Starting phenix.real_space_refine on Tue Aug 26 10:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjf_37578/08_2025/8wjf_37578.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjf_37578/08_2025/8wjf_37578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wjf_37578/08_2025/8wjf_37578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjf_37578/08_2025/8wjf_37578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wjf_37578/08_2025/8wjf_37578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjf_37578/08_2025/8wjf_37578.map" } resolution = 2.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.048 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 168 5.16 5 C 23280 2.51 5 N 6528 2.21 5 O 7128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37104 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "B" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "E" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "F" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "G" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "H" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "I" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "K" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "L" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "M" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "N" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "P" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "Q" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "R" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "S" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "T" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "U" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "V" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "W" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "X" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Time building chain proxies: 7.69, per 1000 atoms: 0.21 Number of scatterers: 37104 At special positions: 0 Unit cell: (137.31, 137.31, 137.31, 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 168 16.00 O 7128 8.00 N 6528 7.00 C 23280 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: 2.82 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 476.8 nanoseconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid -22 through -15 removed outlier: 3.961A pdb=" N LYS A -18 " --> pdb=" O ASN A -22 " (cutoff:3.500A) Processing helix chain 'A' and resid -13 through -8 removed outlier: 3.542A pdb=" N LEU A -8 " --> pdb=" O SER A -11 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.548A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 124 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.694A pdb=" N GLY A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.806A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid -21 through -14 removed outlier: 3.686A pdb=" N GLN B -14 " --> pdb=" O LYS B -18 " (cutoff:3.500A) Processing helix chain 'B' and resid -13 through -8 removed outlier: 3.539A pdb=" N LEU B -8 " --> pdb=" O SER B -11 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 49 through 78 removed outlier: 3.544A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 124 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 removed outlier: 3.702A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.720A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid -21 through -14 removed outlier: 3.663A pdb=" N GLN C -14 " --> pdb=" O LYS C -18 " (cutoff:3.500A) Processing helix chain 'C' and resid -13 through -8 removed outlier: 3.586A pdb=" N LEU C -8 " --> pdb=" O SER C -11 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 removed outlier: 3.657A pdb=" N PHE C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 78 removed outlier: 3.550A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 124 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 removed outlier: 3.705A pdb=" N GLY C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid -21 through -14 removed outlier: 3.703A pdb=" N GLN D -14 " --> pdb=" O LYS D -18 " (cutoff:3.500A) Processing helix chain 'D' and resid -13 through -8 removed outlier: 3.521A pdb=" N LEU D -8 " --> pdb=" O SER D -11 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 49 through 78 removed outlier: 3.548A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 124 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 removed outlier: 3.704A pdb=" N GLY D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.718A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid -21 through -15 Processing helix chain 'E' and resid -13 through -8 removed outlier: 3.580A pdb=" N LEU E -8 " --> pdb=" O SER E -11 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 49 through 77 removed outlier: 3.547A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 124 Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 removed outlier: 3.703A pdb=" N GLY E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid -21 through -15 Processing helix chain 'F' and resid -13 through -8 removed outlier: 3.576A pdb=" N LEU F -8 " --> pdb=" O SER F -11 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.560A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 124 Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 removed outlier: 3.704A pdb=" N GLY F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid -21 through -14 removed outlier: 3.790A pdb=" N GLN G -14 " --> pdb=" O LYS G -18 " (cutoff:3.500A) Processing helix chain 'G' and resid -13 through -8 removed outlier: 3.563A pdb=" N LEU G -8 " --> pdb=" O SER G -11 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 Processing helix chain 'G' and resid 49 through 77 removed outlier: 3.543A pdb=" N ALA G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 124 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 removed outlier: 3.699A pdb=" N GLY G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 175 removed outlier: 3.723A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid -21 through -15 Processing helix chain 'H' and resid -13 through -8 removed outlier: 3.565A pdb=" N LEU H -8 " --> pdb=" O SER H -11 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 Processing helix chain 'H' and resid 49 through 78 removed outlier: 3.555A pdb=" N ALA H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 124 Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 removed outlier: 3.703A pdb=" N GLY H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid -21 through -14 Processing helix chain 'I' and resid -13 through -8 removed outlier: 3.547A pdb=" N LEU I -8 " --> pdb=" O SER I -11 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 Processing helix chain 'I' and resid 49 through 77 removed outlier: 3.558A pdb=" N ALA I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 124 Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 removed outlier: 3.632A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 175 removed outlier: 3.736A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid -21 through -15 Processing helix chain 'J' and resid -13 through -8 removed outlier: 3.634A pdb=" N LEU J -8 " --> pdb=" O SER J -11 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 Processing helix chain 'J' and resid 49 through 78 removed outlier: 3.564A pdb=" N ALA J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 124 Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 removed outlier: 3.704A pdb=" N GLY J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 175 removed outlier: 3.720A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid -21 through -14 removed outlier: 3.701A pdb=" N GLN K -14 " --> pdb=" O LYS K -18 " (cutoff:3.500A) Processing helix chain 'K' and resid -13 through -8 removed outlier: 3.539A pdb=" N LEU K -8 " --> pdb=" O SER K -11 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 Processing helix chain 'K' and resid 49 through 78 removed outlier: 3.563A pdb=" N ALA K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 124 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 removed outlier: 3.706A pdb=" N GLY K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid -21 through -15 Processing helix chain 'L' and resid -13 through -8 removed outlier: 3.549A pdb=" N LEU L -8 " --> pdb=" O SER L -11 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 Processing helix chain 'L' and resid 49 through 78 removed outlier: 3.550A pdb=" N ALA L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 124 Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 removed outlier: 3.694A pdb=" N GLY L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.718A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid -21 through -15 Processing helix chain 'M' and resid -13 through -8 removed outlier: 3.535A pdb=" N LEU M -8 " --> pdb=" O SER M -11 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 Processing helix chain 'M' and resid 49 through 77 removed outlier: 3.546A pdb=" N ALA M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 124 Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 removed outlier: 3.683A pdb=" N GLY M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 175 removed outlier: 3.868A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid -21 through -14 removed outlier: 3.676A pdb=" N GLN N -14 " --> pdb=" O LYS N -18 " (cutoff:3.500A) Processing helix chain 'N' and resid -13 through -8 removed outlier: 3.544A pdb=" N LEU N -8 " --> pdb=" O SER N -11 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 Processing helix chain 'N' and resid 49 through 78 removed outlier: 3.562A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 124 Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 removed outlier: 3.704A pdb=" N GLY N 160 " --> pdb=" O LEU N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 175 removed outlier: 3.720A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid -21 through -14 removed outlier: 3.729A pdb=" N GLN O -14 " --> pdb=" O LYS O -18 " (cutoff:3.500A) Processing helix chain 'O' and resid -13 through -8 removed outlier: 3.542A pdb=" N LEU O -8 " --> pdb=" O SER O -11 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 removed outlier: 3.666A pdb=" N PHE O 42 " --> pdb=" O MET O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 78 removed outlier: 3.550A pdb=" N ALA O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 124 Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 removed outlier: 3.705A pdb=" N GLY O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 175 removed outlier: 3.720A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid -21 through -14 removed outlier: 3.770A pdb=" N GLN P -14 " --> pdb=" O LYS P -18 " (cutoff:3.500A) Processing helix chain 'P' and resid -13 through -8 Processing helix chain 'P' and resid 14 through 42 removed outlier: 3.532A pdb=" N GLU P 18 " --> pdb=" O HIS P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 78 removed outlier: 3.548A pdb=" N ALA P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 124 Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 removed outlier: 3.705A pdb=" N GLY P 160 " --> pdb=" O LEU P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 175 removed outlier: 3.717A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid -21 through -15 Processing helix chain 'Q' and resid -13 through -8 removed outlier: 3.553A pdb=" N LEU Q -8 " --> pdb=" O SER Q -11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 Processing helix chain 'Q' and resid 49 through 77 removed outlier: 3.563A pdb=" N ALA Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 124 Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 removed outlier: 3.703A pdb=" N GLY Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 removed outlier: 3.718A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid -21 through -14 removed outlier: 3.720A pdb=" N GLN R -14 " --> pdb=" O LYS R -18 " (cutoff:3.500A) Processing helix chain 'R' and resid -13 through -8 removed outlier: 3.550A pdb=" N LEU R -8 " --> pdb=" O SER R -11 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.558A pdb=" N ALA R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 124 Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 removed outlier: 3.699A pdb=" N GLY R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 175 removed outlier: 3.723A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid -21 through -15 Processing helix chain 'S' and resid -13 through -8 removed outlier: 3.585A pdb=" N LEU S -8 " --> pdb=" O SER S -11 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 Processing helix chain 'S' and resid 49 through 77 removed outlier: 3.562A pdb=" N ALA S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 124 Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 removed outlier: 3.707A pdb=" N GLY S 160 " --> pdb=" O LEU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 175 removed outlier: 3.718A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid -21 through -15 Processing helix chain 'T' and resid -13 through -8 removed outlier: 3.546A pdb=" N LEU T -8 " --> pdb=" O SER T -11 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 Processing helix chain 'T' and resid 49 through 78 removed outlier: 3.548A pdb=" N ALA T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 124 Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 removed outlier: 3.704A pdb=" N GLY T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid -21 through -15 Processing helix chain 'U' and resid -13 through -8 removed outlier: 3.579A pdb=" N LEU U -8 " --> pdb=" O SER U -11 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 42 Processing helix chain 'U' and resid 49 through 77 removed outlier: 3.550A pdb=" N ALA U 53 " --> pdb=" O LEU U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 124 Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 removed outlier: 3.704A pdb=" N GLY U 160 " --> pdb=" O LEU U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 removed outlier: 3.717A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid -21 through -15 Processing helix chain 'V' and resid -13 through -8 removed outlier: 3.550A pdb=" N LEU V -8 " --> pdb=" O SER V -11 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 42 Processing helix chain 'V' and resid 49 through 78 removed outlier: 3.560A pdb=" N ALA V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 124 Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 removed outlier: 3.699A pdb=" N GLY V 160 " --> pdb=" O LEU V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 175 removed outlier: 3.722A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid -21 through -14 removed outlier: 3.699A pdb=" N GLN W -14 " --> pdb=" O LYS W -18 " (cutoff:3.500A) Processing helix chain 'W' and resid -13 through -8 removed outlier: 3.527A pdb=" N LEU W -8 " --> pdb=" O SER W -11 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 42 Processing helix chain 'W' and resid 49 through 78 removed outlier: 3.548A pdb=" N ALA W 53 " --> pdb=" O LEU W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 124 Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 removed outlier: 3.703A pdb=" N GLY W 160 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 175 removed outlier: 3.718A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid -21 through -15 Processing helix chain 'X' and resid -13 through -8 removed outlier: 3.507A pdb=" N LEU X -8 " --> pdb=" O SER X -11 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 42 Processing helix chain 'X' and resid 49 through 78 removed outlier: 3.550A pdb=" N ALA X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 124 Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 removed outlier: 3.705A pdb=" N GLY X 160 " --> pdb=" O LEU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 175 removed outlier: 3.719A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) 2701 hydrogen bonds defined for protein. 7956 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: 5.22 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9425 1.33 - 1.45: 7363 1.45 - 1.57: 20796 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 37848 Sorted by residual: bond pdb=" N ILE I -17 " pdb=" CA ILE I -17 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.07e+00 bond pdb=" N ASN I -15 " pdb=" CA ASN I -15 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 7.01e+00 bond pdb=" N GLN I -14 " pdb=" CA GLN I -14 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 6.79e+00 bond pdb=" N GLU I -19 " pdb=" CA GLU I -19 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.48e+00 bond pdb=" N ARG I -16 " pdb=" CA ARG I -16 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.19e+00 ... (remaining 37843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 50278 1.90 - 3.80: 521 3.80 - 5.69: 139 5.69 - 7.59: 14 7.59 - 9.49: 24 Bond angle restraints: 50976 Sorted by residual: angle pdb=" C THR V 123 " pdb=" N ASP V 124 " pdb=" CA ASP V 124 " ideal model delta sigma weight residual 122.56 116.36 6.20 1.72e+00 3.38e-01 1.30e+01 angle pdb=" C THR N 123 " pdb=" N ASP N 124 " pdb=" CA ASP N 124 " ideal model delta sigma weight residual 122.56 116.41 6.15 1.72e+00 3.38e-01 1.28e+01 angle pdb=" C THR X 123 " pdb=" N ASP X 124 " pdb=" CA ASP X 124 " ideal model delta sigma weight residual 122.56 116.42 6.14 1.72e+00 3.38e-01 1.28e+01 angle pdb=" C THR C 123 " pdb=" N ASP C 124 " pdb=" CA ASP C 124 " ideal model delta sigma weight residual 122.56 116.43 6.13 1.72e+00 3.38e-01 1.27e+01 angle pdb=" C THR T 123 " pdb=" N ASP T 124 " pdb=" CA ASP T 124 " ideal model delta sigma weight residual 122.56 116.44 6.12 1.72e+00 3.38e-01 1.27e+01 ... (remaining 50971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 21064 17.99 - 35.99: 1445 35.99 - 53.98: 229 53.98 - 71.97: 87 71.97 - 89.96: 71 Dihedral angle restraints: 22896 sinusoidal: 9528 harmonic: 13368 Sorted by residual: dihedral pdb=" CA ALA A 161 " pdb=" C ALA A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta harmonic sigma weight residual 0.00 21.04 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TRP F 94 " pdb=" C TRP F 94 " pdb=" N GLU F 95 " pdb=" CA GLU F 95 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA TRP B 94 " pdb=" C TRP B 94 " pdb=" N GLU B 95 " pdb=" CA GLU B 95 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 22893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3939 0.038 - 0.075: 1022 0.075 - 0.113: 339 0.113 - 0.150: 74 0.150 - 0.188: 2 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CA ILE I -17 " pdb=" N ILE I -17 " pdb=" C ILE I -17 " pdb=" CB ILE I -17 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA LEU I 118 " pdb=" N LEU I 118 " pdb=" C LEU I 118 " pdb=" CB LEU I 118 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA TYR W 40 " pdb=" N TYR W 40 " pdb=" C TYR W 40 " pdb=" CB TYR W 40 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 5373 not shown) Planarity restraints: 6744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 33 " -0.021 2.00e-02 2.50e+03 1.74e-02 6.03e+00 pdb=" CG TYR W 33 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR W 33 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR W 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR W 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR W 33 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR W 33 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR W 33 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 33 " 0.021 2.00e-02 2.50e+03 1.73e-02 5.99e+00 pdb=" CG TYR J 33 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR J 33 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR J 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR J 33 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 33 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR J 33 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 33 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 33 " -0.021 2.00e-02 2.50e+03 1.72e-02 5.94e+00 pdb=" CG TYR H 33 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR H 33 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 33 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 33 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 33 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 33 " -0.002 2.00e-02 2.50e+03 ... (remaining 6741 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4184 2.74 - 3.28: 36645 3.28 - 3.82: 61780 3.82 - 4.36: 71263 4.36 - 4.90: 124301 Nonbonded interactions: 298173 Sorted by model distance: nonbonded pdb=" NH1 ARG J -16 " pdb=" OE1 GLU J 117 " model vdw 2.200 3.120 nonbonded pdb=" NH1 ARG U -16 " pdb=" OE1 GLU U 117 " model vdw 2.202 3.120 nonbonded pdb=" NH1 ARG L -16 " pdb=" OE1 GLU L 117 " model vdw 2.247 3.120 nonbonded pdb=" NH1 ARG F -16 " pdb=" OE1 GLU F 117 " model vdw 2.249 3.120 nonbonded pdb=" NH2 ARG M -16 " pdb=" OE1 GLU M 117 " model vdw 2.270 3.120 ... (remaining 298168 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 28.330 Find NCS groups from input model: 0.580 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: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 37848 Z= 0.260 Angle : 0.611 9.491 50976 Z= 0.360 Chirality : 0.040 0.188 5376 Planarity : 0.003 0.022 6744 Dihedral : 14.456 89.964 14208 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.05 % Allowed : 1.46 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 2.43 (0.11), residues: 4416 helix: 2.64 (0.07), residues: 3264 sheet: None (None), residues: 0 loop : -1.59 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I -16 TYR 0.042 0.003 TYR J 33 PHE 0.012 0.002 PHE Q 42 TRP 0.006 0.002 TRP K 94 HIS 0.003 0.000 HIS K 106 Details of bonding type rmsd covalent geometry : bond 0.00569 (37848) covalent geometry : angle 0.61068 (50976) hydrogen bonds : bond 0.15344 ( 2701) hydrogen bonds : angle 4.47898 ( 7956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 1.471 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 314 average time/residue: 1.2727 time to fit residues: 445.7517 Evaluate side-chains 236 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B -14 GLN G -15 ASN H -15 ASN H -10 ASN H 84 GLN J 84 GLN O -14 GLN P -15 ASN Q -15 ASN Q -10 ASN Q 84 GLN V -15 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.086685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.066140 restraints weight = 89098.958| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.56 r_work: 0.2708 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 37848 Z= 0.171 Angle : 0.565 10.294 50976 Z= 0.298 Chirality : 0.037 0.134 5376 Planarity : 0.003 0.041 6744 Dihedral : 3.968 53.137 4876 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.34 (0.13), residues: 4416 helix: 3.78 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.53 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 23 TYR 0.023 0.002 TYR O 33 PHE 0.023 0.002 PHE P -9 TRP 0.006 0.002 TRP W 94 HIS 0.002 0.000 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00354 (37848) covalent geometry : angle 0.56497 (50976) hydrogen bonds : bond 0.09177 ( 2701) hydrogen bonds : angle 3.65694 ( 7956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8743 (p0) cc_final: 0.8529 (p0) REVERT: M 92 ASP cc_start: 0.8700 (p0) cc_final: 0.8481 (p0) REVERT: O 92 ASP cc_start: 0.8735 (p0) cc_final: 0.8517 (p0) REVERT: P 92 ASP cc_start: 0.8804 (p0) cc_final: 0.8601 (p0) REVERT: X 92 ASP cc_start: 0.8743 (p0) cc_final: 0.8536 (p0) outliers start: 3 outliers final: 1 residues processed: 220 average time/residue: 1.2026 time to fit residues: 299.2419 Evaluate side-chains 217 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 400 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 234 optimal weight: 50.0000 chunk 344 optimal weight: 7.9990 chunk 426 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.083810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062337 restraints weight = 85855.233| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.52 r_work: 0.2695 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9171 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 37848 Z= 0.183 Angle : 0.554 10.015 50976 Z= 0.293 Chirality : 0.037 0.133 5376 Planarity : 0.003 0.027 6744 Dihedral : 3.887 47.717 4876 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.77 (0.13), residues: 4416 helix: 4.07 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.31 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.021 0.002 TYR O 33 PHE 0.022 0.002 PHE B -9 TRP 0.006 0.002 TRP N 94 HIS 0.002 0.000 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00391 (37848) covalent geometry : angle 0.55374 (50976) hydrogen bonds : bond 0.09399 ( 2701) hydrogen bonds : angle 3.63712 ( 7956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 1.367 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 223 average time/residue: 1.1301 time to fit residues: 285.4530 Evaluate side-chains 219 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 193 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 GLN L 84 GLN M 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.060489 restraints weight = 86083.554| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.47 r_work: 0.2652 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 37848 Z= 0.218 Angle : 0.574 9.881 50976 Z= 0.305 Chirality : 0.038 0.136 5376 Planarity : 0.003 0.022 6744 Dihedral : 3.888 44.230 4876 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.10 % Allowed : 7.22 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.75 (0.13), residues: 4416 helix: 4.04 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.25 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 23 TYR 0.020 0.002 TYR C 33 PHE 0.016 0.002 PHE M -9 TRP 0.006 0.002 TRP G 94 HIS 0.002 0.000 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00486 (37848) covalent geometry : angle 0.57412 (50976) hydrogen bonds : bond 0.10223 ( 2701) hydrogen bonds : angle 3.80562 ( 7956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 1.182 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 221 average time/residue: 1.1309 time to fit residues: 282.6790 Evaluate side-chains 217 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 348 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 160 optimal weight: 0.0980 chunk 195 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 387 optimal weight: 20.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.084524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.063207 restraints weight = 86034.937| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.54 r_work: 0.2708 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 37848 Z= 0.166 Angle : 0.538 9.988 50976 Z= 0.283 Chirality : 0.036 0.134 5376 Planarity : 0.003 0.021 6744 Dihedral : 3.792 41.122 4876 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.35 % Allowed : 8.73 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.03 (0.13), residues: 4416 helix: 4.23 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.12 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 23 TYR 0.015 0.002 TYR E 40 PHE 0.011 0.002 PHE W -9 TRP 0.007 0.002 TRP C 94 HIS 0.002 0.000 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00348 (37848) covalent geometry : angle 0.53780 (50976) hydrogen bonds : bond 0.08792 ( 2701) hydrogen bonds : angle 3.49834 ( 7956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 1.627 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 232 average time/residue: 1.3587 time to fit residues: 352.3638 Evaluate side-chains 218 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 386 optimal weight: 10.0000 chunk 163 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 414 optimal weight: 60.0000 chunk 115 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 298 optimal weight: 0.0970 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.083731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.062464 restraints weight = 86010.175| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.53 r_work: 0.2687 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 37848 Z= 0.184 Angle : 0.548 9.883 50976 Z= 0.288 Chirality : 0.037 0.134 5376 Planarity : 0.003 0.021 6744 Dihedral : 3.690 14.656 4872 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.07 % Allowed : 8.80 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.01 (0.13), residues: 4416 helix: 4.20 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.06 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 23 TYR 0.016 0.002 TYR E 40 PHE 0.011 0.002 PHE O -9 TRP 0.007 0.002 TRP P 94 HIS 0.002 0.000 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00400 (37848) covalent geometry : angle 0.54773 (50976) hydrogen bonds : bond 0.09329 ( 2701) hydrogen bonds : angle 3.59922 ( 7956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 1.545 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 219 average time/residue: 1.1235 time to fit residues: 278.7950 Evaluate side-chains 218 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 103 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 188 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G -14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.083721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.062452 restraints weight = 85971.149| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.51 r_work: 0.2689 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 37848 Z= 0.184 Angle : 0.550 9.887 50976 Z= 0.289 Chirality : 0.037 0.134 5376 Planarity : 0.003 0.023 6744 Dihedral : 3.691 14.793 4872 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.07 % Allowed : 9.18 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.05 (0.13), residues: 4416 helix: 4.21 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : 0.03 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 23 TYR 0.016 0.002 TYR E 40 PHE 0.011 0.002 PHE O -9 TRP 0.007 0.002 TRP P 94 HIS 0.002 0.000 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00400 (37848) covalent geometry : angle 0.54968 (50976) hydrogen bonds : bond 0.09315 ( 2701) hydrogen bonds : angle 3.59678 ( 7956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 217 time to evaluate : 1.249 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 1.0605 time to fit residues: 261.8714 Evaluate side-chains 219 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 154 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 72 optimal weight: 60.0000 chunk 330 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.084629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063433 restraints weight = 85612.521| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.48 r_work: 0.2716 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 37848 Z= 0.164 Angle : 0.535 9.904 50976 Z= 0.281 Chirality : 0.036 0.132 5376 Planarity : 0.002 0.021 6744 Dihedral : 3.643 14.508 4872 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.02 % Allowed : 9.28 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.17 (0.13), residues: 4416 helix: 4.29 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : 0.07 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 64 TYR 0.015 0.002 TYR E 40 PHE 0.013 0.002 PHE Q -9 TRP 0.008 0.002 TRP P 94 HIS 0.002 0.000 HIS P 106 Details of bonding type rmsd covalent geometry : bond 0.00344 (37848) covalent geometry : angle 0.53547 (50976) hydrogen bonds : bond 0.08657 ( 2701) hydrogen bonds : angle 3.46084 ( 7956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: Q 23 ARG cc_start: 0.9240 (mtm110) cc_final: 0.8865 (mtm-85) outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 1.0696 time to fit residues: 265.7995 Evaluate side-chains 219 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 87 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 417 optimal weight: 0.9990 chunk 404 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.083517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.062993 restraints weight = 88591.388| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.52 r_work: 0.2648 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 37848 Z= 0.212 Angle : 0.570 9.810 50976 Z= 0.301 Chirality : 0.038 0.134 5376 Planarity : 0.003 0.021 6744 Dihedral : 3.713 14.909 4872 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.02 % Allowed : 9.38 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.96 (0.13), residues: 4416 helix: 4.15 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -0.01 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 64 TYR 0.017 0.002 TYR A 40 PHE 0.013 0.002 PHE Q -9 TRP 0.007 0.002 TRP P 94 HIS 0.002 0.000 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00473 (37848) covalent geometry : angle 0.57048 (50976) hydrogen bonds : bond 0.09952 ( 2701) hydrogen bonds : angle 3.72986 ( 7956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.617 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 219 average time/residue: 1.1176 time to fit residues: 277.0008 Evaluate side-chains 219 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 259 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.084612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063383 restraints weight = 85570.870| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.46 r_work: 0.2714 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 37848 Z= 0.164 Angle : 0.542 9.901 50976 Z= 0.284 Chirality : 0.036 0.133 5376 Planarity : 0.002 0.021 6744 Dihedral : 3.645 14.617 4872 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.05 % Allowed : 9.03 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.17 (0.13), residues: 4416 helix: 4.30 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : 0.04 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 64 TYR 0.015 0.002 TYR E 40 PHE 0.012 0.002 PHE Q -9 TRP 0.008 0.002 TRP P 94 HIS 0.002 0.000 HIS I 106 Details of bonding type rmsd covalent geometry : bond 0.00346 (37848) covalent geometry : angle 0.54205 (50976) hydrogen bonds : bond 0.08673 ( 2701) hydrogen bonds : angle 3.46449 ( 7956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 23 ARG cc_start: 0.9262 (mtm110) cc_final: 0.8791 (mtm-85) REVERT: D 23 ARG cc_start: 0.9233 (mtm110) cc_final: 0.8757 (mtm-85) REVERT: H 23 ARG cc_start: 0.9257 (mtm110) cc_final: 0.8795 (mtm-85) REVERT: K 23 ARG cc_start: 0.9260 (mtm110) cc_final: 0.8792 (mtm-85) REVERT: M 23 ARG cc_start: 0.9262 (mtm110) cc_final: 0.8788 (mtm-85) REVERT: P 23 ARG cc_start: 0.9233 (mtm110) cc_final: 0.8737 (mtm-85) REVERT: R 23 ARG cc_start: 0.9254 (mtm110) cc_final: 0.8784 (mtm-85) REVERT: X 23 ARG cc_start: 0.9271 (mtm110) cc_final: 0.8805 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 217 average time/residue: 1.1407 time to fit residues: 279.6657 Evaluate side-chains 217 residues out of total 4032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue -16 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 204 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 393 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 291 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 356 optimal weight: 9.9990 chunk 306 optimal weight: 60.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.3251 r_free = 0.3251 target = 0.084424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.063730 restraints weight = 88227.083| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.64 r_work: 0.2664 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 37848 Z= 0.193 Angle : 0.559 9.821 50976 Z= 0.295 Chirality : 0.037 0.133 5376 Planarity : 0.003 0.021 6744 Dihedral : 3.680 14.791 4872 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.02 % Allowed : 9.13 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.03 (0.13), residues: 4416 helix: 4.20 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : 0.03 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 64 TYR 0.016 0.002 TYR G 40 PHE 0.012 0.002 PHE Q -9 TRP 0.007 0.002 TRP P 94 HIS 0.002 0.000 HIS R 106 Details of bonding type rmsd covalent geometry : bond 0.00424 (37848) covalent geometry : angle 0.55911 (50976) hydrogen bonds : bond 0.09493 ( 2701) hydrogen bonds : angle 3.62870 ( 7956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14107.69 seconds wall clock time: 240 minutes 31.72 seconds (14431.72 seconds total)