERT: G 39 ASP cc_start: 0.8506 (m-30) cc_final: 0.8245 (m-30) REVERT: I 29 GLU cc_start: 0.8236 (tt0) cc_final: 0.7793 (mt-10) REVERT: I 82 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7300 (mt-10) REVERT: J 29 GLU cc_start: 0.8172 (tt0) cc_final: 0.7792 (mt-10) REVERT: K 135 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8101 (mm-30) REVERT: L 94 TYR cc_start: 0.8498 (m-80) cc_final: 0.8110 (m-80) REVERT: M 39 ASP cc_start: 0.8409 (m-30) cc_final: 0.8181 (m-30) REVERT: M 51 ARG cc_start: 0.8325 (mmt-90) cc_final: 0.7849 (mmt-90) REVERT: N 23 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7479 (mt-10) REVERT: O 51 ARG cc_start: 0.8280 (mmt-90) cc_final: 0.7990 (mmt-90) REVERT: P 23 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7518 (mm-30) REVERT: P 51 ARG cc_start: 0.8436 (mmt-90) cc_final: 0.8118 (mmt-90) REVERT: S 135 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8093 (mm-30) REVERT: T 82 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: U 23 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7495 (mm-30) REVERT: U 51 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.8026 (mmt-90) REVERT: V 20 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7329 (tp30) REVERT: V 51 ARG cc_start: 0.8253 (mmt180) cc_final: 0.8009 (mmt-90) REVERT: W 39 ASP cc_start: 0.8551 (m-30) cc_final: 0.8265 (m-30) REVERT: W 51 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.7951 (mmt180) REVERT: X 23 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7625 (mt-10) outliers start: 14 outliers final: 13 residues processed: 301 average time/residue: 0.4045 time to fit residues: 182.8483 Evaluate side-chains 305 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 291 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 82 GLU Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 241 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 268 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 260 optimal weight: 1.9990 chunk 202 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.128460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.097903 restraints weight = 25894.895| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.90 r_work: 0.2759 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23936 Z= 0.105 Angle : 0.363 5.161 32223 Z= 0.197 Chirality : 0.037 0.121 3852 Planarity : 0.002 0.028 4091 Dihedral : 3.076 14.262 3339 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 9.18 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.14), residues: 3015 helix: 3.64 (0.11), residues: 1800 sheet: 2.61 (0.19), residues: 396 loop : 0.36 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 86 HIS 0.001 0.000 HIS J 46 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.001 TYR D 94 ARG 0.003 0.000 ARG X 51 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1768) hydrogen bonds : angle 3.43411 ( 5124) covalent geometry : bond 0.00234 (23936) covalent geometry : angle 0.36333 (32223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12596.87 seconds wall clock time: 217 minutes 58.50 seconds (13078.50 seconds total)