Starting phenix.real_space_refine on Sun Sep 29 15:23:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9i_7436/09_2024/6c9i_7436.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9i_7436/09_2024/6c9i_7436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9i_7436/09_2024/6c9i_7436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9i_7436/09_2024/6c9i_7436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9i_7436/09_2024/6c9i_7436.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9i_7436/09_2024/6c9i_7436.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 15021 2.51 5 N 4050 2.21 5 O 4533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23700 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Chain: "C" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "D" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "I" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "J" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1090 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Chain: "K" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "L" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "P" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "Q" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1096 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain breaks: 1 Chain: "R" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1084 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1082 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Chain: "T" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1099 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 138} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "V" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "W" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "X" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Time building chain proxies: 14.33, per 1000 atoms: 0.60 Number of scatterers: 23700 At special positions: 0 Unit cell: (129.69, 135.585, 131, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 4533 8.00 N 4050 7.00 C 15021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 4.0 seconds 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5670 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 60.1% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.682A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.545A pdb=" N LEU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 163 Processing helix chain 'B' and resid 24 through 45 Processing helix chain 'B' and resid 49 through 72 Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.680A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 137 removed outlier: 3.546A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 49 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 4.038A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 137 removed outlier: 3.539A pdb=" N LEU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 80 through 96 removed outlier: 4.103A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 73 through 91 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'G' and resid 17 through 31 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 73 through 91 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 36 through 39 Processing helix chain 'H' and resid 73 through 90 Processing helix chain 'I' and resid 24 through 45 Processing helix chain 'I' and resid 49 through 72 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.685A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 163 Processing helix chain 'J' and resid 24 through 45 Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.547A pdb=" N MET J 67 " --> pdb=" O ILE J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 96 removed outlier: 3.679A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 163 Processing helix chain 'K' and resid 24 through 45 Processing helix chain 'K' and resid 49 through 72 Processing helix chain 'K' and resid 80 through 96 removed outlier: 4.041A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 137 removed outlier: 3.547A pdb=" N LEU K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 163 Processing helix chain 'L' and resid 24 through 45 Processing helix chain 'L' and resid 49 through 72 Processing helix chain 'L' and resid 80 through 96 removed outlier: 3.678A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 137 removed outlier: 3.540A pdb=" N LEU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 163 Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 36 through 39 Processing helix chain 'M' and resid 73 through 91 Processing helix chain 'N' and resid 17 through 31 Processing helix chain 'N' and resid 36 through 39 Processing helix chain 'N' and resid 73 through 91 Processing helix chain 'O' and resid 17 through 31 Processing helix chain 'O' and resid 36 through 39 Processing helix chain 'O' and resid 73 through 91 Processing helix chain 'P' and resid 17 through 31 Processing helix chain 'P' and resid 36 through 39 Processing helix chain 'P' and resid 73 through 90 Processing helix chain 'Q' and resid 24 through 45 Processing helix chain 'Q' and resid 49 through 72 Processing helix chain 'Q' and resid 80 through 96 removed outlier: 3.683A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 163 Processing helix chain 'R' and resid 24 through 45 Processing helix chain 'R' and resid 49 through 72 removed outlier: 3.549A pdb=" N MET R 67 " --> pdb=" O ILE R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 96 removed outlier: 3.681A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 137 removed outlier: 3.544A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 163 Processing helix chain 'S' and resid 24 through 45 Processing helix chain 'S' and resid 49 through 72 removed outlier: 3.513A pdb=" N TYR S 64 " --> pdb=" O GLN S 60 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET S 67 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 96 removed outlier: 4.051A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 137 removed outlier: 3.546A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 163 Processing helix chain 'T' and resid 24 through 45 Processing helix chain 'T' and resid 49 through 72 Processing helix chain 'T' and resid 80 through 96 removed outlier: 4.043A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 137 removed outlier: 3.548A pdb=" N LEU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 163 Processing helix chain 'U' and resid 17 through 31 Processing helix chain 'U' and resid 36 through 39 Processing helix chain 'U' and resid 73 through 91 Processing helix chain 'V' and resid 17 through 31 Processing helix chain 'V' and resid 36 through 39 Processing helix chain 'V' and resid 73 through 91 Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 36 through 39 Processing helix chain 'W' and resid 73 through 90 Processing helix chain 'X' and resid 17 through 31 Processing helix chain 'X' and resid 36 through 39 Processing helix chain 'X' and resid 73 through 90 Processing sheet with id=AA1, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.496A pdb=" N ALA M 49 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.495A pdb=" N ALA E 49 " --> pdb=" O PHE U 44 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 6.036A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA U 49 " --> pdb=" O PHE M 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 49 through 52 removed outlier: 4.501A pdb=" N ALA G 49 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 52 removed outlier: 4.498A pdb=" N ALA F 49 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.131A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA P 49 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'V' and resid 49 through 52 removed outlier: 4.501A pdb=" N ALA V 49 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.505A pdb=" N ALA H 49 " --> pdb=" O PHE W 44 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 6.035A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA W 49 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 13 through 14 Processing sheet with id=AB6, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.508A pdb=" N ALA O 49 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.506A pdb=" N ALA N 49 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.039A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA X 49 " --> pdb=" O PHE O 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 Processing sheet with id=AC6, first strand: chain 'X' and resid 13 through 14 1768 hydrogen bonds defined for protein. 5124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4408 1.30 - 1.43: 5522 1.43 - 1.56: 13812 1.56 - 1.68: 44 1.68 - 1.81: 150 Bond restraints: 23936 Sorted by residual: bond pdb=" CB HIS R 46 " pdb=" CG HIS R 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.25e+01 bond pdb=" CB HIS D 46 " pdb=" CG HIS D 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.21e+01 bond pdb=" CB HIS T 46 " pdb=" CG HIS T 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.18e+01 bond pdb=" CB HIS Q 46 " pdb=" CG HIS Q 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.17e+01 bond pdb=" CB HIS C 46 " pdb=" CG HIS C 46 " ideal model delta sigma weight residual 1.497 1.396 0.101 1.40e-02 5.10e+03 5.16e+01 ... (remaining 23931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 22541 1.33 - 2.66: 7204 2.66 - 4.00: 1849 4.00 - 5.33: 500 5.33 - 6.66: 129 Bond angle restraints: 32223 Sorted by residual: angle pdb=" N ILE D 84 " pdb=" CA ILE D 84 " pdb=" C ILE D 84 " ideal model delta sigma weight residual 111.00 104.34 6.66 1.09e+00 8.42e-01 3.73e+01 angle pdb=" C LEU Q 105 " pdb=" N PRO Q 106 " pdb=" CA PRO Q 106 " ideal model delta sigma weight residual 119.78 125.75 -5.97 1.03e+00 9.43e-01 3.36e+01 angle pdb=" C LEU J 105 " pdb=" N PRO J 106 " pdb=" CA PRO J 106 " ideal model delta sigma weight residual 119.78 125.73 -5.95 1.03e+00 9.43e-01 3.34e+01 angle pdb=" C LEU B 105 " pdb=" N PRO B 106 " pdb=" CA PRO B 106 " ideal model delta sigma weight residual 119.78 125.70 -5.92 1.03e+00 9.43e-01 3.31e+01 angle pdb=" C LEU A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta sigma weight residual 119.78 125.69 -5.91 1.03e+00 9.43e-01 3.29e+01 ... (remaining 32218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 13943 13.62 - 27.24: 532 27.24 - 40.86: 73 40.86 - 54.48: 49 54.48 - 68.10: 32 Dihedral angle restraints: 14629 sinusoidal: 5824 harmonic: 8805 Sorted by residual: dihedral pdb=" C SER T 25 " pdb=" N SER T 25 " pdb=" CA SER T 25 " pdb=" CB SER T 25 " ideal model delta harmonic sigma weight residual -122.60 -130.37 7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" CA LYS S 65 " pdb=" CB LYS S 65 " pdb=" CG LYS S 65 " pdb=" CD LYS S 65 " ideal model delta sinusoidal sigma weight residual 60.00 112.77 -52.77 3 1.50e+01 4.44e-03 9.15e+00 dihedral pdb=" C SER K 25 " pdb=" N SER K 25 " pdb=" CA SER K 25 " pdb=" CB SER K 25 " ideal model delta harmonic sigma weight residual -122.60 -130.14 7.54 0 2.50e+00 1.60e-01 9.10e+00 ... (remaining 14626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1687 0.074 - 0.149: 1383 0.149 - 0.223: 612 0.223 - 0.297: 154 0.297 - 0.371: 16 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA SER K 25 " pdb=" N SER K 25 " pdb=" C SER K 25 " pdb=" CB SER K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA SER T 25 " pdb=" N SER T 25 " pdb=" C SER T 25 " pdb=" CB SER T 25 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA SER C 25 " pdb=" N SER C 25 " pdb=" C SER C 25 " pdb=" CB SER C 25 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 3849 not shown) Planarity restraints: 4091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 50 " -0.046 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR O 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR O 50 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR O 50 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR O 50 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR O 50 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR O 50 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR O 50 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 50 " -0.045 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" CG TYR P 50 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR P 50 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR P 50 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR P 50 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR P 50 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR P 50 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 50 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 50 " -0.045 2.00e-02 2.50e+03 2.42e-02 1.17e+01 pdb=" CG TYR H 50 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR H 50 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR H 50 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR H 50 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR H 50 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR H 50 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 50 " -0.036 2.00e-02 2.50e+03 ... (remaining 4088 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 10696 2.91 - 3.41: 23862 3.41 - 3.91: 39885 3.91 - 4.40: 49391 4.40 - 4.90: 75800 Nonbonded interactions: 199634 Sorted by model distance: nonbonded pdb=" N ASN O 11 " pdb=" OD1 ASN O 11 " model vdw 2.417 3.120 nonbonded pdb=" N ASN W 11 " pdb=" OD1 ASN W 11 " model vdw 2.426 3.120 nonbonded pdb=" N ASN G 11 " pdb=" OD1 ASN G 11 " model vdw 2.428 3.120 nonbonded pdb=" N ASN N 11 " pdb=" OD1 ASN N 11 " model vdw 2.432 3.120 nonbonded pdb=" N ASN V 11 " pdb=" OD1 ASN V 11 " model vdw 2.432 3.120 ... (remaining 199629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'B' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'C' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'D' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'I' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'J' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'K' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'L' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'Q' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'R' and (resid 23 through 99 or resid 103 through 163)) selection = (chain 'S' and (resid 23 through 99 or (resid 103 and (name N or name CA or name \ C or name O or name CB )) or resid 104 through 163)) selection = (chain 'T' and (resid 23 through 99 or resid 103 through 163)) } ncs_group { reference = (chain 'E' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'F' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'G' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'H' selection = (chain 'M' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'N' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'O' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'P' selection = (chain 'U' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'V' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'W' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 53.530 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.860 ------------------------------------------------------------------------------- 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= 1.919 Angle : 1.477 6.660 32223 Z= 0.991 Chirality : 0.115 0.371 3852 Planarity : 0.008 0.048 4091 Dihedral : 9.221 68.100 8959 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.64 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.14), residues: 3015 helix: 1.70 (0.11), residues: 1776 sheet: 2.83 (0.22), residues: 396 loop : 0.78 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.009 TRP R 86 HIS 0.004 0.002 HIS X 63 PHE 0.020 0.003 PHE J 103 TYR 0.046 0.009 TYR O 50 ARG 0.008 0.001 ARG U 43 *********************** 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 fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 2.769 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: 0.4375 time to fit residues: 290.2099 Evaluate side-chains 325 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2350 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= 0.194 Angle : 0.473 5.306 32223 Z= 0.258 Chirality : 0.040 0.129 3852 Planarity : 0.003 0.033 4091 Dihedral : 3.520 13.802 3339 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.32 % Allowed : 4.08 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.14), residues: 3015 helix: 3.42 (0.11), residues: 1764 sheet: 2.34 (0.20), residues: 396 loop : 0.18 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP R 86 HIS 0.001 0.000 HIS M 3 PHE 0.007 0.001 PHE E 44 TYR 0.013 0.002 TYR X 61 ARG 0.004 0.001 ARG M 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6030 Ramachandran restraints generated. 3015 Oldfield, 0 Emsley, 3015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 368 time to evaluate : 2.989 Fit side-chains REVERT: D 36 GLU cc_start: 0.7863 (tt0) cc_final: 0.7662 (tt0) REVERT: E 39 ASP cc_start: 0.7549 (m-30) cc_final: 0.7316 (m-30) REVERT: F 39 ASP cc_start: 0.7464 (m-30) cc_final: 0.7184 (m-30) REVERT: M 39 ASP cc_start: 0.7552 (m-30) cc_final: 0.7335 (m-30) REVERT: O 39 ASP cc_start: 0.7378 (m-30) cc_final: 0.7158 (m-30) REVERT: R 36 GLU cc_start: 0.7923 (tt0) cc_final: 0.7718 (tt0) REVERT: U 39 ASP cc_start: 0.7556 (m-30) cc_final: 0.7309 (m-30) REVERT: V 39 ASP cc_start: 0.7547 (m-30) cc_final: 0.7340 (m-30) REVERT: V 105 GLU cc_start: 0.8507 (tt0) cc_final: 0.8271 (tt0) REVERT: W 39 ASP cc_start: 0.7496 (m-30) cc_final: 0.7219 (m-30) REVERT: X 39 ASP cc_start: 0.7431 (m-30) cc_final: 0.7213 (m-30) outliers start: 8 outliers final: 4 residues processed: 369 average time/residue: 0.3813 time to fit residues: 214.2680 Evaluate side-chains 290 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 286 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain R residue 95 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 265 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23936 Z= 0.311 Angle : 0.485 5.465 32223 Z= 0.258 Chirality : 0.040 0.131 3852 Planarity : 0.004 0.032 4091 Dihedral : 3.503 14.793 3339 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.09 % Allowed : 5.98 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.14), residues: 3015 helix: 3.31 (0.11), residues: 1752 sheet: 2.06 (0.19), residues: 396 loop : -0.04 (0.18), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP R 86 HIS 0.002 0.001 HIS J 46 PHE 0.007 0.001 PHE D 40 TYR 0.011 0.002 TYR X 61 ARG 0.004 0.001 ARG H 43 *********************** 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 349 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 322 time to evaluate : 2.567 Fit side-chains REVERT: E 39 ASP cc_start: 0.7549 (m-30) cc_final: 0.7321 (m-30) REVERT: M 39 ASP cc_start: 0.7552 (m-30) cc_final: 0.7310 (m-30) REVERT: N 39 ASP cc_start: 0.7570 (m-30) cc_final: 0.7335 (m-30) REVERT: O 39 ASP cc_start: 0.7431 (m-30) cc_final: 0.7207 (m-30) REVERT: U 39 ASP cc_start: 0.7565 (m-30) cc_final: 0.7304 (m-30) REVERT: W 39 ASP cc_start: 0.7539 (m-30) cc_final: 0.7285 (m-30) REVERT: X 39 ASP cc_start: 0.7440 (m-30) cc_final: 0.7231 (m-30) outliers start: 27 outliers final: 15 residues processed: 328 average time/residue: 0.3928 time to fit residues: 192.3478 Evaluate side-chains 308 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 293 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain F residue 103 SER 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 160 ILE Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain W residue 103 SER 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 264 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 140 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23936 Z= 0.161 Angle : 0.389 5.183 32223 Z= 0.213 Chirality : 0.038 0.124 3852 Planarity : 0.003 0.030 4091 Dihedral : 3.225 14.155 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.85 % Allowed : 7.32 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.14), residues: 3015 helix: 3.53 (0.11), residues: 1776 sheet: 2.27 (0.18), residues: 396 loop : 0.15 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 86 HIS 0.001 0.000 HIS J 46 PHE 0.005 0.001 PHE R 154 TYR 0.011 0.001 TYR H 61 ARG 0.003 0.000 ARG G 51 *********************** 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 325 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 304 time to evaluate : 2.756 Fit side-chains REVERT: E 39 ASP cc_start: 0.7474 (m-30) cc_final: 0.7223 (m-30) REVERT: M 39 ASP cc_start: 0.7471 (m-30) cc_final: 0.7246 (m-30) REVERT: O 39 ASP cc_start: 0.7364 (m-30) cc_final: 0.7157 (m-30) REVERT: U 39 ASP cc_start: 0.7512 (m-30) cc_final: 0.7227 (m-30) REVERT: W 39 ASP cc_start: 0.7480 (m-30) cc_final: 0.7204 (m-30) outliers start: 21 outliers final: 12 residues processed: 311 average time/residue: 0.3968 time to fit residues: 184.9892 Evaluate side-chains 297 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 285 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 160 ILE 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 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 236 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 chunk 242 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 145 optimal weight: 0.0020 chunk 255 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23936 Z= 0.135 Angle : 0.368 5.155 32223 Z= 0.202 Chirality : 0.037 0.124 3852 Planarity : 0.002 0.029 4091 Dihedral : 3.080 14.133 3339 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.57 % Allowed : 8.00 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.14), residues: 3015 helix: 3.57 (0.11), residues: 1800 sheet: 2.52 (0.18), residues: 396 loop : 0.31 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP S 86 HIS 0.001 0.000 HIS I 46 PHE 0.009 0.001 PHE B 40 TYR 0.010 0.001 TYR V 61 ARG 0.002 0.000 ARG W 51 *********************** 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 315 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 301 time to evaluate : 2.759 Fit side-chains REVERT: E 39 ASP cc_start: 0.7358 (m-30) cc_final: 0.7122 (m-30) REVERT: M 39 ASP cc_start: 0.7434 (m-30) cc_final: 0.7231 (m-30) REVERT: U 39 ASP cc_start: 0.7427 (m-30) cc_final: 0.7217 (m-30) REVERT: W 39 ASP cc_start: 0.7452 (m-30) cc_final: 0.7172 (m-30) outliers start: 14 outliers final: 9 residues processed: 305 average time/residue: 0.3886 time to fit residues: 178.5866 Evaluate side-chains 291 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 282 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain 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 95 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 149 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23936 Z= 0.146 Angle : 0.370 5.190 32223 Z= 0.201 Chirality : 0.037 0.122 3852 Planarity : 0.002 0.028 4091 Dihedral : 3.063 14.224 3339 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 7.80 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.14), residues: 3015 helix: 3.54 (0.11), residues: 1812 sheet: 2.63 (0.18), residues: 396 loop : 0.37 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 86 HIS 0.001 0.000 HIS J 46 PHE 0.008 0.001 PHE B 40 TYR 0.010 0.001 TYR V 61 ARG 0.003 0.000 ARG W 51 *********************** 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 295 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 2.601 Fit side-chains REVERT: A 121 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8764 (mp) REVERT: E 39 ASP cc_start: 0.7359 (m-30) cc_final: 0.7116 (m-30) REVERT: U 39 ASP cc_start: 0.7416 (m-30) cc_final: 0.7173 (m-30) REVERT: W 39 ASP cc_start: 0.7443 (m-30) cc_final: 0.7143 (m-30) outliers start: 20 outliers final: 17 residues processed: 281 average time/residue: 0.3956 time to fit residues: 167.0298 Evaluate side-chains 289 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 160 ILE Chi-restraints excluded: chain U residue 103 SER 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 274 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 239 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 177 optimal weight: 0.3980 chunk 172 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23936 Z= 0.146 Angle : 0.366 5.191 32223 Z= 0.199 Chirality : 0.037 0.121 3852 Planarity : 0.002 0.028 4091 Dihedral : 3.046 14.184 3339 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.73 % Allowed : 8.12 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.14), residues: 3015 helix: 3.59 (0.11), residues: 1806 sheet: 2.64 (0.18), residues: 396 loop : 0.40 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 86 HIS 0.001 0.000 HIS J 46 PHE 0.007 0.001 PHE B 40 TYR 0.009 0.001 TYR V 61 ARG 0.003 0.000 ARG W 51 *********************** 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 297 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 2.617 Fit side-chains REVERT: A 121 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8753 (mp) REVERT: E 39 ASP cc_start: 0.7337 (m-30) cc_final: 0.7109 (m-30) REVERT: U 39 ASP cc_start: 0.7385 (m-30) cc_final: 0.7168 (m-30) REVERT: W 39 ASP cc_start: 0.7433 (m-30) cc_final: 0.7134 (m-30) outliers start: 18 outliers final: 16 residues processed: 287 average time/residue: 0.3927 time to fit residues: 169.3650 Evaluate side-chains 292 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 275 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain 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 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 175 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23936 Z= 0.248 Angle : 0.426 5.343 32223 Z= 0.226 Chirality : 0.038 0.125 3852 Planarity : 0.003 0.027 4091 Dihedral : 3.267 14.720 3339 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.81 % Allowed : 8.33 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.14), residues: 3015 helix: 3.42 (0.11), residues: 1779 sheet: 2.50 (0.19), residues: 396 loop : 0.24 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 86 HIS 0.002 0.000 HIS J 46 PHE 0.007 0.001 PHE B 40 TYR 0.016 0.001 TYR D 64 ARG 0.004 0.000 ARG W 51 *********************** 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 284 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 264 time to evaluate : 2.724 Fit side-chains REVERT: A 121 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8791 (mp) REVERT: E 39 ASP cc_start: 0.7434 (m-30) cc_final: 0.7204 (m-30) REVERT: U 39 ASP cc_start: 0.7478 (m-30) cc_final: 0.7248 (m-30) REVERT: W 39 ASP cc_start: 0.7511 (m-30) cc_final: 0.7258 (m-30) outliers start: 20 outliers final: 15 residues processed: 271 average time/residue: 0.4083 time to fit residues: 164.3476 Evaluate side-chains 280 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain 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 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 257 optimal weight: 0.9990 chunk 271 optimal weight: 0.9980 chunk 247 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 chunk 263 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23936 Z= 0.167 Angle : 0.381 5.242 32223 Z= 0.206 Chirality : 0.037 0.122 3852 Planarity : 0.002 0.027 4091 Dihedral : 3.151 14.348 3339 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.69 % Allowed : 8.65 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.14), residues: 3015 helix: 3.52 (0.11), residues: 1794 sheet: 2.55 (0.19), residues: 396 loop : 0.32 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 86 HIS 0.001 0.000 HIS J 46 PHE 0.007 0.001 PHE B 40 TYR 0.010 0.001 TYR N 61 ARG 0.003 0.000 ARG W 51 *********************** 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 284 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 267 time to evaluate : 2.794 Fit side-chains REVERT: A 121 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8760 (mp) REVERT: E 39 ASP cc_start: 0.7375 (m-30) cc_final: 0.7151 (m-30) REVERT: U 39 ASP cc_start: 0.7434 (m-30) cc_final: 0.7205 (m-30) REVERT: W 39 ASP cc_start: 0.7492 (m-30) cc_final: 0.7191 (m-30) outliers start: 17 outliers final: 14 residues processed: 271 average time/residue: 0.4155 time to fit residues: 168.6181 Evaluate side-chains 280 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 265 time to evaluate : 2.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain 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 160 ILE Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 160 ILE Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 9.9990 chunk 269 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23936 Z= 0.282 Angle : 0.442 5.407 32223 Z= 0.234 Chirality : 0.039 0.127 3852 Planarity : 0.003 0.027 4091 Dihedral : 3.359 14.864 3339 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.65 % Allowed : 8.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.14), residues: 3015 helix: 3.37 (0.11), residues: 1764 sheet: 2.47 (0.19), residues: 396 loop : 0.07 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 86 HIS 0.002 0.001 HIS J 46 PHE 0.005 0.001 PHE B 40 TYR 0.018 0.002 TYR D 64 ARG 0.004 0.001 ARG W 51 ********************** 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 283 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 267 time to evaluate : 2.525 Fit side-chains REVERT: A 121 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8790 (mp) REVERT: E 39 ASP cc_start: 0.7468 (m-30) cc_final: 0.7249 (m-30) REVERT: T 141 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7080 (mt-10) REVERT: U 39 ASP cc_start: 0.7504 (m-30) cc_final: 0.7264 (m-30) REVERT: W 39 ASP cc_start: 0.7520 (m-30) cc_final: 0.7241 (m-30) outliers start: 16 outliers final: 14 residues processed: 271 average time/residue: 0.4056 time to fit residues: 162.8684 Evaluate side-chains 277 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 262 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain 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 U residue 103 SER Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.096053 restraints weight = 26217.230| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.90 r_work: 0.2732 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3237 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= 0.188 Angle : 0.392 5.273 32223 Z= 0.212 Chirality : 0.037 0.124 3852 Planarity : 0.003 0.027 4091 Dihedral : 3.226 14.385 3339 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.61 % Allowed : 8.73 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.14), residues: 3015 helix: 3.45 (0.11), residues: 1788 sheet: 2.51 (0.19), residues: 396 loop : 0.23 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 86 HIS 0.001 0.000 HIS J 46 PHE 0.006 0.001 PHE B 40 TYR 0.011 0.001 TYR D 94 ARG 0.003 0.000 ARG O 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.84 seconds wall clock time: 86 minutes 40.14 seconds (5200.14 seconds total)