Starting phenix.real_space_refine on Tue Aug 26 00:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/4v1w_2788/08_2025/4v1w_2788.cif Found real_map, /net/cci-nas-00/data/ceres_data/4v1w_2788/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/4v1w_2788/08_2025/4v1w_2788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/4v1w_2788/08_2025/4v1w_2788.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/4v1w_2788/08_2025/4v1w_2788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/4v1w_2788/08_2025/4v1w_2788.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.49, per 1000 atoms: 0.20 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: 2.12 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.69 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: 5.66 Time building geometry restraints manager: 2.83 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set 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: 0.080 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.490 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.080 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (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 ARG 0.019 0.002 ARG S 168 TYR 0.026 0.006 TYR A 8 PHE 0.065 0.008 PHE I 166 TRP 0.016 0.006 TRP F 89 HIS 0.017 0.004 HIS O 49 Details of bonding type rmsd covalent geometry : bond 0.01974 (33264) covalent geometry : angle 2.44915 (44784) hydrogen bonds : bond 0.18274 ( 2657) hydrogen bonds : angle 6.23322 ( 7971) *********************** 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 : 0.042 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: 0.7359 (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: 0.8914 (tm-30) REVERT: A 64 ARG cc_start: 0.9190 (ttm110) cc_final: 0.8846 (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: 0.8409 (mmtt) REVERT: A 86 GLN cc_start: 0.9250 (mt0) cc_final: 0.9047 (mt0) REVERT: A 88 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8636 (pp20) REVERT: A 104 LYS cc_start: 0.9507 (mttt) cc_final: 0.9200 (tptt) REVERT: A 126 CYS cc_start: 0.9077 (m) cc_final: 0.8617 (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: 0.8836 (mt) REVERT: A 142 LYS cc_start: 0.9164 (tptp) cc_final: 0.8730 (tptt) REVERT: A 147 HIS cc_start: 0.9059 (m-70) cc_final: 0.8664 (m-70) REVERT: A 153 ARG cc_start: 0.8907 (ptp90) cc_final: 0.6954 (tmt170) REVERT: A 157 SER cc_start: 0.5092 (OUTLIER) cc_final: 0.4257 (p) REVERT: A 166 PHE cc_start: 0.9085 (t80) cc_final: 0.8731 (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: 0.0650 time to fit residues: 8.3490 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 : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.092243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084380 restraints weight = 3875.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086711 restraints weight = 2091.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.088221 restraints weight = 1263.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089268 restraints weight = 817.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089828 restraints weight = 556.960| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 33264 Z= 0.227 Angle : 0.751 5.907 44784 Z= 0.406 Chirality : 0.042 0.145 4920 Planarity : 0.007 0.071 5880 Dihedral : 4.650 14.098 4464 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.69 % Allowed : 9.03 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.12), residues: 4032 helix: 1.45 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.29 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG P 75 TYR 0.028 0.003 TYR U 28 PHE 0.021 0.003 PHE P 50 TRP 0.012 0.003 TRP J 89 HIS 0.004 0.001 HIS O 124 Details of bonding type rmsd covalent geometry : bond 0.00463 (33264) covalent geometry : angle 0.75148 (44784) hydrogen bonds : bond 0.05033 ( 2657) hydrogen bonds : angle 4.36944 ( 7971) *********************** 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 110 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8529 (pt0) cc_final: 0.8198 (tt0) REVERT: B 13 GLU cc_start: 0.9266 (tt0) cc_final: 0.8703 (tt0) REVERT: B 30 TYR cc_start: 0.8752 (m-10) cc_final: 0.8127 (m-10) REVERT: B 65 LEU cc_start: 0.9126 (mt) cc_final: 0.8880 (mt) REVERT: B 67 LYS cc_start: 0.9446 (tptt) cc_final: 0.9071 (tppt) REVERT: B 69 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8208 (tp40) REVERT: B 72 ARG cc_start: 0.8872 (mmm-85) cc_final: 0.8160 (mmm-85) REVERT: B 104 LYS cc_start: 0.9375 (mmmt) cc_final: 0.8965 (mmmt) REVERT: B 132 HIS cc_start: 0.7635 (m90) cc_final: 0.7182 (m-70) REVERT: B 133 PHE cc_start: 0.8652 (m-80) cc_final: 0.7667 (m-80) REVERT: B 135 ASP cc_start: 0.8876 (t70) cc_final: 0.8172 (t70) REVERT: B 141 ILE cc_start: 0.9055 (mt) cc_final: 0.8404 (mt) REVERT: B 142 LYS cc_start: 0.8983 (tptp) cc_final: 0.8059 (tppt) REVERT: B 144 MET cc_start: 0.9195 (mtp) cc_final: 0.8976 (mtp) REVERT: B 153 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7233 (tmt170) REVERT: B 168 ARG cc_start: 0.8829 (tpm170) cc_final: 0.6985 (ttt180) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0654 time to fit residues: 7.6666 Evaluate side-chains 77 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 62 optimal weight: 3.9990 chunk 209 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 256 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 338 optimal weight: 0.0000 chunk 263 optimal weight: 0.9990 chunk 375 optimal weight: 6.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.088801 restraints weight = 3958.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091404 restraints weight = 2158.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093153 restraints weight = 1319.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094328 restraints weight = 869.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.095118 restraints weight = 603.159| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33264 Z= 0.169 Angle : 0.753 8.263 44784 Z= 0.379 Chirality : 0.040 0.118 4920 Planarity : 0.007 0.057 5880 Dihedral : 4.798 21.036 4464 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.13), residues: 4032 helix: 2.29 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.87 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG F 75 TYR 0.024 0.003 TYR F 23 PHE 0.016 0.002 PHE H 128 TRP 0.007 0.002 TRP Q 89 HIS 0.003 0.001 HIS H 124 Details of bonding type rmsd covalent geometry : bond 0.00364 (33264) covalent geometry : angle 0.75288 (44784) hydrogen bonds : bond 0.04018 ( 2657) hydrogen bonds : angle 3.82277 ( 7971) *********************** 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 110 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 6 GLN cc_start: 0.7295 (tt0) cc_final: 0.6830 (tt0) REVERT: D 8 TYR cc_start: 0.7240 (t80) cc_final: 0.6372 (t80) REVERT: D 17 ASN cc_start: 0.9110 (m-40) cc_final: 0.8808 (m-40) REVERT: D 18 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.8006 (mmp80) REVERT: D 22 LEU cc_start: 0.9239 (mt) cc_final: 0.8989 (mm) REVERT: D 30 TYR cc_start: 0.8899 (m-10) cc_final: 0.8284 (m-10) REVERT: D 60 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7794 (tm-30) REVERT: D 69 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8153 (tp-100) REVERT: D 72 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.7410 (mmm160) REVERT: D 122 ASP cc_start: 0.8550 (m-30) cc_final: 0.7978 (m-30) REVERT: D 142 LYS cc_start: 0.8583 (tptp) cc_final: 0.8030 (tttt) REVERT: D 150 ASN cc_start: 0.8167 (m110) cc_final: 0.7820 (m-40) REVERT: D 153 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7164 (tmt170) REVERT: D 161 LEU cc_start: 0.9243 (tp) cc_final: 0.8986 (tp) REVERT: D 168 ARG cc_start: 0.8776 (tpm170) cc_final: 0.7189 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0784 time to fit residues: 9.2683 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 : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 214 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 160 optimal weight: 0.2980 chunk 272 optimal weight: 20.0000 chunk 250 optimal weight: 20.0000 chunk 229 optimal weight: 0.7980 chunk 362 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 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 = 0.3463 r_free = 0.3463 target = 0.102139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092827 restraints weight = 4054.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095561 restraints weight = 2231.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097426 restraints weight = 1364.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098705 restraints weight = 888.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099248 restraints weight = 600.605| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.7832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33264 Z= 0.158 Angle : 0.727 8.108 44784 Z= 0.370 Chirality : 0.041 0.150 4920 Planarity : 0.007 0.063 5880 Dihedral : 5.071 29.798 4464 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.14), residues: 4032 helix: 2.62 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.27 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 59 TYR 0.013 0.002 TYR J 28 PHE 0.015 0.002 PHE X 128 TRP 0.006 0.003 TRP J 89 HIS 0.004 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00348 (33264) covalent geometry : angle 0.72740 (44784) hydrogen bonds : bond 0.03704 ( 2657) hydrogen bonds : angle 3.68456 ( 7971) *********************** 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 98 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.057 Fit side-chains revert: symmetry clash REVERT: K 30 TYR cc_start: 0.8716 (m-10) cc_final: 0.7020 (m-10) REVERT: K 44 LEU cc_start: 0.9336 (mp) cc_final: 0.9070 (mt) REVERT: K 45 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8289 (tm-30) REVERT: K 47 VAL cc_start: 0.9438 (t) cc_final: 0.8795 (t) REVERT: K 65 LEU cc_start: 0.9047 (mt) cc_final: 0.8721 (mt) REVERT: K 67 LYS cc_start: 0.9513 (tppt) cc_final: 0.8994 (tppt) REVERT: K 69 GLN cc_start: 0.8789 (tp-100) cc_final: 0.7780 (tp-100) REVERT: K 72 ARG cc_start: 0.8497 (mmm-85) cc_final: 0.8191 (mmm-85) REVERT: K 104 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8849 (tptt) REVERT: K 122 ASP cc_start: 0.8237 (m-30) cc_final: 0.7697 (m-30) REVERT: K 129 LEU cc_start: 0.9286 (mt) cc_final: 0.8808 (tt) REVERT: K 135 ASP cc_start: 0.9289 (m-30) cc_final: 0.8951 (m-30) REVERT: K 141 ILE cc_start: 0.8587 (mt) cc_final: 0.8009 (pt) REVERT: K 142 LYS cc_start: 0.8677 (tptp) cc_final: 0.8165 (tppt) REVERT: K 161 LEU cc_start: 0.9254 (tp) cc_final: 0.9008 (tt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0636 time to fit residues: 6.7716 Evaluate side-chains 68 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 192 optimal weight: 9.9990 chunk 12 optimal weight: 0.0970 chunk 319 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 397 optimal weight: 9.9990 chunk 50 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.101061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091740 restraints weight = 3946.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094533 restraints weight = 2102.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096430 restraints weight = 1262.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097648 restraints weight = 813.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098602 restraints weight = 555.740| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.8536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33264 Z= 0.155 Angle : 0.768 7.204 44784 Z= 0.387 Chirality : 0.042 0.191 4920 Planarity : 0.006 0.043 5880 Dihedral : 4.846 21.407 4464 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.14), residues: 4032 helix: 2.17 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : 0.11 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG P 59 TYR 0.022 0.003 TYR S 23 PHE 0.010 0.001 PHE X 128 TRP 0.004 0.001 TRP C 89 HIS 0.003 0.001 HIS O 114 Details of bonding type rmsd covalent geometry : bond 0.00363 (33264) covalent geometry : angle 0.76783 (44784) hydrogen bonds : bond 0.03653 ( 2657) hydrogen bonds : angle 3.82788 ( 7971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 30 TYR cc_start: 0.8459 (m-10) cc_final: 0.8245 (m-10) REVERT: J 54 LEU cc_start: 0.9577 (tp) cc_final: 0.9294 (tp) REVERT: J 67 LYS cc_start: 0.9492 (tppt) cc_final: 0.8728 (tppt) REVERT: J 69 GLN cc_start: 0.8730 (tp-100) cc_final: 0.7778 (tp-100) REVERT: J 72 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8336 (mmm-85) REVERT: J 104 LYS cc_start: 0.9366 (mmmm) cc_final: 0.8934 (mmmt) REVERT: J 122 ASP cc_start: 0.8256 (m-30) cc_final: 0.7767 (m-30) REVERT: J 142 LYS cc_start: 0.8485 (tptp) cc_final: 0.7988 (tttt) REVERT: J 144 MET cc_start: 0.9158 (ptm) cc_final: 0.8786 (ptm) REVERT: J 150 ASN cc_start: 0.8789 (m-40) cc_final: 0.8302 (p0) REVERT: J 161 LEU cc_start: 0.9208 (tp) cc_final: 0.8933 (tt) REVERT: J 168 ARG cc_start: 0.8643 (tpm170) cc_final: 0.6675 (ttt180) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0703 time to fit residues: 7.1594 Evaluate side-chains 68 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 297 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 157 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 406 optimal weight: 0.0060 chunk 308 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 279 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 160 optimal weight: 0.0070 chunk 12 optimal weight: 3.9990 overall best weight: 1.1016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 ASN J 21 ASN J 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094302 restraints weight = 3972.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096973 restraints weight = 2151.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098593 restraints weight = 1283.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099758 restraints weight = 826.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100567 restraints weight = 558.744| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.8879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33264 Z= 0.136 Angle : 0.742 8.769 44784 Z= 0.373 Chirality : 0.041 0.169 4920 Planarity : 0.005 0.034 5880 Dihedral : 4.698 17.441 4464 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.67 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.14), residues: 4032 helix: 2.21 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.07 (0.27), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Q 59 TYR 0.013 0.002 TYR B 164 PHE 0.013 0.002 PHE R 128 TRP 0.003 0.001 TRP H 89 HIS 0.002 0.001 HIS F 114 Details of bonding type rmsd covalent geometry : bond 0.00307 (33264) covalent geometry : angle 0.74214 (44784) hydrogen bonds : bond 0.03519 ( 2657) hydrogen bonds : angle 3.78044 ( 7971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 18 ARG cc_start: 0.8354 (mmp80) cc_final: 0.7730 (mmp80) REVERT: J 22 LEU cc_start: 0.9408 (mm) cc_final: 0.8931 (mm) REVERT: J 65 LEU cc_start: 0.8847 (mt) cc_final: 0.8610 (mt) REVERT: J 67 LYS cc_start: 0.9533 (tppt) cc_final: 0.8867 (tppt) REVERT: J 69 GLN cc_start: 0.8657 (tp40) cc_final: 0.7676 (tp-100) REVERT: J 122 ASP cc_start: 0.8181 (m-30) cc_final: 0.7727 (m-30) REVERT: J 142 LYS cc_start: 0.8804 (tptp) cc_final: 0.8417 (tptt) REVERT: J 144 MET cc_start: 0.8980 (ptm) cc_final: 0.8244 (ptm) REVERT: J 147 HIS cc_start: 0.8766 (m-70) cc_final: 0.8505 (m-70) REVERT: J 149 THR cc_start: 0.7843 (m) cc_final: 0.7635 (m) REVERT: J 150 ASN cc_start: 0.8849 (m-40) cc_final: 0.8567 (m-40) REVERT: J 153 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7164 (mtm110) REVERT: J 161 LEU cc_start: 0.9209 (tp) cc_final: 0.8913 (tp) REVERT: J 168 ARG cc_start: 0.8388 (tpm170) cc_final: 0.7225 (ttt180) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0792 time to fit residues: 8.7876 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 : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 23 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 216 optimal weight: 8.9990 chunk 394 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 305 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 0.0470 overall best weight: 1.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094786 restraints weight = 3920.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097613 restraints weight = 2088.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099499 restraints weight = 1249.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100779 restraints weight = 803.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101632 restraints weight = 550.798| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.9189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33264 Z= 0.153 Angle : 0.807 11.410 44784 Z= 0.412 Chirality : 0.044 0.183 4920 Planarity : 0.007 0.084 5880 Dihedral : 4.791 16.857 4464 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.14), residues: 4032 helix: 2.34 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.26 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 52 TYR 0.024 0.003 TYR Q 164 PHE 0.018 0.003 PHE J 166 TRP 0.003 0.001 TRP L 89 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00346 (33264) covalent geometry : angle 0.80659 (44784) hydrogen bonds : bond 0.03590 ( 2657) hydrogen bonds : angle 4.04837 ( 7971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 18 ARG cc_start: 0.8366 (mmp80) cc_final: 0.7763 (mmp80) REVERT: K 22 LEU cc_start: 0.9328 (mm) cc_final: 0.8909 (mm) REVERT: K 30 TYR cc_start: 0.8621 (m-10) cc_final: 0.8313 (m-10) REVERT: K 57 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9040 (mt-10) REVERT: K 65 LEU cc_start: 0.8797 (mt) cc_final: 0.8585 (mt) REVERT: K 67 LYS cc_start: 0.9544 (tppt) cc_final: 0.8842 (tppt) REVERT: K 69 GLN cc_start: 0.8454 (tp40) cc_final: 0.7595 (tp-100) REVERT: K 103 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8185 (mm-30) REVERT: K 104 LYS cc_start: 0.9220 (mmtt) cc_final: 0.8501 (mmtt) REVERT: K 122 ASP cc_start: 0.8269 (m-30) cc_final: 0.7729 (m-30) REVERT: K 142 LYS cc_start: 0.8845 (tptp) cc_final: 0.8405 (tppt) REVERT: K 144 MET cc_start: 0.9035 (ptm) cc_final: 0.8429 (ptm) REVERT: K 147 HIS cc_start: 0.9166 (m-70) cc_final: 0.8736 (m-70) REVERT: K 149 THR cc_start: 0.7663 (m) cc_final: 0.7442 (m) REVERT: K 150 ASN cc_start: 0.8865 (m-40) cc_final: 0.8599 (m-40) REVERT: K 153 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7057 (mtm110) REVERT: K 168 ARG cc_start: 0.8358 (tpm170) cc_final: 0.6942 (ttt180) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0584 time to fit residues: 6.6460 Evaluate side-chains 80 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 111 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 157 optimal weight: 0.0370 chunk 236 optimal weight: 9.9990 chunk 347 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 358 optimal weight: 0.0030 chunk 221 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 overall best weight: 3.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 17 ASN ** J 21 ASN ** 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 = 0.3500 r_free = 0.3500 target = 0.104802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094097 restraints weight = 3962.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.096988 restraints weight = 2296.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099047 restraints weight = 1471.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100490 restraints weight = 993.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.101446 restraints weight = 696.036| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.9480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33264 Z= 0.184 Angle : 0.795 9.067 44784 Z= 0.409 Chirality : 0.042 0.179 4920 Planarity : 0.006 0.062 5880 Dihedral : 4.749 16.525 4464 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.13), residues: 4032 helix: 2.43 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.79 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 75 TYR 0.015 0.002 TYR T 8 PHE 0.012 0.002 PHE U 128 TRP 0.003 0.001 TRP I 89 HIS 0.002 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00425 (33264) covalent geometry : angle 0.79483 (44784) hydrogen bonds : bond 0.03486 ( 2657) hydrogen bonds : angle 3.97730 ( 7971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 30 TYR cc_start: 0.8635 (m-10) cc_final: 0.8409 (m-10) REVERT: J 67 LYS cc_start: 0.9464 (tppt) cc_final: 0.8748 (tppt) REVERT: J 104 LYS cc_start: 0.9256 (mmtt) cc_final: 0.8642 (mmtt) REVERT: J 142 LYS cc_start: 0.8863 (tptp) cc_final: 0.8586 (tppt) REVERT: J 144 MET cc_start: 0.9033 (ptm) cc_final: 0.8465 (ptm) REVERT: J 147 HIS cc_start: 0.9125 (m-70) cc_final: 0.8800 (m-70) REVERT: J 168 ARG cc_start: 0.8493 (tpm170) cc_final: 0.6931 (ttt180) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0550 time to fit residues: 5.3444 Evaluate side-chains 68 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 382 optimal weight: 5.9990 chunk 259 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 262 optimal weight: 0.0770 chunk 85 optimal weight: 30.0000 chunk 161 optimal weight: 20.0000 chunk 363 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.106236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095107 restraints weight = 4012.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098092 restraints weight = 2352.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100080 restraints weight = 1514.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101654 restraints weight = 1045.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.102673 restraints weight = 744.736| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.9698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 33264 Z= 0.175 Angle : 0.828 8.271 44784 Z= 0.429 Chirality : 0.043 0.173 4920 Planarity : 0.006 0.067 5880 Dihedral : 4.728 16.722 4464 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.13), residues: 4032 helix: 2.17 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.23 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG O 75 TYR 0.031 0.004 TYR X 23 PHE 0.018 0.002 PHE Q 166 TRP 0.003 0.001 TRP N 89 HIS 0.002 0.001 HIS K 124 Details of bonding type rmsd covalent geometry : bond 0.00395 (33264) covalent geometry : angle 0.82838 (44784) hydrogen bonds : bond 0.03657 ( 2657) hydrogen bonds : angle 4.12695 ( 7971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 67 LYS cc_start: 0.9435 (tppt) cc_final: 0.8872 (tppt) REVERT: H 100 ILE cc_start: 0.9463 (tt) cc_final: 0.9252 (tt) REVERT: H 104 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8584 (mmmt) REVERT: H 142 LYS cc_start: 0.8901 (tptp) cc_final: 0.8686 (tppt) REVERT: H 144 MET cc_start: 0.8723 (ptm) cc_final: 0.7500 (ptm) REVERT: H 147 HIS cc_start: 0.9013 (m-70) cc_final: 0.8654 (m170) REVERT: H 168 ARG cc_start: 0.8505 (tpm170) cc_final: 0.6926 (ttt180) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0565 time to fit residues: 5.6437 Evaluate side-chains 67 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 295 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 405 optimal weight: 1.9990 chunk 211 optimal weight: 10.0000 chunk 392 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 180 optimal weight: 6.9990 chunk 24 optimal weight: 0.0370 overall best weight: 0.7358 ------------------------------------------------------------------------------- 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 ** 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 = 0.3608 r_free = 0.3608 target = 0.110952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100100 restraints weight = 3966.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102824 restraints weight = 2368.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.104968 restraints weight = 1563.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.105932 restraints weight = 1071.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107276 restraints weight = 826.937| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 1.0171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33264 Z= 0.162 Angle : 0.856 6.667 44784 Z= 0.444 Chirality : 0.043 0.162 4920 Planarity : 0.005 0.040 5880 Dihedral : 4.786 17.920 4464 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.13), residues: 4032 helix: 1.83 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -1.61 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 75 TYR 0.011 0.002 TYR M 30 PHE 0.020 0.003 PHE I 166 TRP 0.003 0.001 TRP O 89 HIS 0.002 0.001 HIS U 124 Details of bonding type rmsd covalent geometry : bond 0.00355 (33264) covalent geometry : angle 0.85645 (44784) hydrogen bonds : bond 0.03892 ( 2657) hydrogen bonds : angle 4.32967 ( 7971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6384 Ramachandran restraints generated. 3192 Oldfield, 0 Emsley, 3192 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 : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 21 ASN cc_start: 0.9123 (t0) cc_final: 0.8852 (t0) REVERT: K 22 LEU cc_start: 0.9277 (mm) cc_final: 0.8966 (mm) REVERT: K 67 LYS cc_start: 0.9450 (tppt) cc_final: 0.8803 (tppt) REVERT: K 77 LEU cc_start: 0.8279 (mt) cc_final: 0.7589 (mt) REVERT: K 89 TRP cc_start: 0.8698 (m100) cc_final: 0.7800 (m100) REVERT: K 104 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8492 (mmmt) REVERT: K 122 ASP cc_start: 0.8323 (m-30) cc_final: 0.7840 (m-30) REVERT: K 142 LYS cc_start: 0.8508 (tptp) cc_final: 0.8119 (tptt) REVERT: K 146 ASP cc_start: 0.8597 (m-30) cc_final: 0.8265 (m-30) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0508 time to fit residues: 5.1846 Evaluate side-chains 67 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 144 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 268 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.107912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096649 restraints weight = 3870.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099673 restraints weight = 2388.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101643 restraints weight = 1565.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102986 restraints weight = 1085.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104213 restraints weight = 793.739| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 1.0220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33264 Z= 0.188 Angle : 0.784 6.612 44784 Z= 0.423 Chirality : 0.045 0.217 4920 Planarity : 0.006 0.048 5880 Dihedral : 4.835 15.902 4464 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.13), residues: 4032 helix: 1.59 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.57 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 64 TYR 0.027 0.003 TYR T 164 PHE 0.017 0.002 PHE I 166 TRP 0.004 0.001 TRP D 89 HIS 0.002 0.001 HIS S 147 Details of bonding type rmsd covalent geometry : bond 0.00428 (33264) covalent geometry : angle 0.78448 (44784) hydrogen bonds : bond 0.03731 ( 2657) hydrogen bonds : angle 4.67307 ( 7971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.94 seconds wall clock time: 33 minutes 14.89 seconds (1994.89 seconds total)