Starting phenix.real_space_refine on Mon Sep 14 16:27:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/4v1w_2788/09_2026/4v1w_2788.cif Found real_map, /net/cci-nas-00/data/ceres_data/4v1w_2788/09_2026/4v1w_2788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/4v1w_2788/09_2026/4v1w_2788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/4v1w_2788/09_2026/4v1w_2788.map" model { file = "/net/cci-nas-00/data/ceres_data/4v1w_2788/09_2026/4v1w_2788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/4v1w_2788/09_2026/4v1w_2788.cif" } 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-2.2.1-6174/lib/python3.11/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: 7.05, per 1000 atoms: 0.22 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: 2.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 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: 6.35 Time building geometry restraints manager: 3.74 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: 0.13 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.160 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 are 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/Z covalent geometry : bond 0.01974 / 1.31 (33264) covalent geometry : angle 2.44915 / 1.57 (44784) hydrogen bonds : bond 0.18274 / 12.16 ( 2657) hydrogen bonds : angle 6.23322 / 4.55 ( 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 : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8954 (pt0) cc_final: 0.8735 (tp40) REVERT: A 6 GLN cc_start: 0.8732 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 7 ASN cc_start: 0.7729 (t0) cc_final: 0.7360 (t0) REVERT: A 12 VAL cc_start: 0.9706 (t) cc_final: 0.9445 (p) REVERT: A 17 ASN cc_start: 0.9800 (m-40) cc_final: 0.9411 (m110) REVERT: A 38 ASP cc_start: 0.9162 (t70) cc_final: 0.8814 (m-30) REVERT: A 45 GLU cc_start: 0.9187 (tt0) cc_final: 0.8914 (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: 0.9460 (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: 0.9396 (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: 0.9508 (mttt) cc_final: 0.9200 (tptt) REVERT: A 126 CYS cc_start: 0.9077 (m) cc_final: 0.8618 (m) REVERT: A 128 PHE cc_start: 0.9548 (t80) cc_final: 0.9261 (t80) REVERT: A 141 ILE cc_start: 0.9223 (mt) cc_final: 0.8836 (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: 0.8908 (ptp90) cc_final: 0.6954 (tmt170) REVERT: A 157 SER cc_start: 0.5093 (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: 0.0810 time to fit residues: 10.3748 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 : 0.050 ------------------------------------------------------------------------------- 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... A 71 GLN A 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 = 0.092240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084357 restraints weight = 3863.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.086703 restraints weight = 2100.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088204 restraints weight = 1272.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.089278 restraints weight = 825.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090058 restraints weight = 559.039| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5660 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 : 14.17 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 are 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/Z covalent geometry : bond 0.00463 / 0.23 (33264) covalent geometry : angle 0.75148 / 0.41 (44784) hydrogen bonds : bond 0.05033 / 3.29 ( 2657) hydrogen bonds : angle 4.36944 / 3.18 ( 7971) *********************** REFINEMENT MACRO_CYCLE 2 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 110 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8534 (pt0) cc_final: 0.8201 (tt0) REVERT: B 13 GLU cc_start: 0.9267 (tt0) cc_final: 0.8709 (tt0) REVERT: B 30 TYR cc_start: 0.8755 (m-10) cc_final: 0.8134 (m-10) REVERT: B 65 LEU cc_start: 0.9130 (mt) cc_final: 0.8885 (mt) REVERT: B 67 LYS cc_start: 0.9443 (tptt) cc_final: 0.9076 (tppt) REVERT: B 69 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8217 (tp40) REVERT: B 72 ARG cc_start: 0.8875 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: B 104 LYS cc_start: 0.9379 (mmmt) cc_final: 0.8971 (mmmt) REVERT: B 132 HIS cc_start: 0.7637 (m90) cc_final: 0.7184 (m-70) REVERT: B 133 PHE cc_start: 0.8650 (m-80) cc_final: 0.7666 (m-80) REVERT: B 135 ASP cc_start: 0.8880 (t70) cc_final: 0.8180 (t70) REVERT: B 141 ILE cc_start: 0.9056 (mt) cc_final: 0.8403 (mt) REVERT: B 142 LYS cc_start: 0.8983 (tptp) cc_final: 0.8057 (tppt) REVERT: B 144 MET cc_start: 0.9190 (mtp) cc_final: 0.8974 (mtp) REVERT: B 153 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7233 (tmt170) REVERT: B 168 ARG cc_start: 0.8832 (tpm170) cc_final: 0.6982 (ttt180) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.0826 time to fit residues: 9.7058 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 : 0.053 ------------------------------------------------------------------------------- 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: 2.9990 chunk 338 optimal weight: 0.0000 chunk 263 optimal weight: 0.7980 chunk 375 optimal weight: 6.9990 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 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 = 0.3388 r_free = 0.3388 target = 0.098707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089577 restraints weight = 3878.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092234 restraints weight = 2154.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.093962 restraints weight = 1339.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095098 restraints weight = 888.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096003 restraints weight = 630.223| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33264 Z= 0.162 Angle : 0.758 8.647 44784 Z= 0.379 Chirality : 0.040 0.115 4920 Planarity : 0.007 0.055 5880 Dihedral : 4.817 21.732 4464 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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 are not related in a simple way. whole: 2.71 (0.13), residues: 4032 helix: 2.38 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.94 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG P 75 TYR 0.025 0.002 TYR X 23 PHE 0.015 0.002 PHE F 128 TRP 0.007 0.002 TRP H 89 HIS 0.003 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (33264) covalent geometry : angle 0.75777 / 0.38 (44784) hydrogen bonds : bond 0.04003 / 2.60 ( 2657) hydrogen bonds : angle 3.76589 / 2.75 ( 7971) *********************** REFINEMENT MACRO_CYCLE 3 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 107 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8274 (pt0) cc_final: 0.8003 (tt0) REVERT: A 13 GLU cc_start: 0.9093 (tt0) cc_final: 0.8589 (tt0) REVERT: A 17 ASN cc_start: 0.9011 (m-40) cc_final: 0.8692 (m-40) REVERT: A 30 TYR cc_start: 0.8762 (m-10) cc_final: 0.8175 (m-10) REVERT: A 45 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8262 (tm-30) REVERT: A 60 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7379 (tm-30) REVERT: A 67 LYS cc_start: 0.9469 (tptt) cc_final: 0.9126 (tppt) REVERT: A 68 MET cc_start: 0.8273 (tmm) cc_final: 0.8003 (tmm) REVERT: A 69 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8156 (tp-100) REVERT: A 71 GLN cc_start: 0.9345 (pt0) cc_final: 0.9122 (pt0) REVERT: A 72 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8244 (mmm-85) REVERT: A 104 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8999 (mmmt) REVERT: A 120 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 122 ASP cc_start: 0.8358 (m-30) cc_final: 0.7684 (m-30) REVERT: A 141 ILE cc_start: 0.8918 (mt) cc_final: 0.8187 (pt) REVERT: A 142 LYS cc_start: 0.8837 (tptp) cc_final: 0.8088 (tttt) REVERT: A 161 LEU cc_start: 0.9246 (tp) cc_final: 0.8931 (tp) REVERT: A 168 ARG cc_start: 0.8562 (tpm170) cc_final: 0.6981 (ttt180) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0789 time to fit residues: 9.1091 Evaluate side-chains 76 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.058 ------------------------------------------------------------------------------- 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: 10.0000 chunk 143 optimal weight: 0.0050 chunk 298 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 160 optimal weight: 0.0570 chunk 272 optimal weight: 20.0000 chunk 250 optimal weight: 0.0170 chunk 229 optimal weight: 0.0970 chunk 362 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 overall best weight: 0.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 147 HIS A 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094317 restraints weight = 4145.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097003 restraints weight = 2382.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098929 restraints weight = 1524.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100245 restraints weight = 1027.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101187 restraints weight = 720.642| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33264 Z= 0.150 Angle : 0.806 10.440 44784 Z= 0.392 Chirality : 0.042 0.230 4920 Planarity : 0.006 0.046 5880 Dihedral : 4.973 30.453 4464 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 : 0.60 % 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 are not related in a simple way. whole: 3.23 (0.13), residues: 4032 helix: 2.68 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 39 TYR 0.011 0.002 TYR M 164 PHE 0.010 0.002 PHE C 78 TRP 0.004 0.001 TRP C 89 HIS 0.003 0.001 HIS I 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (33264) covalent geometry : angle 0.80616 / 0.39 (44784) hydrogen bonds : bond 0.03924 / 2.52 ( 2657) hydrogen bonds : angle 3.62496 / 2.64 ( 7971) *********************** REFINEMENT MACRO_CYCLE 4 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 101 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: K 30 TYR cc_start: 0.8452 (m-10) cc_final: 0.6944 (m-10) REVERT: K 45 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8103 (tm-30) REVERT: K 47 VAL cc_start: 0.9290 (t) cc_final: 0.8343 (t) REVERT: K 64 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7475 (mmm-85) REVERT: K 65 LEU cc_start: 0.9032 (mt) cc_final: 0.8629 (mt) REVERT: K 67 LYS cc_start: 0.9527 (tptt) cc_final: 0.8988 (tppt) REVERT: K 68 MET cc_start: 0.8169 (tmm) cc_final: 0.7893 (tmm) REVERT: K 69 GLN cc_start: 0.8680 (tp-100) cc_final: 0.7782 (tp-100) REVERT: K 71 GLN cc_start: 0.9367 (pt0) cc_final: 0.9047 (pt0) REVERT: K 72 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8222 (mmm-85) REVERT: K 89 TRP cc_start: 0.8853 (m100) cc_final: 0.8334 (m100) REVERT: K 122 ASP cc_start: 0.8066 (m-30) cc_final: 0.7480 (m-30) REVERT: K 129 LEU cc_start: 0.9159 (mt) cc_final: 0.8729 (tt) REVERT: K 135 ASP cc_start: 0.8265 (t70) cc_final: 0.7799 (t70) REVERT: K 141 ILE cc_start: 0.8725 (mt) cc_final: 0.8063 (pt) REVERT: K 142 LYS cc_start: 0.8833 (tptp) cc_final: 0.8306 (tptt) REVERT: K 161 LEU cc_start: 0.9270 (tp) cc_final: 0.8949 (tp) REVERT: K 168 ARG cc_start: 0.8562 (tpm170) cc_final: 0.6976 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0627 time to fit residues: 6.9733 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 : 0.052 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 20.0000 chunk 319 optimal weight: 0.0060 chunk 173 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 254 optimal weight: 0.0770 chunk 35 optimal weight: 0.1980 chunk 397 optimal weight: 8.9990 chunk 50 optimal weight: 0.0970 chunk 90 optimal weight: 7.9990 overall best weight: 0.0950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3507 r_free = 0.3507 target = 0.104533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.095897 restraints weight = 3847.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098480 restraints weight = 2131.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100212 restraints weight = 1301.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101449 restraints weight = 840.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102244 restraints weight = 560.233| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.8875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33264 Z= 0.152 Angle : 0.751 7.411 44784 Z= 0.379 Chirality : 0.040 0.166 4920 Planarity : 0.005 0.038 5880 Dihedral : 4.761 21.743 4464 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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 are not related in a simple way. whole: 2.92 (0.13), residues: 4032 helix: 2.37 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.09 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 39 TYR 0.021 0.003 TYR N 164 PHE 0.021 0.003 PHE O 166 TRP 0.003 0.001 TRP Q 89 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (33264) covalent geometry : angle 0.75133 / 0.38 (44784) hydrogen bonds : bond 0.03943 / 2.50 ( 2657) hydrogen bonds : angle 3.89910 / 2.83 ( 7971) *********************** REFINEMENT MACRO_CYCLE 5 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 102 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7965 (tt0) cc_final: 0.7676 (pm20) REVERT: H 18 ARG cc_start: 0.8096 (mmp80) cc_final: 0.7696 (mmp80) REVERT: H 22 LEU cc_start: 0.9306 (mm) cc_final: 0.8941 (mm) REVERT: H 45 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7618 (tm-30) REVERT: H 60 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7120 (tm-30) REVERT: H 67 LYS cc_start: 0.9527 (tptt) cc_final: 0.8864 (tppt) REVERT: H 68 MET cc_start: 0.8245 (tmm) cc_final: 0.7898 (tmm) REVERT: H 71 GLN cc_start: 0.9391 (pt0) cc_final: 0.8920 (pt0) REVERT: H 72 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8243 (mmm-85) REVERT: H 88 GLU cc_start: 0.7944 (pm20) cc_final: 0.7703 (pm20) REVERT: H 89 TRP cc_start: 0.8798 (m100) cc_final: 0.7429 (m100) REVERT: H 135 ASP cc_start: 0.8193 (t70) cc_final: 0.7826 (t70) REVERT: H 142 LYS cc_start: 0.8612 (tptp) cc_final: 0.8128 (tppt) REVERT: H 144 MET cc_start: 0.9201 (ptm) cc_final: 0.8725 (ptm) REVERT: H 161 LEU cc_start: 0.9233 (tp) cc_final: 0.8878 (tp) REVERT: H 168 ARG cc_start: 0.8321 (tpm170) cc_final: 0.6758 (ttt180) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0783 time to fit residues: 8.6340 Evaluate side-chains 71 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.052 ------------------------------------------------------------------------------- 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: 0.0070 chunk 275 optimal weight: 4.9990 chunk 157 optimal weight: 0.0970 chunk 205 optimal weight: 0.0670 chunk 406 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 21 ASN H 49 HIS H 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.103552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.094221 restraints weight = 3851.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.096711 restraints weight = 2178.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098431 restraints weight = 1366.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099717 restraints weight = 914.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100572 restraints weight = 638.590| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.9249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33264 Z= 0.146 Angle : 0.761 10.836 44784 Z= 0.387 Chirality : 0.042 0.142 4920 Planarity : 0.005 0.048 5880 Dihedral : 4.589 18.250 4464 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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 are not related in a simple way. whole: 2.87 (0.14), residues: 4032 helix: 2.40 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.17 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG W 39 TYR 0.018 0.003 TYR T 164 PHE 0.014 0.002 PHE D 128 TRP 0.003 0.001 TRP H 89 HIS 0.005 0.002 HIS P 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (33264) covalent geometry : angle 0.76150 / 0.39 (44784) hydrogen bonds : bond 0.03713 / 2.31 ( 2657) hydrogen bonds : angle 4.14982 / 3.01 ( 7971) *********************** REFINEMENT MACRO_CYCLE 6 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 100 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 18 ARG cc_start: 0.8046 (mmp80) cc_final: 0.7799 (mmp80) REVERT: K 22 LEU cc_start: 0.9300 (mm) cc_final: 0.8914 (mm) REVERT: K 38 ASP cc_start: 0.8890 (t70) cc_final: 0.8657 (t0) REVERT: K 65 LEU cc_start: 0.8866 (mt) cc_final: 0.8442 (mt) REVERT: K 68 MET cc_start: 0.8063 (tmm) cc_final: 0.7678 (tmm) REVERT: K 69 GLN cc_start: 0.8672 (tp40) cc_final: 0.8261 (tm-30) REVERT: K 72 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8193 (mmm-85) REVERT: K 88 GLU cc_start: 0.7974 (pm20) cc_final: 0.7730 (pm20) REVERT: K 89 TRP cc_start: 0.8880 (m100) cc_final: 0.7764 (m100) REVERT: K 104 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8520 (mmmt) REVERT: K 122 ASP cc_start: 0.8130 (m-30) cc_final: 0.7630 (m-30) REVERT: K 135 ASP cc_start: 0.8300 (t70) cc_final: 0.7857 (t70) REVERT: K 142 LYS cc_start: 0.8515 (tptp) cc_final: 0.8082 (tppt) REVERT: K 144 MET cc_start: 0.9125 (ptm) cc_final: 0.8730 (ptm) REVERT: K 161 LEU cc_start: 0.9248 (tp) cc_final: 0.8995 (tp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0700 time to fit residues: 7.6548 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 : 0.054 ------------------------------------------------------------------------------- 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: 9.9990 chunk 127 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 394 optimal weight: 0.0970 chunk 333 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 305 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 17 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 HIS K 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.105263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094477 restraints weight = 3936.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097416 restraints weight = 2308.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099383 restraints weight = 1479.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100839 restraints weight = 1003.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.101919 restraints weight = 708.057| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.9313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33264 Z= 0.144 Angle : 0.746 9.437 44784 Z= 0.381 Chirality : 0.040 0.131 4920 Planarity : 0.007 0.083 5880 Dihedral : 4.786 19.830 4464 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.43 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 are not related in a simple way. whole: 2.99 (0.13), residues: 4032 helix: 2.56 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.45 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG T 39 TYR 0.024 0.003 TYR J 23 PHE 0.011 0.002 PHE H 37 TRP 0.001 0.000 TRP A 89 HIS 0.006 0.002 HIS P 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (33264) covalent geometry : angle 0.74557 / 0.38 (44784) hydrogen bonds : bond 0.03749 / 2.39 ( 2657) hydrogen bonds : angle 4.09383 / 2.96 ( 7971) *********************** REFINEMENT MACRO_CYCLE 7 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 95 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 22 LEU cc_start: 0.9303 (mm) cc_final: 0.8858 (mm) REVERT: J 47 VAL cc_start: 0.9243 (t) cc_final: 0.8723 (t) REVERT: J 68 MET cc_start: 0.8482 (tmm) cc_final: 0.8015 (tmm) REVERT: J 69 GLN cc_start: 0.8670 (tp40) cc_final: 0.8353 (tm-30) REVERT: J 72 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.7547 (mmm160) REVERT: J 104 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8707 (mmmt) REVERT: J 122 ASP cc_start: 0.8194 (m-30) cc_final: 0.7731 (m-30) REVERT: J 142 LYS cc_start: 0.8641 (tptp) cc_final: 0.8074 (tttt) REVERT: J 144 MET cc_start: 0.9068 (ptm) cc_final: 0.8785 (ptm) REVERT: J 146 ASP cc_start: 0.8529 (m-30) cc_final: 0.8321 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0607 time to fit residues: 6.4037 Evaluate side-chains 75 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.053 ------------------------------------------------------------------------------- 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: 8.9990 chunk 178 optimal weight: 0.0770 chunk 332 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 347 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 17 ASN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS J 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.101499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.091832 restraints weight = 3942.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094610 restraints weight = 2214.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096483 restraints weight = 1375.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.097753 restraints weight = 908.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.098706 restraints weight = 626.969| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.9354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33264 Z= 0.184 Angle : 0.740 7.289 44784 Z= 0.377 Chirality : 0.042 0.137 4920 Planarity : 0.006 0.049 5880 Dihedral : 4.752 20.666 4464 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.14), residues: 4032 helix: 2.44 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.55 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 52 TYR 0.021 0.003 TYR P 164 PHE 0.013 0.002 PHE O 128 TRP 0.004 0.001 TRP C 89 HIS 0.003 0.001 HIS G 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (33264) covalent geometry : angle 0.74030 / 0.38 (44784) hydrogen bonds : bond 0.03543 / 2.25 ( 2657) hydrogen bonds : angle 4.19666 / 3.04 ( 7971) *********************** REFINEMENT MACRO_CYCLE 8 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 95 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 65 LEU cc_start: 0.9001 (mt) cc_final: 0.8650 (mt) REVERT: K 68 MET cc_start: 0.8084 (tmm) cc_final: 0.7686 (tmm) REVERT: K 69 GLN cc_start: 0.8716 (tp40) cc_final: 0.8289 (tm-30) REVERT: K 72 ARG cc_start: 0.8500 (mmm-85) cc_final: 0.8011 (mmm-85) REVERT: K 104 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8693 (mmmt) REVERT: K 122 ASP cc_start: 0.8119 (m-30) cc_final: 0.7621 (m-30) REVERT: K 126 CYS cc_start: 0.8979 (m) cc_final: 0.8775 (m) REVERT: K 167 GLU cc_start: 0.7486 (tp30) cc_final: 0.7054 (tp30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0716 time to fit residues: 7.4212 Evaluate side-chains 73 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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: 6.9990 chunk 259 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 161 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 17 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 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 = 0.3494 r_free = 0.3494 target = 0.103229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.092754 restraints weight = 3999.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095496 restraints weight = 2377.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097448 restraints weight = 1537.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098889 restraints weight = 1051.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.099788 restraints weight = 746.605| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.9890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 33264 Z= 0.243 Angle : 0.970 20.098 44784 Z= 0.479 Chirality : 0.044 0.148 4920 Planarity : 0.006 0.049 5880 Dihedral : 4.860 21.060 4464 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.13), residues: 4032 helix: 1.76 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.69 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 64 TYR 0.016 0.003 TYR I 30 PHE 0.017 0.002 PHE B 128 TRP 0.002 0.001 TRP E 89 HIS 0.003 0.001 HIS I 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (33264) covalent geometry : angle 0.97036 / 0.48 (44784) hydrogen bonds : bond 0.04394 / 2.85 ( 2657) hydrogen bonds : angle 4.52882 / 3.26 ( 7971) *********************** REFINEMENT MACRO_CYCLE 9 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 94 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 22 LEU cc_start: 0.9347 (mm) cc_final: 0.8959 (mm) REVERT: H 65 LEU cc_start: 0.9178 (mt) cc_final: 0.8822 (mt) REVERT: H 69 GLN cc_start: 0.8629 (tp40) cc_final: 0.8416 (tm-30) REVERT: H 88 GLU cc_start: 0.7999 (pm20) cc_final: 0.7708 (pm20) REVERT: H 104 LYS cc_start: 0.9292 (mmtt) cc_final: 0.8915 (mmmt) REVERT: H 122 ASP cc_start: 0.8415 (m-30) cc_final: 0.7889 (m-30) REVERT: H 144 MET cc_start: 0.8831 (ptm) cc_final: 0.7691 (ppp) REVERT: H 147 HIS cc_start: 0.8948 (m170) cc_final: 0.8574 (m170) REVERT: H 167 GLU cc_start: 0.7408 (tp30) cc_final: 0.7020 (tp30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0616 time to fit residues: 6.4398 Evaluate side-chains 73 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.052 ------------------------------------------------------------------------------- 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: 10.0000 chunk 165 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 251 optimal weight: 0.1980 chunk 405 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 392 optimal weight: 0.0570 chunk 60 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS H 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095730 restraints weight = 3849.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098293 restraints weight = 2254.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100470 restraints weight = 1474.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.101843 restraints weight = 1005.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.102943 restraints weight = 716.393| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 1.0204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33264 Z= 0.153 Angle : 0.806 7.595 44784 Z= 0.399 Chirality : 0.042 0.148 4920 Planarity : 0.005 0.031 5880 Dihedral : 4.855 18.786 4464 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.13), residues: 4032 helix: 2.28 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.66 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 64 TYR 0.024 0.003 TYR P 164 PHE 0.013 0.002 PHE D 128 TRP 0.001 0.000 TRP M 89 HIS 0.002 0.001 HIS W 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (33264) covalent geometry : angle 0.80643 / 0.40 (44784) hydrogen bonds : bond 0.03714 / 2.39 ( 2657) hydrogen bonds : angle 4.13087 / 2.98 ( 7971) ********************** REFINEMENT MACRO_CYCLE 10 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 93 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 ARG cc_start: 0.8325 (mmp80) cc_final: 0.7778 (mmp80) REVERT: H 22 LEU cc_start: 0.9345 (mm) cc_final: 0.8948 (mm) REVERT: H 65 LEU cc_start: 0.9034 (mt) cc_final: 0.8575 (mt) REVERT: H 72 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: H 88 GLU cc_start: 0.7782 (pm20) cc_final: 0.7503 (pm20) REVERT: H 104 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8676 (mmmt) REVERT: H 144 MET cc_start: 0.8955 (ptm) cc_final: 0.8228 (ptm) REVERT: H 147 HIS cc_start: 0.8849 (m170) cc_final: 0.8564 (m-70) REVERT: H 167 GLU cc_start: 0.7416 (tp30) cc_final: 0.7194 (tp30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0662 time to fit residues: 6.7604 Evaluate side-chains 70 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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: 5.9990 chunk 164 optimal weight: 9.9990 chunk 268 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 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 = 0.3466 r_free = 0.3466 target = 0.101217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.091471 restraints weight = 3885.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.094362 restraints weight = 2237.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096318 restraints weight = 1401.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097684 restraints weight = 924.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098632 restraints weight = 632.514| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 1.0071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33264 Z= 0.242 Angle : 0.798 7.089 44784 Z= 0.422 Chirality : 0.047 0.172 4920 Planarity : 0.006 0.052 5880 Dihedral : 5.017 19.696 4464 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.13), residues: 4032 helix: 1.89 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -1.11 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 64 TYR 0.014 0.002 TYR J 30 PHE 0.022 0.003 PHE D 128 TRP 0.007 0.002 TRP H 89 HIS 0.004 0.001 HIS O 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.24 (33264) covalent geometry : angle 0.79820 / 0.42 (44784) hydrogen bonds : bond 0.04338 / 2.82 ( 2657) hydrogen bonds : angle 4.43564 / 3.19 ( 7971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2081.61 seconds wall clock time: 38 minutes 33.24 seconds (2313.24 seconds total)