Starting phenix.real_space_refine on Fri Jun 27 12:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/4v1w_2788/06_2025/4v1w_2788.cif Found real_map, /net/cci-nas-00/data/ceres_data/4v1w_2788/06_2025/4v1w_2788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/4v1w_2788/06_2025/4v1w_2788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/4v1w_2788/06_2025/4v1w_2788.map" model { file = "/net/cci-nas-00/data/ceres_data/4v1w_2788/06_2025/4v1w_2788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/4v1w_2788/06_2025/4v1w_2788.cif" } resolution = 4.7 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= 0.009 sd= 0.053 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 120 5.16 5 C 20640 2.51 5 N 5736 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32736 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "B" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "C" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "D" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "F" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "G" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "H" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "I" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "J" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "K" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "L" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "M" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "N" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "O" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "P" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "Q" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "R" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "S" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "T" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "U" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "V" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "W" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "X" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Time building chain proxies: 17.78, per 1000 atoms: 0.54 Number of scatterers: 32736 At special positions: 0 Unit cell: (135.946, 135.946, 135.946, 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 120 16.00 O 6240 8.00 N 5736 7.00 C 20640 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: 7.78 Conformation dependent library (CDL) restraints added in 4.4 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 9 through 37 Processing helix chain 'A' and resid 44 through 73 removed outlier: 3.595A pdb=" N ARG A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.677A pdb=" N GLY A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 removed outlier: 3.508A pdb=" N GLY A 162 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 37 Processing helix chain 'B' and resid 44 through 73 removed outlier: 3.587A pdb=" N ARG B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 120 Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.516A pdb=" N HIS B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 156 removed outlier: 3.678A pdb=" N GLY B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.507A pdb=" N GLY B 162 " --> pdb=" O GLN B 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 73 removed outlier: 3.597A pdb=" N ARG C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 removed outlier: 3.510A pdb=" N HIS C 132 " --> pdb=" O PHE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 156 removed outlier: 3.676A pdb=" N GLY C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.505A pdb=" N GLY C 162 " --> pdb=" O GLN C 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 73 removed outlier: 3.599A pdb=" N ARG D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 removed outlier: 3.519A pdb=" N HIS D 132 " --> pdb=" O PHE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 156 removed outlier: 3.691A pdb=" N GLY D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 170 Processing helix chain 'E' and resid 9 through 37 Processing helix chain 'E' and resid 44 through 73 removed outlier: 3.591A pdb=" N ARG E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.513A pdb=" N HIS E 132 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 156 removed outlier: 3.690A pdb=" N GLY E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 170 Processing helix chain 'F' and resid 9 through 37 Processing helix chain 'F' and resid 44 through 73 removed outlier: 3.607A pdb=" N ARG F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 removed outlier: 3.513A pdb=" N HIS F 132 " --> pdb=" O PHE F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 156 removed outlier: 3.692A pdb=" N GLY F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 170 Processing helix chain 'G' and resid 9 through 37 Processing helix chain 'G' and resid 44 through 73 removed outlier: 3.600A pdb=" N ARG G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 removed outlier: 3.510A pdb=" N HIS G 132 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 156 removed outlier: 3.682A pdb=" N GLY G 156 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 170 Processing helix chain 'H' and resid 9 through 37 Processing helix chain 'H' and resid 44 through 73 removed outlier: 3.595A pdb=" N ARG H 59 " --> pdb=" O ALA H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 removed outlier: 3.515A pdb=" N HIS H 132 " --> pdb=" O PHE H 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 156 removed outlier: 3.674A pdb=" N GLY H 156 " --> pdb=" O GLN H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 170 removed outlier: 3.509A pdb=" N GLY H 162 " --> pdb=" O GLN H 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'I' and resid 44 through 73 removed outlier: 3.595A pdb=" N ARG I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 removed outlier: 3.513A pdb=" N HIS I 132 " --> pdb=" O PHE I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 156 removed outlier: 3.695A pdb=" N GLY I 156 " --> pdb=" O GLN I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 170 Processing helix chain 'J' and resid 9 through 37 Processing helix chain 'J' and resid 44 through 73 removed outlier: 3.594A pdb=" N ARG J 59 " --> pdb=" O ALA J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 removed outlier: 3.515A pdb=" N HIS J 132 " --> pdb=" O PHE J 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 156 removed outlier: 3.692A pdb=" N GLY J 156 " --> pdb=" O GLN J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'K' and resid 9 through 37 Processing helix chain 'K' and resid 44 through 73 removed outlier: 3.592A pdb=" N ARG K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 removed outlier: 3.510A pdb=" N HIS K 132 " --> pdb=" O PHE K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 156 removed outlier: 3.687A pdb=" N GLY K 156 " --> pdb=" O GLN K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 170 Processing helix chain 'L' and resid 9 through 37 Processing helix chain 'L' and resid 44 through 73 removed outlier: 3.591A pdb=" N ARG L 59 " --> pdb=" O ALA L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 removed outlier: 3.514A pdb=" N HIS L 132 " --> pdb=" O PHE L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 156 removed outlier: 3.693A pdb=" N GLY L 156 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 170 Processing helix chain 'M' and resid 9 through 37 Processing helix chain 'M' and resid 44 through 73 removed outlier: 3.596A pdb=" N ARG M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 removed outlier: 3.520A pdb=" N HIS M 132 " --> pdb=" O PHE M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 156 removed outlier: 3.693A pdb=" N GLY M 156 " --> pdb=" O GLN M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 170 Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 73 removed outlier: 3.600A pdb=" N ARG N 59 " --> pdb=" O ALA N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 removed outlier: 3.512A pdb=" N HIS N 132 " --> pdb=" O PHE N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 156 removed outlier: 3.687A pdb=" N GLY N 156 " --> pdb=" O GLN N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 170 Processing helix chain 'O' and resid 9 through 37 Processing helix chain 'O' and resid 44 through 73 removed outlier: 3.594A pdb=" N ARG O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 removed outlier: 3.517A pdb=" N HIS O 132 " --> pdb=" O PHE O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 156 removed outlier: 3.683A pdb=" N GLY O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 170 Processing helix chain 'P' and resid 9 through 37 Processing helix chain 'P' and resid 44 through 73 removed outlier: 3.596A pdb=" N ARG P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 removed outlier: 3.515A pdb=" N HIS P 132 " --> pdb=" O PHE P 128 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 156 removed outlier: 3.687A pdb=" N GLY P 156 " --> pdb=" O GLN P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 170 Processing helix chain 'Q' and resid 9 through 37 Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.599A pdb=" N ARG Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 removed outlier: 3.520A pdb=" N HIS Q 132 " --> pdb=" O PHE Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 156 removed outlier: 3.692A pdb=" N GLY Q 156 " --> pdb=" O GLN Q 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 158 through 170 Processing helix chain 'R' and resid 9 through 37 Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.589A pdb=" N ARG R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 removed outlier: 3.511A pdb=" N HIS R 132 " --> pdb=" O PHE R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 156 removed outlier: 3.686A pdb=" N GLY R 156 " --> pdb=" O GLN R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 170 removed outlier: 3.500A pdb=" N GLY R 162 " --> pdb=" O GLN R 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 37 Processing helix chain 'S' and resid 44 through 73 removed outlier: 3.590A pdb=" N ARG S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 removed outlier: 3.517A pdb=" N HIS S 132 " --> pdb=" O PHE S 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 156 removed outlier: 3.670A pdb=" N GLY S 156 " --> pdb=" O GLN S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 158 through 170 removed outlier: 3.505A pdb=" N GLY S 162 " --> pdb=" O GLN S 158 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 37 Processing helix chain 'T' and resid 44 through 73 removed outlier: 3.589A pdb=" N ARG T 59 " --> pdb=" O ALA T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 removed outlier: 3.505A pdb=" N HIS T 132 " --> pdb=" O PHE T 128 " (cutoff:3.500A) Processing helix chain 'T' and resid 133 through 156 removed outlier: 3.675A pdb=" N GLY T 156 " --> pdb=" O GLN T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 158 through 170 removed outlier: 3.507A pdb=" N GLY T 162 " --> pdb=" O GLN T 158 " (cutoff:3.500A) Processing helix chain 'U' and resid 9 through 37 Processing helix chain 'U' and resid 44 through 73 removed outlier: 3.590A pdb=" N ARG U 59 " --> pdb=" O ALA U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 91 through 120 Processing helix chain 'U' and resid 122 through 133 removed outlier: 3.512A pdb=" N HIS U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) Processing helix chain 'U' and resid 133 through 156 removed outlier: 3.678A pdb=" N GLY U 156 " --> pdb=" O GLN U 152 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 170 removed outlier: 3.506A pdb=" N GLY U 162 " --> pdb=" O GLN U 158 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 37 Processing helix chain 'V' and resid 44 through 73 removed outlier: 3.599A pdb=" N ARG V 59 " --> pdb=" O ALA V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 removed outlier: 3.520A pdb=" N HIS V 132 " --> pdb=" O PHE V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 156 removed outlier: 3.689A pdb=" N GLY V 156 " --> pdb=" O GLN V 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 158 through 170 Processing helix chain 'W' and resid 9 through 37 Processing helix chain 'W' and resid 44 through 73 removed outlier: 3.596A pdb=" N ARG W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 removed outlier: 3.516A pdb=" N HIS W 132 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 156 removed outlier: 3.687A pdb=" N GLY W 156 " --> pdb=" O GLN W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 170 Processing helix chain 'X' and resid 9 through 37 Processing helix chain 'X' and resid 44 through 73 removed outlier: 3.599A pdb=" N ARG X 59 " --> pdb=" O ALA X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 removed outlier: 3.513A pdb=" N HIS X 132 " --> pdb=" O PHE X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 156 removed outlier: 3.688A pdb=" N GLY X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 170 2657 hydrogen bonds defined for protein. 7971 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: 11.20 Time building geometry restraints manager: 9.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6924 1.33 - 1.45: 8358 1.45 - 1.58: 17384 1.58 - 1.70: 406 1.70 - 1.82: 192 Bond restraints: 33264 Sorted by residual: bond pdb=" CA MET M 96 " pdb=" C MET M 96 " ideal model delta sigma weight residual 1.523 1.601 -0.078 1.35e-02 5.49e+03 3.32e+01 bond pdb=" CA MET P 96 " pdb=" C MET P 96 " ideal model delta sigma weight residual 1.523 1.600 -0.077 1.35e-02 5.49e+03 3.23e+01 bond pdb=" CA MET L 96 " pdb=" C MET L 96 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.35e-02 5.49e+03 3.19e+01 bond pdb=" CA MET E 96 " pdb=" C MET E 96 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.35e-02 5.49e+03 3.18e+01 bond pdb=" CA MET W 96 " pdb=" C MET W 96 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.35e-02 5.49e+03 3.17e+01 ... (remaining 33259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 32798 2.40 - 4.81: 9407 4.81 - 7.21: 1923 7.21 - 9.62: 536 9.62 - 12.02: 120 Bond angle restraints: 44784 Sorted by residual: angle pdb=" N LEU J 54 " pdb=" CA LEU J 54 " pdb=" C LEU J 54 " ideal model delta sigma weight residual 111.28 119.22 -7.94 1.09e+00 8.42e-01 5.31e+01 angle pdb=" N LEU F 54 " pdb=" CA LEU F 54 " pdb=" C LEU F 54 " ideal model delta sigma weight residual 111.28 119.19 -7.91 1.09e+00 8.42e-01 5.27e+01 angle pdb=" N LEU L 54 " pdb=" CA LEU L 54 " pdb=" C LEU L 54 " ideal model delta sigma weight residual 111.28 119.12 -7.84 1.09e+00 8.42e-01 5.18e+01 angle pdb=" N LEU X 54 " pdb=" CA LEU X 54 " pdb=" C LEU X 54 " ideal model delta sigma weight residual 111.28 119.06 -7.78 1.09e+00 8.42e-01 5.09e+01 angle pdb=" N ALA R 159 " pdb=" CA ALA R 159 " pdb=" C ALA R 159 " ideal model delta sigma weight residual 110.97 118.70 -7.73 1.09e+00 8.42e-01 5.03e+01 ... (remaining 44779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 16633 16.90 - 33.79: 2388 33.79 - 50.69: 737 50.69 - 67.59: 234 67.59 - 84.48: 72 Dihedral angle restraints: 20064 sinusoidal: 8232 harmonic: 11832 Sorted by residual: dihedral pdb=" C PHE A 78 " pdb=" N PHE A 78 " pdb=" CA PHE A 78 " pdb=" CB PHE A 78 " ideal model delta harmonic sigma weight residual -122.60 -139.97 17.37 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C PHE E 35 " pdb=" N PHE E 35 " pdb=" CA PHE E 35 " pdb=" CB PHE E 35 " ideal model delta harmonic sigma weight residual -122.60 -139.73 17.13 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" C PHE K 35 " pdb=" N PHE K 35 " pdb=" CA PHE K 35 " pdb=" CB PHE K 35 " ideal model delta harmonic sigma weight residual -122.60 -139.56 16.96 0 2.50e+00 1.60e-01 4.60e+01 ... (remaining 20061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3357 0.144 - 0.289: 1065 0.289 - 0.433: 440 0.433 - 0.577: 11 0.577 - 0.721: 47 Chirality restraints: 4920 Sorted by residual: chirality pdb=" CA PHE A 78 " pdb=" N PHE A 78 " pdb=" C PHE A 78 " pdb=" CB PHE A 78 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA PHE E 35 " pdb=" N PHE E 35 " pdb=" C PHE E 35 " pdb=" CB PHE E 35 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CA PHE K 35 " pdb=" N PHE K 35 " pdb=" C PHE K 35 " pdb=" CB PHE K 35 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 4917 not shown) Planarity restraints: 5880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 166 " -0.045 2.00e-02 2.50e+03 3.10e-02 1.68e+01 pdb=" CG PHE I 166 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE I 166 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE I 166 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE I 166 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE I 166 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE I 166 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 166 " -0.045 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE J 166 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE J 166 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE J 166 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 166 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE J 166 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE J 166 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 166 " -0.045 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE O 166 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE O 166 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE O 166 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE O 166 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE O 166 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE O 166 " -0.011 2.00e-02 2.50e+03 ... (remaining 5877 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 16550 3.01 - 3.48: 36523 3.48 - 3.95: 55714 3.95 - 4.43: 68502 4.43 - 4.90: 98156 Nonbonded interactions: 275445 Sorted by model distance: nonbonded pdb=" O VAL M 16 " pdb=" CA ASN M 17 " model vdw 2.533 2.776 nonbonded pdb=" O VAL W 16 " pdb=" CA ASN W 17 " model vdw 2.534 2.776 nonbonded pdb=" O VAL J 16 " pdb=" CA ASN J 17 " model vdw 2.536 2.776 nonbonded pdb=" O VAL T 16 " pdb=" CA ASN T 17 " model vdw 2.536 2.776 nonbonded pdb=" O VAL C 16 " pdb=" CA ASN C 17 " model vdw 2.536 2.776 ... (remaining 275440 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: 0.32 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.290 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 69.900 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.020 0.130 33264 Z= 1.313 Angle : 2.449 12.023 44784 Z= 1.573 Chirality : 0.171 0.721 4920 Planarity : 0.008 0.033 5880 Dihedral : 18.968 84.484 12432 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.95 % Favored : 96.45 % Rotamer: Outliers : 7.67 % Allowed : 12.64 % Favored : 79.69 % Cbeta Deviations : 4.51 % 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: -2.40 (0.11), residues: 4032 helix: -1.53 (0.07), residues: 3192 sheet: None (None), residues: 0 loop : -0.89 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP F 89 HIS 0.017 0.004 HIS O 49 PHE 0.065 0.008 PHE I 166 TYR 0.026 0.006 TYR A 8 ARG 0.019 0.002 ARG S 168 Details of bonding type rmsd hydrogen bonds : bond 0.18274 ( 2657) hydrogen bonds : angle 6.23322 ( 7971) covalent geometry : bond 0.01974 (33264) covalent geometry : angle 2.44915 (44784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8954 (pt0) cc_final: 0.8735 (tp40) REVERT: A 6 GLN cc_start: 0.8732 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 7 ASN cc_start: 0.7729 (t0) cc_final: 0.7360 (t0) REVERT: A 12 VAL cc_start: 0.9706 (t) cc_final: 0.9445 (p) REVERT: A 17 ASN cc_start: 0.9800 (m-40) cc_final: 0.9411 (m110) REVERT: A 38 ASP cc_start: 0.9162 (t70) cc_final: 0.8814 (m-30) REVERT: A 45 GLU cc_start: 0.9187 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 64 ARG cc_start: 0.9190 (ttm110) cc_final: 0.8847 (ttm110) REVERT: A 65 LEU cc_start: 0.9593 (mt) cc_final: 0.9326 (mm) REVERT: A 67 LYS cc_start: 0.9461 (tptt) cc_final: 0.9205 (tppt) REVERT: A 69 GLN cc_start: 0.9632 (tp-100) cc_final: 0.9233 (tp40) REVERT: A 71 GLN cc_start: 0.9690 (mt0) cc_final: 0.9395 (mt0) REVERT: A 83 LYS cc_start: 0.8823 (pttt) cc_final: 0.8410 (mmtt) REVERT: A 86 GLN cc_start: 0.9250 (mt0) cc_final: 0.9048 (mt0) REVERT: A 88 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8636 (pp20) REVERT: A 96 MET cc_start: 0.9339 (tpp) cc_final: 0.9134 (mmm) REVERT: A 104 LYS cc_start: 0.9507 (mttt) cc_final: 0.9199 (tptt) REVERT: A 126 CYS cc_start: 0.9077 (m) cc_final: 0.8618 (m) REVERT: A 128 PHE cc_start: 0.9548 (t80) cc_final: 0.9261 (t80) REVERT: A 141 ILE cc_start: 0.9223 (mt) cc_final: 0.8871 (mt) REVERT: A 142 LYS cc_start: 0.9164 (tptp) cc_final: 0.8727 (tptt) REVERT: A 147 HIS cc_start: 0.9059 (m-70) cc_final: 0.8654 (m-70) REVERT: A 153 ARG cc_start: 0.8907 (ptp90) cc_final: 0.6953 (tmt170) REVERT: A 157 SER cc_start: 0.5092 (OUTLIER) cc_final: 0.4258 (p) REVERT: A 166 PHE cc_start: 0.9085 (t80) cc_final: 0.8719 (t80) REVERT: A 168 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7090 (mmm160) outliers start: 11 outliers final: 1 residues processed: 119 average time/residue: 0.1813 time to fit residues: 23.1549 Evaluate side-chains 91 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 105 optimal weight: 0.1980 chunk 208 optimal weight: 10.0000 chunk 165 optimal weight: 0.0010 chunk 319 optimal weight: 0.0970 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 0.9990 chunk 238 optimal weight: 20.0000 chunk 370 optimal weight: 8.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088361 restraints weight = 3795.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.090767 restraints weight = 2045.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092409 restraints weight = 1233.245| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33264 Z= 0.152 Angle : 0.725 6.578 44784 Z= 0.373 Chirality : 0.040 0.142 4920 Planarity : 0.006 0.051 5880 Dihedral : 4.533 14.623 4464 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.69 % Allowed : 6.94 % Favored : 92.36 % 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: 2.10 (0.12), residues: 4032 helix: 1.79 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.32 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 89 HIS 0.004 0.002 HIS U 124 PHE 0.026 0.003 PHE V 50 TYR 0.028 0.002 TYR U 28 ARG 0.012 0.001 ARG K 75 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 2657) hydrogen bonds : angle 3.89945 ( 7971) covalent geometry : bond 0.00294 (33264) covalent geometry : angle 0.72534 (44784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLU cc_start: 0.9317 (tt0) cc_final: 0.8746 (tt0) REVERT: B 22 LEU cc_start: 0.9166 (mm) cc_final: 0.8863 (mm) REVERT: B 36 TYR cc_start: 0.8629 (t80) cc_final: 0.8121 (t80) REVERT: B 38 ASP cc_start: 0.8682 (t0) cc_final: 0.8397 (m-30) REVERT: B 64 ARG cc_start: 0.8230 (ttm110) cc_final: 0.7866 (mmm-85) REVERT: B 67 LYS cc_start: 0.9406 (tptt) cc_final: 0.9093 (tppt) REVERT: B 69 GLN cc_start: 0.8900 (tp-100) cc_final: 0.8190 (tp40) REVERT: B 71 GLN cc_start: 0.9075 (mt0) cc_final: 0.8808 (mt0) REVERT: B 72 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8446 (mmm-85) REVERT: B 104 LYS cc_start: 0.9321 (mmmt) cc_final: 0.8933 (mmmt) REVERT: B 132 HIS cc_start: 0.7528 (m90) cc_final: 0.6342 (m90) REVERT: B 133 PHE cc_start: 0.8487 (m-80) cc_final: 0.7676 (m-80) REVERT: B 141 ILE cc_start: 0.8994 (mt) cc_final: 0.8713 (mt) REVERT: B 142 LYS cc_start: 0.9027 (tptp) cc_final: 0.8146 (tppt) REVERT: B 146 ASP cc_start: 0.8810 (m-30) cc_final: 0.8475 (m-30) REVERT: B 168 ARG cc_start: 0.8577 (tpm170) cc_final: 0.6933 (ttt-90) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.2053 time to fit residues: 23.8238 Evaluate side-chains 78 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 331 optimal weight: 10.0000 chunk 278 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 242 optimal weight: 0.0370 chunk 287 optimal weight: 4.9990 chunk 381 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.088826 restraints weight = 3737.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091615 restraints weight = 2072.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093466 restraints weight = 1272.366| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.7432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33264 Z= 0.180 Angle : 0.723 7.625 44784 Z= 0.361 Chirality : 0.040 0.123 4920 Planarity : 0.007 0.060 5880 Dihedral : 4.805 24.427 4464 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 2.87 (0.13), residues: 4032 helix: 2.45 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.70 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP J 89 HIS 0.003 0.001 HIS O 124 PHE 0.014 0.002 PHE P 78 TYR 0.020 0.003 TYR K 23 ARG 0.009 0.001 ARG W 59 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 2657) hydrogen bonds : angle 3.72858 ( 7971) covalent geometry : bond 0.00403 (33264) covalent geometry : angle 0.72344 (44784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 6 GLN cc_start: 0.7419 (tt0) cc_final: 0.6875 (tt0) REVERT: J 13 GLU cc_start: 0.9309 (tt0) cc_final: 0.8623 (tt0) REVERT: J 30 TYR cc_start: 0.9085 (m-10) cc_final: 0.8591 (m-10) REVERT: J 48 CYS cc_start: 0.8463 (t) cc_final: 0.8194 (t) REVERT: J 66 LEU cc_start: 0.9663 (mt) cc_final: 0.9452 (mm) REVERT: J 67 LYS cc_start: 0.9377 (tptt) cc_final: 0.8924 (tppt) REVERT: J 69 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8047 (tp-100) REVERT: J 71 GLN cc_start: 0.8839 (mt0) cc_final: 0.8610 (mt0) REVERT: J 72 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8472 (mmm-85) REVERT: J 89 TRP cc_start: 0.9140 (m100) cc_final: 0.8595 (m100) REVERT: J 132 HIS cc_start: 0.7932 (m90) cc_final: 0.7300 (m90) REVERT: J 142 LYS cc_start: 0.8865 (tptp) cc_final: 0.8168 (tppt) REVERT: J 146 ASP cc_start: 0.8840 (m-30) cc_final: 0.8490 (m-30) REVERT: J 149 THR cc_start: 0.7956 (m) cc_final: 0.6716 (m) REVERT: J 153 ARG cc_start: 0.8910 (ptm160) cc_final: 0.7960 (ptp-170) REVERT: J 168 ARG cc_start: 0.8778 (tpm170) cc_final: 0.7076 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1869 time to fit residues: 22.6886 Evaluate side-chains 78 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 335 optimal weight: 20.0000 chunk 202 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 384 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 chunk 402 optimal weight: 7.9990 chunk 374 optimal weight: 30.0000 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 21 ASN H 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089267 restraints weight = 3929.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092015 restraints weight = 2195.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.093941 restraints weight = 1368.321| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 33264 Z= 0.187 Angle : 0.754 8.736 44784 Z= 0.384 Chirality : 0.042 0.181 4920 Planarity : 0.007 0.062 5880 Dihedral : 4.884 30.707 4464 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: 3.09 (0.13), residues: 4032 helix: 2.67 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.98 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP J 89 HIS 0.004 0.002 HIS M 132 PHE 0.016 0.002 PHE I 35 TYR 0.017 0.002 TYR M 164 ARG 0.011 0.002 ARG W 59 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 2657) hydrogen bonds : angle 3.91139 ( 7971) covalent geometry : bond 0.00396 (33264) covalent geometry : angle 0.75402 (44784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ASN cc_start: 0.8007 (t0) cc_final: 0.7768 (t0) REVERT: H 8 TYR cc_start: 0.6953 (t80) cc_final: 0.6740 (t80) REVERT: H 22 LEU cc_start: 0.9351 (mm) cc_final: 0.9043 (mt) REVERT: H 30 TYR cc_start: 0.8945 (m-10) cc_final: 0.8544 (m-10) REVERT: H 38 ASP cc_start: 0.8783 (t70) cc_final: 0.8168 (m-30) REVERT: H 44 LEU cc_start: 0.9292 (mp) cc_final: 0.9009 (mm) REVERT: H 45 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8344 (tm-30) REVERT: H 47 VAL cc_start: 0.9479 (t) cc_final: 0.9239 (p) REVERT: H 65 LEU cc_start: 0.8937 (mt) cc_final: 0.8689 (mt) REVERT: H 67 LYS cc_start: 0.9444 (tptt) cc_final: 0.8900 (tppt) REVERT: H 69 GLN cc_start: 0.8836 (tp-100) cc_final: 0.7756 (tp-100) REVERT: H 71 GLN cc_start: 0.8913 (mt0) cc_final: 0.8687 (mt0) REVERT: H 72 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: H 106 LEU cc_start: 0.9513 (mt) cc_final: 0.9170 (mt) REVERT: H 122 ASP cc_start: 0.8438 (t0) cc_final: 0.8060 (t0) REVERT: H 129 LEU cc_start: 0.9309 (mt) cc_final: 0.8820 (tt) REVERT: H 142 LYS cc_start: 0.9159 (tptp) cc_final: 0.8535 (tptt) REVERT: H 146 ASP cc_start: 0.8866 (m-30) cc_final: 0.8545 (m-30) REVERT: H 161 LEU cc_start: 0.9230 (tt) cc_final: 0.8926 (tp) REVERT: H 168 ARG cc_start: 0.8865 (tpm170) cc_final: 0.7103 (tpt170) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1522 time to fit residues: 16.1909 Evaluate side-chains 71 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 397 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 4 optimal weight: 0.0570 chunk 213 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 21 ASN J 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.090107 restraints weight = 3999.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.092921 restraints weight = 2235.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094946 restraints weight = 1403.102| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.7984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33264 Z= 0.201 Angle : 0.707 7.143 44784 Z= 0.363 Chirality : 0.042 0.169 4920 Planarity : 0.005 0.035 5880 Dihedral : 4.515 23.222 4464 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: 2.96 (0.13), residues: 4032 helix: 2.59 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.97 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 89 HIS 0.004 0.001 HIS Q 132 PHE 0.013 0.002 PHE C 128 TYR 0.022 0.003 TYR U 23 ARG 0.006 0.001 ARG P 64 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 2657) hydrogen bonds : angle 3.99845 ( 7971) covalent geometry : bond 0.00417 (33264) covalent geometry : angle 0.70750 (44784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 22 LEU cc_start: 0.9317 (mm) cc_final: 0.8855 (mm) REVERT: J 30 TYR cc_start: 0.9093 (m-10) cc_final: 0.8622 (m-10) REVERT: J 38 ASP cc_start: 0.8783 (t70) cc_final: 0.8143 (m-30) REVERT: J 44 LEU cc_start: 0.9372 (mp) cc_final: 0.8604 (mm) REVERT: J 48 CYS cc_start: 0.8201 (t) cc_final: 0.7264 (m) REVERT: J 67 LYS cc_start: 0.9375 (tptt) cc_final: 0.8869 (tppt) REVERT: J 69 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8018 (tp-100) REVERT: J 71 GLN cc_start: 0.9074 (mt0) cc_final: 0.8743 (mt0) REVERT: J 72 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.7879 (mmm-85) REVERT: J 104 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8760 (mmmt) REVERT: J 106 LEU cc_start: 0.9588 (mt) cc_final: 0.9332 (mt) REVERT: J 122 ASP cc_start: 0.8342 (t0) cc_final: 0.8036 (t0) REVERT: J 142 LYS cc_start: 0.9063 (tptp) cc_final: 0.8543 (tptt) REVERT: J 146 ASP cc_start: 0.8792 (m-30) cc_final: 0.8501 (m-30) REVERT: J 168 ARG cc_start: 0.8570 (tpm170) cc_final: 0.8149 (tpm170) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1521 time to fit residues: 16.4536 Evaluate side-chains 71 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 276 optimal weight: 8.9990 chunk 382 optimal weight: 3.9990 chunk 277 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.100575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091030 restraints weight = 3851.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093719 restraints weight = 2189.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095614 restraints weight = 1379.662| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 33264 Z= 0.169 Angle : 0.731 7.277 44784 Z= 0.373 Chirality : 0.042 0.136 4920 Planarity : 0.007 0.065 5880 Dihedral : 4.651 21.671 4464 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 2.65 (0.13), residues: 4032 helix: 2.30 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.68 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.004 TRP J 89 HIS 0.003 0.001 HIS Q 132 PHE 0.016 0.002 PHE K 128 TYR 0.019 0.002 TYR Q 164 ARG 0.010 0.001 ARG P 39 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 2657) hydrogen bonds : angle 3.86664 ( 7971) covalent geometry : bond 0.00368 (33264) covalent geometry : angle 0.73088 (44784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 18 ARG cc_start: 0.8161 (mmp80) cc_final: 0.7723 (mmp80) REVERT: J 22 LEU cc_start: 0.9376 (mm) cc_final: 0.8914 (mm) REVERT: J 30 TYR cc_start: 0.8983 (m-10) cc_final: 0.8647 (m-10) REVERT: J 45 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8174 (tm-30) REVERT: J 48 CYS cc_start: 0.8386 (t) cc_final: 0.8084 (t) REVERT: J 67 LYS cc_start: 0.9410 (tptt) cc_final: 0.8898 (tppt) REVERT: J 69 GLN cc_start: 0.8880 (tp-100) cc_final: 0.7955 (tp-100) REVERT: J 71 GLN cc_start: 0.9023 (mt0) cc_final: 0.8665 (mt0) REVERT: J 72 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.7976 (mmm-85) REVERT: J 88 GLU cc_start: 0.7969 (pm20) cc_final: 0.7528 (pm20) REVERT: J 89 TRP cc_start: 0.9053 (m100) cc_final: 0.8422 (m100) REVERT: J 104 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8834 (mmmt) REVERT: J 106 LEU cc_start: 0.9592 (mt) cc_final: 0.9324 (mt) REVERT: J 122 ASP cc_start: 0.8396 (t0) cc_final: 0.8003 (t0) REVERT: J 142 LYS cc_start: 0.8978 (tptp) cc_final: 0.8476 (tppt) REVERT: J 146 ASP cc_start: 0.8844 (m-30) cc_final: 0.8590 (m-30) REVERT: J 161 LEU cc_start: 0.9266 (tp) cc_final: 0.9058 (tt) REVERT: J 168 ARG cc_start: 0.8521 (tpm170) cc_final: 0.7997 (tpm170) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2108 time to fit residues: 22.8132 Evaluate side-chains 73 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 351 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 327 optimal weight: 0.0050 chunk 85 optimal weight: 20.0000 overall best weight: 2.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 21 ASN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.093497 restraints weight = 3882.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096416 restraints weight = 2323.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098431 restraints weight = 1510.573| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.8379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33264 Z= 0.151 Angle : 0.781 8.736 44784 Z= 0.393 Chirality : 0.044 0.182 4920 Planarity : 0.004 0.031 5880 Dihedral : 4.656 19.836 4464 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 2.25 (0.13), residues: 4032 helix: 1.98 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.64 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP W 89 HIS 0.003 0.001 HIS I 132 PHE 0.015 0.002 PHE H 128 TYR 0.020 0.002 TYR D 23 ARG 0.006 0.001 ARG X 64 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 2657) hydrogen bonds : angle 3.87493 ( 7971) covalent geometry : bond 0.00328 (33264) covalent geometry : angle 0.78141 (44784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 30 TYR cc_start: 0.8954 (m-10) cc_final: 0.8615 (m-10) REVERT: J 36 TYR cc_start: 0.8418 (t80) cc_final: 0.8069 (t80) REVERT: J 38 ASP cc_start: 0.8684 (t70) cc_final: 0.8127 (m-30) REVERT: J 67 LYS cc_start: 0.9380 (tptt) cc_final: 0.8871 (tppt) REVERT: J 69 GLN cc_start: 0.8716 (tp-100) cc_final: 0.7632 (tp-100) REVERT: J 71 GLN cc_start: 0.8957 (mt0) cc_final: 0.8552 (mt0) REVERT: J 72 ARG cc_start: 0.8694 (mmm-85) cc_final: 0.8109 (mmm-85) REVERT: J 88 GLU cc_start: 0.7634 (pm20) cc_final: 0.7334 (pm20) REVERT: J 89 TRP cc_start: 0.8895 (m100) cc_final: 0.8215 (m100) REVERT: J 106 LEU cc_start: 0.9591 (mt) cc_final: 0.9359 (mt) REVERT: J 122 ASP cc_start: 0.8408 (t0) cc_final: 0.8181 (t0) REVERT: J 142 LYS cc_start: 0.8896 (tptp) cc_final: 0.8550 (tppt) REVERT: J 147 HIS cc_start: 0.9062 (m-70) cc_final: 0.8410 (m170) REVERT: J 161 LEU cc_start: 0.9255 (tp) cc_final: 0.9010 (tt) REVERT: J 168 ARG cc_start: 0.8561 (tpm170) cc_final: 0.7855 (tpm170) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2042 time to fit residues: 19.7788 Evaluate side-chains 76 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 130 optimal weight: 7.9990 chunk 375 optimal weight: 0.0040 chunk 169 optimal weight: 0.0870 chunk 307 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 21 optimal weight: 0.0770 chunk 127 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.104172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092916 restraints weight = 3727.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095724 restraints weight = 2281.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097665 restraints weight = 1519.363| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.8861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33264 Z= 0.166 Angle : 0.773 6.796 44784 Z= 0.407 Chirality : 0.041 0.127 4920 Planarity : 0.007 0.064 5880 Dihedral : 4.860 18.974 4464 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: 2.10 (0.13), residues: 4032 helix: 1.98 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP W 89 HIS 0.001 0.001 HIS M 114 PHE 0.016 0.002 PHE D 128 TYR 0.024 0.003 TYR T 164 ARG 0.017 0.002 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 2657) hydrogen bonds : angle 3.89059 ( 7971) covalent geometry : bond 0.00366 (33264) covalent geometry : angle 0.77302 (44784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 22 LEU cc_start: 0.9306 (mm) cc_final: 0.8874 (mm) REVERT: J 30 TYR cc_start: 0.8866 (m-10) cc_final: 0.8404 (m-10) REVERT: J 35 PHE cc_start: 0.8867 (m-10) cc_final: 0.8327 (m-10) REVERT: J 38 ASP cc_start: 0.8553 (t70) cc_final: 0.7750 (m-30) REVERT: J 45 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7998 (tm-30) REVERT: J 48 CYS cc_start: 0.7780 (t) cc_final: 0.4427 (t) REVERT: J 67 LYS cc_start: 0.9326 (tptt) cc_final: 0.8853 (tppt) REVERT: J 71 GLN cc_start: 0.8841 (mt0) cc_final: 0.8457 (mt0) REVERT: J 72 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8058 (mmm-85) REVERT: J 89 TRP cc_start: 0.8905 (m100) cc_final: 0.8016 (m100) REVERT: J 104 LYS cc_start: 0.9459 (mmtt) cc_final: 0.8998 (mmmt) REVERT: J 106 LEU cc_start: 0.9592 (mt) cc_final: 0.9372 (mt) REVERT: J 122 ASP cc_start: 0.8379 (t0) cc_final: 0.8142 (t0) REVERT: J 142 LYS cc_start: 0.8878 (tptp) cc_final: 0.8241 (tppt) REVERT: J 147 HIS cc_start: 0.9133 (m-70) cc_final: 0.8699 (m-70) REVERT: J 161 LEU cc_start: 0.9268 (tp) cc_final: 0.9022 (tp) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2620 time to fit residues: 27.5223 Evaluate side-chains 76 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 165 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 287 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 399 optimal weight: 20.0000 chunk 18 optimal weight: 0.0570 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 17 ASN H 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.105579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094675 restraints weight = 3574.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.097525 restraints weight = 2115.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099309 restraints weight = 1370.599| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.9356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33264 Z= 0.146 Angle : 0.707 7.096 44784 Z= 0.361 Chirality : 0.039 0.128 4920 Planarity : 0.007 0.100 5880 Dihedral : 4.700 17.508 4464 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 2.38 (0.13), residues: 4032 helix: 2.09 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.70 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 89 HIS 0.010 0.002 HIS D 132 PHE 0.020 0.002 PHE L 35 TYR 0.026 0.003 TYR P 30 ARG 0.011 0.001 ARG C 75 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 2657) hydrogen bonds : angle 3.67230 ( 7971) covalent geometry : bond 0.00324 (33264) covalent geometry : angle 0.70680 (44784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8059 (tm-30) REVERT: H 48 CYS cc_start: 0.8097 (t) cc_final: 0.7852 (t) REVERT: H 67 LYS cc_start: 0.9349 (tptt) cc_final: 0.8839 (tppt) REVERT: H 71 GLN cc_start: 0.8820 (mt0) cc_final: 0.8400 (mt0) REVERT: H 104 LYS cc_start: 0.9499 (mmmm) cc_final: 0.9115 (mmmt) REVERT: H 106 LEU cc_start: 0.9650 (mt) cc_final: 0.9416 (mt) REVERT: H 126 CYS cc_start: 0.9087 (m) cc_final: 0.8835 (m) REVERT: H 142 LYS cc_start: 0.8942 (tptp) cc_final: 0.8631 (tptt) REVERT: H 147 HIS cc_start: 0.9062 (m-70) cc_final: 0.8752 (m-70) REVERT: H 168 ARG cc_start: 0.8604 (tpm170) cc_final: 0.6625 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1816 time to fit residues: 16.3379 Evaluate side-chains 76 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 284 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 377 optimal weight: 0.0030 chunk 294 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 214 optimal weight: 0.0050 chunk 334 optimal weight: 0.0970 chunk 185 optimal weight: 0.4980 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.111629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.100423 restraints weight = 3658.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103343 restraints weight = 2111.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105173 restraints weight = 1356.040| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.9901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33264 Z= 0.140 Angle : 0.744 7.536 44784 Z= 0.370 Chirality : 0.038 0.135 4920 Planarity : 0.006 0.067 5880 Dihedral : 4.550 18.615 4464 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 2.16 (0.13), residues: 4032 helix: 1.93 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.71 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 89 HIS 0.003 0.001 HIS C 124 PHE 0.021 0.002 PHE P 35 TYR 0.029 0.004 TYR J 23 ARG 0.010 0.001 ARG W 64 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 2657) hydrogen bonds : angle 3.86842 ( 7971) covalent geometry : bond 0.00291 (33264) covalent geometry : angle 0.74368 (44784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 7 ASN cc_start: 0.7777 (t0) cc_final: 0.7521 (t0) REVERT: H 36 TYR cc_start: 0.8384 (t80) cc_final: 0.8144 (t80) REVERT: H 38 ASP cc_start: 0.8399 (t70) cc_final: 0.8120 (m-30) REVERT: H 45 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 48 CYS cc_start: 0.7948 (t) cc_final: 0.7338 (m) REVERT: H 59 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8392 (tpp80) REVERT: H 67 LYS cc_start: 0.9301 (tptt) cc_final: 0.8790 (tppt) REVERT: H 69 GLN cc_start: 0.8474 (tp40) cc_final: 0.7670 (tp-100) REVERT: H 71 GLN cc_start: 0.8718 (mt0) cc_final: 0.8291 (mt0) REVERT: H 89 TRP cc_start: 0.8736 (m100) cc_final: 0.7903 (m100) REVERT: H 104 LYS cc_start: 0.9479 (mmmm) cc_final: 0.9048 (mmmt) REVERT: H 122 ASP cc_start: 0.8524 (t0) cc_final: 0.8070 (m-30) REVERT: H 127 ASP cc_start: 0.9055 (p0) cc_final: 0.8839 (t70) REVERT: H 142 LYS cc_start: 0.8950 (tptp) cc_final: 0.8659 (tptt) REVERT: H 149 THR cc_start: 0.8494 (m) cc_final: 0.7647 (m) REVERT: H 153 ARG cc_start: 0.8413 (ptm160) cc_final: 0.8138 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2114 time to fit residues: 20.8127 Evaluate side-chains 83 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 253 optimal weight: 0.0060 chunk 164 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 371 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 377 optimal weight: 0.0470 chunk 285 optimal weight: 7.9990 chunk 309 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 344 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 overall best weight: 3.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 17 ASN K 21 ASN K 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.099053 restraints weight = 3614.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102018 restraints weight = 2099.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103979 restraints weight = 1346.351| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.9841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 33264 Z= 0.164 Angle : 0.749 7.341 44784 Z= 0.382 Chirality : 0.040 0.136 4920 Planarity : 0.007 0.082 5880 Dihedral : 4.870 16.142 4464 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 1.99 (0.13), residues: 4032 helix: 1.76 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 89 HIS 0.006 0.002 HIS I 147 PHE 0.013 0.001 PHE K 128 TYR 0.022 0.002 TYR M 30 ARG 0.006 0.001 ARG F 64 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 2657) hydrogen bonds : angle 4.07717 ( 7971) covalent geometry : bond 0.00363 (33264) covalent geometry : angle 0.74939 (44784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.79 seconds wall clock time: 90 minutes 24.48 seconds (5424.48 seconds total)