Starting phenix.real_space_refine on Fri Sep 19 03:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c9i_7436/09_2025/6c9i_7436.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c9i_7436/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6c9i_7436/09_2025/6c9i_7436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c9i_7436/09_2025/6c9i_7436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c9i_7436/09_2025/6c9i_7436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c9i_7436/09_2025/6c9i_7436.map" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.08, per 1000 atoms: 0.21 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: 1.84 Conformation dependent library (CDL) restraints added in 822.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.76 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: 4.38 Time building geometry restraints manager: 2.35 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.070 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG U 43 TYR 0.046 0.009 TYR O 50 PHE 0.020 0.003 PHE J 103 TRP 0.026 0.009 TRP R 86 HIS 0.004 0.002 HIS X 63 Details of bonding type rmsd covalent geometry : bond 0.02940 (23936) covalent geometry : angle 1.47677 (32223) hydrogen bonds : bond 0.15043 ( 1768) hydrogen bonds : angle 6.04845 ( 5124) *********************** 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 : 0.775 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: 0.1836 time to fit residues: 122.6958 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 : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.129059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098993 restraints weight = 25955.466| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.90 r_work: 0.2765 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23936 Z= 0.129 Angle : 0.468 5.279 32223 Z= 0.255 Chirality : 0.039 0.129 3852 Planarity : 0.004 0.034 4091 Dihedral : 3.528 13.910 3339 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.28 % Allowed : 4.32 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.14), residues: 3015 helix: 3.43 (0.11), residues: 1764 sheet: 2.30 (0.20), residues: 396 loop : 0.20 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 77 TYR 0.014 0.002 TYR X 61 PHE 0.007 0.001 PHE C 154 TRP 0.015 0.003 TRP R 86 HIS 0.001 0.000 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00276 (23936) covalent geometry : angle 0.46757 (32223) hydrogen bonds : bond 0.05075 ( 1768) hydrogen bonds : angle 3.95626 ( 5124) *********************** 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 381 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 374 time to evaluate : 0.874 Fit side-chains REVERT: A 29 GLU cc_start: 0.8056 (tt0) cc_final: 0.7636 (mt-10) REVERT: A 36 GLU cc_start: 0.8724 (tt0) cc_final: 0.8359 (tt0) REVERT: B 29 GLU cc_start: 0.8050 (tt0) cc_final: 0.7666 (mt-10) REVERT: C 36 GLU cc_start: 0.8675 (tt0) cc_final: 0.8424 (tt0) REVERT: D 36 GLU cc_start: 0.8701 (tt0) cc_final: 0.8422 (tt0) REVERT: E 39 ASP cc_start: 0.8641 (m-30) cc_final: 0.8429 (m-30) REVERT: E 51 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.8060 (mmt-90) REVERT: F 51 ARG cc_start: 0.8140 (mmp80) cc_final: 0.7886 (mmp80) REVERT: G 39 ASP cc_start: 0.8514 (m-30) cc_final: 0.8280 (m-30) REVERT: H 51 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.8086 (mmt-90) REVERT: I 29 GLU cc_start: 0.8169 (tt0) cc_final: 0.7677 (mt-10) REVERT: I 36 GLU cc_start: 0.8730 (tt0) cc_final: 0.8454 (tt0) REVERT: J 29 GLU cc_start: 0.8083 (tt0) cc_final: 0.7648 (mt-10) REVERT: K 135 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8171 (mm-30) REVERT: M 39 ASP cc_start: 0.8610 (m-30) cc_final: 0.8383 (m-30) REVERT: M 51 ARG cc_start: 0.8375 (mmt-90) cc_final: 0.8093 (mmt-90) REVERT: N 51 ARG cc_start: 0.8334 (mmt-90) cc_final: 0.8031 (mmt-90) REVERT: P 51 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.8037 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8179 (tt0) cc_final: 0.7661 (mt-10) REVERT: Q 36 GLU cc_start: 0.8681 (tt0) cc_final: 0.8460 (tt0) REVERT: R 29 GLU cc_start: 0.8099 (tt0) cc_final: 0.7757 (mt-10) REVERT: R 36 GLU cc_start: 0.8722 (tt0) cc_final: 0.8400 (tt0) REVERT: R 77 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7850 (tp30) REVERT: R 135 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8340 (mm-30) REVERT: S 77 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7531 (tp30) REVERT: S 135 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8088 (mm-30) REVERT: T 82 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: U 39 ASP cc_start: 0.8584 (m-30) cc_final: 0.8348 (m-30) REVERT: U 51 ARG cc_start: 0.8358 (mmt-90) cc_final: 0.7393 (mmm160) REVERT: U 110 GLU cc_start: 0.8699 (tt0) cc_final: 0.8407 (tt0) REVERT: V 20 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7533 (tp30) REVERT: V 39 ASP cc_start: 0.8519 (m-30) cc_final: 0.8310 (m-30) REVERT: V 51 ARG cc_start: 0.8256 (mmt180) cc_final: 0.7811 (mmp80) REVERT: W 23 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7553 (mm-30) REVERT: W 39 ASP cc_start: 0.8624 (m-30) cc_final: 0.8353 (m-30) REVERT: W 51 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.7985 (mmt-90) REVERT: X 51 ARG cc_start: 0.8363 (mmt-90) cc_final: 0.8091 (mmt-90) outliers start: 7 outliers final: 3 residues processed: 375 average time/residue: 0.1603 time to fit residues: 91.8761 Evaluate side-chains 307 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 303 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain I residue 97 MET 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 178 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 244 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.130479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.100619 restraints weight = 25792.639| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.87 r_work: 0.2781 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2812 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= 0.110 Angle : 0.394 5.220 32223 Z= 0.215 Chirality : 0.038 0.126 3852 Planarity : 0.003 0.029 4091 Dihedral : 3.198 14.178 3339 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.85 % Allowed : 5.90 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.88 (0.14), residues: 3015 helix: 3.63 (0.11), residues: 1782 sheet: 2.20 (0.19), residues: 396 loop : 0.27 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 51 TYR 0.012 0.001 TYR X 61 PHE 0.005 0.001 PHE E 44 TRP 0.014 0.003 TRP R 86 HIS 0.001 0.000 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00235 (23936) covalent geometry : angle 0.39370 (32223) hydrogen bonds : bond 0.04301 ( 1768) hydrogen bonds : angle 3.69645 ( 5124) *********************** 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 336 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 0.898 Fit side-chains REVERT: A 29 GLU cc_start: 0.8054 (tt0) cc_final: 0.7694 (mt-10) REVERT: B 29 GLU cc_start: 0.8137 (tt0) cc_final: 0.7756 (mt-10) REVERT: D 29 GLU cc_start: 0.8088 (tt0) cc_final: 0.7615 (mt-10) REVERT: D 97 MET cc_start: 0.7560 (mtm) cc_final: 0.7278 (mtp) REVERT: E 39 ASP cc_start: 0.8580 (m-30) cc_final: 0.8349 (m-30) REVERT: E 51 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7315 (mmm160) REVERT: F 51 ARG cc_start: 0.8067 (mmp80) cc_final: 0.7299 (mmm160) REVERT: G 39 ASP cc_start: 0.8499 (m-30) cc_final: 0.8245 (m-30) REVERT: G 51 ARG cc_start: 0.8095 (mmt-90) cc_final: 0.7754 (mmt-90) REVERT: I 29 GLU cc_start: 0.8174 (tt0) cc_final: 0.7757 (mt-10) REVERT: I 36 GLU cc_start: 0.8717 (tt0) cc_final: 0.8306 (tt0) REVERT: J 29 GLU cc_start: 0.8112 (tt0) cc_final: 0.7682 (mt-10) REVERT: J 36 GLU cc_start: 0.8618 (tt0) cc_final: 0.8362 (tt0) REVERT: J 43 GLU cc_start: 0.8730 (tt0) cc_final: 0.8499 (tm-30) REVERT: K 135 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8040 (mm-30) REVERT: M 39 ASP cc_start: 0.8539 (m-30) cc_final: 0.8276 (m-30) REVERT: M 51 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7985 (mmt-90) REVERT: N 42 SER cc_start: 0.9436 (p) cc_final: 0.9154 (m) REVERT: N 51 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7943 (mmt-90) REVERT: P 51 ARG cc_start: 0.8231 (mmt-90) cc_final: 0.7322 (mmm160) REVERT: Q 29 GLU cc_start: 0.8151 (tt0) cc_final: 0.7694 (mt-10) REVERT: R 36 GLU cc_start: 0.8678 (tt0) cc_final: 0.8297 (tt0) REVERT: S 135 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8016 (mm-30) REVERT: T 82 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: U 39 ASP cc_start: 0.8549 (m-30) cc_final: 0.8299 (m-30) REVERT: U 51 ARG cc_start: 0.8200 (mmt-90) cc_final: 0.7349 (mmm160) REVERT: V 20 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7411 (tp30) REVERT: V 51 ARG cc_start: 0.8235 (mmt180) cc_final: 0.7268 (mmm160) REVERT: W 39 ASP cc_start: 0.8566 (m-30) cc_final: 0.8285 (m-30) REVERT: W 51 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7864 (mmt-90) REVERT: X 51 ARG cc_start: 0.8279 (mmt-90) cc_final: 0.7968 (mmp80) outliers start: 21 outliers final: 8 residues processed: 320 average time/residue: 0.1644 time to fit residues: 80.2101 Evaluate side-chains 295 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 286 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain H residue 103 SER 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 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 285 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 0.0470 chunk 101 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.2082 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.127818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.097453 restraints weight = 25827.061| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.86 r_work: 0.2734 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23936 Z= 0.132 Angle : 0.406 5.249 32223 Z= 0.219 Chirality : 0.038 0.126 3852 Planarity : 0.003 0.030 4091 Dihedral : 3.229 14.835 3339 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.85 % Allowed : 6.39 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.14), residues: 3015 helix: 3.53 (0.11), residues: 1776 sheet: 2.31 (0.18), residues: 396 loop : 0.27 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 51 TYR 0.011 0.001 TYR H 61 PHE 0.008 0.001 PHE C 40 TRP 0.011 0.002 TRP I 86 HIS 0.001 0.000 HIS Q 46 Details of bonding type rmsd covalent geometry : bond 0.00306 (23936) covalent geometry : angle 0.40637 (32223) hydrogen bonds : bond 0.04520 ( 1768) hydrogen bonds : angle 3.64238 ( 5124) *********************** 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 318 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 297 time to evaluate : 0.975 Fit side-chains REVERT: A 29 GLU cc_start: 0.8101 (tt0) cc_final: 0.7715 (mt-10) REVERT: A 43 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8464 (tt0) REVERT: B 29 GLU cc_start: 0.8171 (tt0) cc_final: 0.7775 (mt-10) REVERT: D 29 GLU cc_start: 0.8118 (tt0) cc_final: 0.7685 (mt-10) REVERT: D 97 MET cc_start: 0.7467 (mtm) cc_final: 0.7156 (mtp) REVERT: E 39 ASP cc_start: 0.8559 (m-30) cc_final: 0.8322 (m-30) REVERT: E 51 ARG cc_start: 0.8319 (mmt-90) cc_final: 0.8064 (mmt-90) REVERT: F 23 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7404 (mm-30) REVERT: F 51 ARG cc_start: 0.8128 (mmp80) cc_final: 0.7846 (mmp80) REVERT: G 39 ASP cc_start: 0.8561 (m-30) cc_final: 0.8320 (m-30) REVERT: G 51 ARG cc_start: 0.8162 (mmt-90) cc_final: 0.7760 (mmt-90) REVERT: H 51 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.7991 (mmt-90) REVERT: I 29 GLU cc_start: 0.8239 (tt0) cc_final: 0.7809 (mt-10) REVERT: J 29 GLU cc_start: 0.8145 (tt0) cc_final: 0.7769 (mt-10) REVERT: J 77 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7825 (tp30) REVERT: K 135 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8114 (mm-30) REVERT: M 39 ASP cc_start: 0.8512 (m-30) cc_final: 0.8255 (m-30) REVERT: M 51 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.8017 (mmt-90) REVERT: N 51 ARG cc_start: 0.8218 (mmt-90) cc_final: 0.7973 (mmt-90) REVERT: P 51 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.8051 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8180 (tt0) cc_final: 0.7664 (mt-10) REVERT: R 77 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7822 (tp30) REVERT: S 135 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8116 (mm-30) REVERT: T 82 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: U 39 ASP cc_start: 0.8524 (m-30) cc_final: 0.8266 (m-30) REVERT: U 51 ARG cc_start: 0.8213 (mmt-90) cc_final: 0.7920 (mmt-90) REVERT: V 20 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7468 (tp30) REVERT: V 51 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7969 (mmt-90) REVERT: W 23 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7571 (mm-30) REVERT: W 39 ASP cc_start: 0.8608 (m-30) cc_final: 0.8331 (m-30) REVERT: X 51 ARG cc_start: 0.8261 (mmt-90) cc_final: 0.7982 (mmp80) outliers start: 21 outliers final: 11 residues processed: 307 average time/residue: 0.1691 time to fit residues: 78.2020 Evaluate side-chains 291 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 279 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 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 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 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 117 optimal weight: 0.0870 chunk 210 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.125353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.094303 restraints weight = 25901.170| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.92 r_work: 0.2692 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2849 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= 0.167 Angle : 0.430 5.354 32223 Z= 0.229 Chirality : 0.039 0.128 3852 Planarity : 0.003 0.030 4091 Dihedral : 3.334 14.977 3339 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 7.80 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.63 (0.14), residues: 3015 helix: 3.41 (0.11), residues: 1767 sheet: 2.35 (0.18), residues: 396 loop : 0.14 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 43 TYR 0.010 0.001 TYR N 61 PHE 0.006 0.001 PHE C 40 TRP 0.009 0.002 TRP I 86 HIS 0.002 0.000 HIS J 46 Details of bonding type rmsd covalent geometry : bond 0.00405 (23936) covalent geometry : angle 0.43033 (32223) hydrogen bonds : bond 0.04815 ( 1768) hydrogen bonds : angle 3.70736 ( 5124) *********************** 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 308 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.934 Fit side-chains REVERT: A 29 GLU cc_start: 0.8190 (tt0) cc_final: 0.7778 (mt-10) REVERT: D 29 GLU cc_start: 0.8153 (tt0) cc_final: 0.7759 (mt-10) REVERT: D 97 MET cc_start: 0.7489 (mtm) cc_final: 0.7170 (mtp) REVERT: E 39 ASP cc_start: 0.8552 (m-30) cc_final: 0.8309 (m-30) REVERT: E 51 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.8129 (mmt-90) REVERT: F 51 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7905 (mmp80) REVERT: G 39 ASP cc_start: 0.8606 (m-30) cc_final: 0.8368 (m-30) REVERT: G 51 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.7852 (mmt180) REVERT: I 29 GLU cc_start: 0.8244 (tt0) cc_final: 0.7802 (mt-10) REVERT: J 29 GLU cc_start: 0.8210 (tt0) cc_final: 0.7795 (mt-10) REVERT: K 77 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7907 (tp30) REVERT: K 135 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8201 (mm-30) REVERT: L 94 TYR cc_start: 0.8517 (m-80) cc_final: 0.8164 (m-80) REVERT: M 39 ASP cc_start: 0.8544 (m-30) cc_final: 0.8300 (m-30) REVERT: M 51 ARG cc_start: 0.8301 (mmt-90) cc_final: 0.8075 (mmt-90) REVERT: N 51 ARG cc_start: 0.8285 (mmt-90) cc_final: 0.7960 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8269 (tt0) cc_final: 0.7781 (mt-10) REVERT: R 77 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7860 (tp30) REVERT: S 135 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8155 (mm-30) REVERT: T 82 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: U 23 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7441 (mm-30) REVERT: U 39 ASP cc_start: 0.8540 (m-30) cc_final: 0.8286 (m-30) REVERT: U 51 ARG cc_start: 0.8289 (mmt-90) cc_final: 0.8081 (mmt-90) REVERT: V 20 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7498 (tp30) REVERT: V 51 ARG cc_start: 0.8318 (mmt180) cc_final: 0.8073 (mmt-90) REVERT: W 23 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7634 (mm-30) REVERT: W 39 ASP cc_start: 0.8655 (m-30) cc_final: 0.8369 (m-30) REVERT: W 51 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.8153 (mmt-90) REVERT: X 15 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7322 (mt-10) REVERT: X 51 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.8008 (mmt-90) outliers start: 17 outliers final: 12 residues processed: 294 average time/residue: 0.1737 time to fit residues: 76.3406 Evaluate side-chains 296 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 283 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 97 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 208 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.126562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.096283 restraints weight = 26238.795| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.90 r_work: 0.2735 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3043 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= 0.121 Angle : 0.383 5.250 32223 Z= 0.208 Chirality : 0.038 0.124 3852 Planarity : 0.003 0.029 4091 Dihedral : 3.192 14.437 3339 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.57 % Allowed : 8.37 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.82 (0.14), residues: 3015 helix: 3.55 (0.11), residues: 1776 sheet: 2.45 (0.18), residues: 396 loop : 0.20 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 51 TYR 0.010 0.001 TYR D 64 PHE 0.005 0.001 PHE C 40 TRP 0.011 0.002 TRP I 86 HIS 0.001 0.000 HIS Q 46 Details of bonding type rmsd covalent geometry : bond 0.00279 (23936) covalent geometry : angle 0.38345 (32223) hydrogen bonds : bond 0.04276 ( 1768) hydrogen bonds : angle 3.54569 ( 5124) *********************** 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 309 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 295 time to evaluate : 0.819 Fit side-chains REVERT: A 29 GLU cc_start: 0.8088 (tt0) cc_final: 0.7700 (mt-10) REVERT: D 29 GLU cc_start: 0.8147 (tt0) cc_final: 0.7785 (mt-10) REVERT: E 39 ASP cc_start: 0.8519 (m-30) cc_final: 0.8295 (m-30) REVERT: F 23 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7296 (mt-10) REVERT: G 39 ASP cc_start: 0.8555 (m-30) cc_final: 0.8305 (m-30) REVERT: G 51 ARG cc_start: 0.8209 (mmt-90) cc_final: 0.7660 (mmt180) REVERT: I 29 GLU cc_start: 0.8220 (tt0) cc_final: 0.7779 (mt-10) REVERT: J 29 GLU cc_start: 0.8156 (tt0) cc_final: 0.7784 (mt-10) REVERT: K 135 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8109 (mm-30) REVERT: L 94 TYR cc_start: 0.8494 (m-80) cc_final: 0.8129 (m-80) REVERT: M 51 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.8010 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8239 (tt0) cc_final: 0.7756 (mt-10) REVERT: S 135 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8107 (mm-30) REVERT: T 82 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: U 23 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7360 (mm-30) REVERT: U 51 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.8009 (mmt-90) REVERT: V 20 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7451 (tp30) REVERT: V 23 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7503 (mm-30) REVERT: V 51 ARG cc_start: 0.8267 (mmt180) cc_final: 0.8014 (mmt-90) REVERT: W 23 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7586 (mm-30) REVERT: W 39 ASP cc_start: 0.8600 (m-30) cc_final: 0.8317 (m-30) REVERT: W 51 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.7938 (mmt-90) REVERT: X 15 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7377 (mt-10) REVERT: X 23 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7291 (mm-30) outliers start: 14 outliers final: 11 residues processed: 298 average time/residue: 0.1769 time to fit residues: 78.6790 Evaluate side-chains 301 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 289 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 291 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3287 r_free = 0.3287 target = 0.125563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.095242 restraints weight = 26127.091| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.89 r_work: 0.2718 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23936 Z= 0.138 Angle : 0.401 5.269 32223 Z= 0.215 Chirality : 0.038 0.125 3852 Planarity : 0.003 0.029 4091 Dihedral : 3.226 14.585 3339 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 8.49 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.75 (0.14), residues: 3015 helix: 3.48 (0.11), residues: 1776 sheet: 2.46 (0.19), residues: 396 loop : 0.15 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 51 TYR 0.013 0.001 TYR D 64 PHE 0.006 0.001 PHE C 40 TRP 0.009 0.002 TRP I 86 HIS 0.001 0.000 HIS J 46 Details of bonding type rmsd covalent geometry : bond 0.00327 (23936) covalent geometry : angle 0.40065 (32223) hydrogen bonds : bond 0.04471 ( 1768) hydrogen bonds : angle 3.58910 ( 5124) *********************** 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 299 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.927 Fit side-chains REVERT: A 29 GLU cc_start: 0.8119 (tt0) cc_final: 0.7723 (mt-10) REVERT: C 141 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: D 29 GLU cc_start: 0.8166 (tt0) cc_final: 0.7798 (mt-10) REVERT: E 39 ASP cc_start: 0.8528 (m-30) cc_final: 0.8324 (m-30) REVERT: F 23 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7458 (mt-10) REVERT: F 51 ARG cc_start: 0.8058 (mpt180) cc_final: 0.7037 (mmm160) REVERT: G 39 ASP cc_start: 0.8574 (m-30) cc_final: 0.8332 (m-30) REVERT: G 51 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7671 (mmt180) REVERT: I 29 GLU cc_start: 0.8237 (tt0) cc_final: 0.7791 (mt-10) REVERT: J 29 GLU cc_start: 0.8158 (tt0) cc_final: 0.7782 (mt-10) REVERT: K 135 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8163 (mm-30) REVERT: L 94 TYR cc_start: 0.8521 (m-80) cc_final: 0.8141 (m-80) REVERT: M 51 ARG cc_start: 0.8270 (mmt-90) cc_final: 0.8020 (mmt-90) REVERT: P 51 ARG cc_start: 0.8411 (mmt-90) cc_final: 0.8165 (mmt-90) REVERT: Q 29 GLU cc_start: 0.8273 (tt0) cc_final: 0.7790 (mt-10) REVERT: S 135 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8136 (mm-30) REVERT: T 82 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7204 (pm20) REVERT: U 23 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7406 (mm-30) REVERT: U 51 ARG cc_start: 0.8330 (mmt-90) cc_final: 0.8008 (mmt-90) REVERT: V 20 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7362 (tp30) REVERT: V 51 ARG cc_start: 0.8296 (mmt180) cc_final: 0.8049 (mmt-90) REVERT: W 39 ASP cc_start: 0.8613 (m-30) cc_final: 0.8331 (m-30) REVERT: W 51 ARG cc_start: 0.8367 (mmt-90) cc_final: 0.8060 (mmt180) REVERT: X 15 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7348 (mt-10) REVERT: X 51 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.8105 (mmt-90) outliers start: 17 outliers final: 15 residues processed: 286 average time/residue: 0.1860 time to fit residues: 78.8996 Evaluate side-chains 285 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 268 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 157 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 21 optimal weight: 0.0000 chunk 279 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 226 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- 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 = 0.124398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.094044 restraints weight = 26248.802| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.89 r_work: 0.2694 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23936 Z= 0.164 Angle : 0.424 5.316 32223 Z= 0.226 Chirality : 0.039 0.127 3852 Planarity : 0.003 0.029 4091 Dihedral : 3.319 14.811 3339 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.73 % Allowed : 8.53 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.14), residues: 3015 helix: 3.45 (0.11), residues: 1764 sheet: 2.43 (0.19), residues: 396 loop : 0.05 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 43 TYR 0.010 0.001 TYR N 61 PHE 0.005 0.001 PHE Q 40 TRP 0.008 0.002 TRP B 86 HIS 0.002 0.000 HIS J 46 Details of bonding type rmsd covalent geometry : bond 0.00397 (23936) covalent geometry : angle 0.42430 (32223) hydrogen bonds : bond 0.04712 ( 1768) hydrogen bonds : angle 3.66020 ( 5124) *********************** 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 303 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 285 time to evaluate : 0.793 Fit side-chains REVERT: A 29 GLU cc_start: 0.8139 (tt0) cc_final: 0.7736 (mt-10) REVERT: C 141 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: E 23 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 39 ASP cc_start: 0.8549 (m-30) cc_final: 0.8331 (m-30) REVERT: G 39 ASP cc_start: 0.8602 (m-30) cc_final: 0.8370 (m-30) REVERT: G 51 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7804 (mmt180) REVERT: I 29 GLU cc_start: 0.8241 (tt0) cc_final: 0.7780 (mt-10) REVERT: I 82 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7287 (mt-10) REVERT: J 29 GLU cc_start: 0.8164 (tt0) cc_final: 0.7773 (mt-10) REVERT: K 135 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8204 (mm-30) REVERT: M 23 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7575 (mm-30) REVERT: M 51 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.8111 (mmt-90) REVERT: O 23 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7611 (mm-30) REVERT: P 23 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7514 (mm-30) REVERT: P 51 ARG cc_start: 0.8423 (mmt-90) cc_final: 0.8146 (mmt-90) REVERT: S 135 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8093 (mm-30) REVERT: T 82 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: V 20 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7486 (tp30) REVERT: V 51 ARG cc_start: 0.8326 (mmt180) cc_final: 0.8084 (mmt-90) REVERT: W 23 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7548 (mm-30) REVERT: W 39 ASP cc_start: 0.8633 (m-30) cc_final: 0.8351 (m-30) REVERT: W 51 ARG cc_start: 0.8349 (mmt-90) cc_final: 0.7995 (mmt180) outliers start: 18 outliers final: 15 residues processed: 289 average time/residue: 0.1792 time to fit residues: 77.0684 Evaluate side-chains 293 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 276 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 188 optimal weight: 4.9990 chunk 145 optimal weight: 0.0010 chunk 183 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.125907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.095596 restraints weight = 26186.424| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.89 r_work: 0.2723 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3121 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= 0.125 Angle : 0.391 5.222 32223 Z= 0.211 Chirality : 0.038 0.125 3852 Planarity : 0.003 0.029 4091 Dihedral : 3.219 14.418 3339 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.57 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.14), residues: 3015 helix: 3.56 (0.11), residues: 1773 sheet: 2.48 (0.19), residues: 396 loop : 0.12 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 51 TYR 0.010 0.001 TYR N 61 PHE 0.005 0.001 PHE C 40 TRP 0.010 0.002 TRP J 86 HIS 0.001 0.000 HIS Q 46 Details of bonding type rmsd covalent geometry : bond 0.00289 (23936) covalent geometry : angle 0.39068 (32223) hydrogen bonds : bond 0.04329 ( 1768) hydrogen bonds : angle 3.55206 ( 5124) *********************** 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 294 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 278 time to evaluate : 0.838 Fit side-chains REVERT: A 29 GLU cc_start: 0.8114 (tt0) cc_final: 0.7719 (mt-10) REVERT: C 141 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: E 39 ASP cc_start: 0.8519 (m-30) cc_final: 0.8299 (m-30) REVERT: G 39 ASP cc_start: 0.8569 (m-30) cc_final: 0.8321 (m-30) REVERT: I 29 GLU cc_start: 0.8208 (tt0) cc_final: 0.7750 (mt-10) REVERT: J 29 GLU cc_start: 0.8150 (tt0) cc_final: 0.7762 (mt-10) REVERT: K 135 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8138 (mm-30) REVERT: M 51 ARG cc_start: 0.8299 (mmt-90) cc_final: 0.7899 (mmt-90) REVERT: N 23 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7679 (mm-30) REVERT: P 23 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7480 (mm-30) REVERT: P 51 ARG cc_start: 0.8396 (mmt-90) cc_final: 0.8109 (mmt-90) REVERT: S 135 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8059 (mm-30) REVERT: T 82 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: U 23 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7657 (mm-30) REVERT: U 51 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8170 (mmt-90) REVERT: V 20 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7424 (tp30) REVERT: V 23 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7479 (mm-30) REVERT: V 51 ARG cc_start: 0.8279 (mmt180) cc_final: 0.8057 (mmt-90) REVERT: W 23 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7524 (mm-30) REVERT: W 39 ASP cc_start: 0.8598 (m-30) cc_final: 0.8316 (m-30) REVERT: W 51 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.8071 (mmt180) outliers start: 16 outliers final: 13 residues processed: 281 average time/residue: 0.1762 time to fit residues: 73.2936 Evaluate side-chains 287 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 272 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 59 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 144 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.126790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.096399 restraints weight = 26078.588| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.90 r_work: 0.2740 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23936 Z= 0.116 Angle : 0.379 5.194 32223 Z= 0.205 Chirality : 0.037 0.124 3852 Planarity : 0.003 0.032 4091 Dihedral : 3.157 14.287 3339 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.89 (0.14), residues: 3015 helix: 3.62 (0.11), residues: 1776 sheet: 2.52 (0.19), residues: 396 loop : 0.16 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 51 TYR 0.011 0.001 TYR D 64 PHE 0.005 0.001 PHE C 40 TRP 0.011 0.002 TRP B 86 HIS 0.001 0.000 HIS Q 46 Details of bonding type rmsd covalent geometry : bond 0.00265 (23936) covalent geometry : angle 0.37921 (32223) hydrogen bonds : bond 0.04169 ( 1768) hydrogen bonds : angle 3.50232 ( 5124) ********************** 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 301 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 285 time to evaluate : 0.709 Fit side-chains REVERT: A 29 GLU cc_start: 0.8099 (tt0) cc_final: 0.7711 (mt-10) REVERT: C 141 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: E 39 ASP cc_start: 0.8491 (m-30) cc_final: 0.8270 (m-30) REVERT: G 39 ASP cc_start: 0.8514 (m-30) cc_final: 0.8220 (m-30) REVERT: I 29 GLU cc_start: 0.8193 (tt0) cc_final: 0.7745 (mt-10) REVERT: J 29 GLU cc_start: 0.8150 (tt0) cc_final: 0.7772 (mt-10) REVERT: K 135 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8089 (mm-30) REVERT: L 94 TYR cc_start: 0.8481 (m-80) cc_final: 0.8161 (m-80) REVERT: M 51 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.7884 (mmt-90) REVERT: N 23 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7673 (mm-30) REVERT: P 23 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7493 (mm-30) REVERT: P 51 ARG cc_start: 0.8410 (mmt-90) cc_final: 0.8139 (mmt-90) REVERT: S 135 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8066 (mm-30) REVERT: T 82 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: U 23 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7660 (mm-30) REVERT: V 20 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7420 (tp30) REVERT: V 23 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7481 (mm-30) REVERT: V 51 ARG cc_start: 0.8275 (mmt180) cc_final: 0.8027 (mmt-90) REVERT: W 39 ASP cc_start: 0.8567 (m-30) cc_final: 0.8283 (m-30) REVERT: W 51 ARG cc_start: 0.8312 (mmt-90) cc_final: 0.8052 (mmt180) outliers start: 16 outliers final: 13 residues processed: 288 average time/residue: 0.1754 time to fit residues: 75.4044 Evaluate side-chains 291 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 276 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 55 optimal weight: 0.0970 chunk 228 optimal weight: 0.3980 chunk 208 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 261 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.128598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.098310 restraints weight = 25991.127| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.89 r_work: 0.2764 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3324 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= 0.100 Angle : 0.362 5.149 32223 Z= 0.197 Chirality : 0.037 0.120 3852 Planarity : 0.002 0.028 4091 Dihedral : 3.071 14.104 3339 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.81 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.99 (0.14), residues: 3015 helix: 3.60 (0.11), residues: 1806 sheet: 2.56 (0.19), residues: 396 loop : 0.31 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 51 TYR 0.010 0.001 TYR H 61 PHE 0.005 0.001 PHE R 154 TRP 0.012 0.002 TRP I 86 HIS 0.001 0.000 HIS Q 46 Details of bonding type rmsd covalent geometry : bond 0.00217 (23936) covalent geometry : angle 0.36170 (32223) hydrogen bonds : bond 0.03927 ( 1768) hydrogen bonds : angle 3.42418 ( 5124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5396.76 seconds wall clock time: 93 minutes 14.65 seconds (5594.65 seconds total)