Starting phenix.real_space_refine on Fri Mar 22 07:32:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1w_2788/03_2024/4v1w_2788.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1w_2788/03_2024/4v1w_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1w_2788/03_2024/4v1w_2788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1w_2788/03_2024/4v1w_2788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1w_2788/03_2024/4v1w_2788.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4v1w_2788/03_2024/4v1w_2788.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 20640 2.51 5 N 5736 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32736 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "B" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "C" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "D" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "F" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "G" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "H" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "I" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "J" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "K" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "L" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "M" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "N" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "O" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "P" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "Q" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "R" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "S" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "T" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "U" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "V" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "W" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain: "X" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1364 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Time building chain proxies: 16.24, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 12.56 Conformation dependent library (CDL) restraints added in 6.3 seconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7632 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 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: 10.29 Time building geometry restraints manager: 13.50 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: 97.30 - 104.61: 369 104.61 - 111.91: 10587 111.91 - 119.22: 17076 119.22 - 126.52: 16242 126.52 - 133.83: 510 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 2.320 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 80.200 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.280 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.130 33264 Z= 1.278 Angle : 2.449 12.023 44784 Z= 1.573 Chirality : 0.171 0.721 4920 Planarity : 0.008 0.033 5880 Dihedral : 18.968 84.484 12432 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.95 % Favored : 96.45 % Rotamer: Outliers : 7.67 % Allowed : 12.64 % Favored : 79.69 % Cbeta Deviations : 4.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.11), residues: 4032 helix: -1.53 (0.07), residues: 3192 sheet: None (None), residues: 0 loop : -0.89 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP F 89 HIS 0.017 0.004 HIS O 49 PHE 0.065 0.008 PHE I 166 TYR 0.026 0.006 TYR A 8 ARG 0.019 0.002 ARG S 168 *********************** 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 fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLN cc_start: 0.8954 (pt0) cc_final: 0.8735 (tp40) REVERT: A 6 GLN cc_start: 0.8732 (tt0) cc_final: 0.7358 (tm-30) REVERT: A 7 ASN cc_start: 0.7729 (t0) cc_final: 0.7360 (t0) REVERT: A 12 VAL cc_start: 0.9706 (t) cc_final: 0.9445 (p) REVERT: A 17 ASN cc_start: 0.9800 (m-40) cc_final: 0.9411 (m110) REVERT: A 38 ASP cc_start: 0.9162 (t70) cc_final: 0.8814 (m-30) REVERT: A 45 GLU cc_start: 0.9187 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 64 ARG cc_start: 0.9190 (ttm110) cc_final: 0.8847 (ttm110) REVERT: A 65 LEU cc_start: 0.9593 (mt) cc_final: 0.9326 (mm) REVERT: A 67 LYS cc_start: 0.9461 (tptt) cc_final: 0.9205 (tppt) REVERT: A 69 GLN cc_start: 0.9632 (tp-100) cc_final: 0.9233 (tp40) REVERT: A 71 GLN cc_start: 0.9690 (mt0) cc_final: 0.9395 (mt0) REVERT: A 83 LYS cc_start: 0.8823 (pttt) cc_final: 0.8410 (mmtt) REVERT: A 86 GLN cc_start: 0.9250 (mt0) cc_final: 0.9048 (mt0) REVERT: A 88 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8636 (pp20) REVERT: A 96 MET cc_start: 0.9339 (tpp) cc_final: 0.9134 (mmm) REVERT: A 104 LYS cc_start: 0.9507 (mttt) cc_final: 0.9199 (tptt) REVERT: A 126 CYS cc_start: 0.9077 (m) cc_final: 0.8618 (m) REVERT: A 128 PHE cc_start: 0.9548 (t80) cc_final: 0.9261 (t80) REVERT: A 141 ILE cc_start: 0.9223 (mt) cc_final: 0.8871 (mt) REVERT: A 142 LYS cc_start: 0.9164 (tptp) cc_final: 0.8727 (tptt) REVERT: A 147 HIS cc_start: 0.9059 (m-70) cc_final: 0.8654 (m-70) REVERT: A 153 ARG cc_start: 0.8907 (ptp90) cc_final: 0.6953 (tmt170) REVERT: A 157 SER cc_start: 0.5092 (OUTLIER) cc_final: 0.4258 (p) REVERT: A 166 PHE cc_start: 0.9085 (t80) cc_final: 0.8719 (t80) REVERT: A 168 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7090 (mmm160) outliers start: 11 outliers final: 1 residues processed: 119 average time/residue: 0.1867 time to fit residues: 23.8850 Evaluate side-chains 91 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 105 optimal weight: 0.0020 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 194 optimal weight: 0.0970 chunk 238 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 overall best weight: 2.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5820 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= 0.192 Angle : 0.718 6.310 44784 Z= 0.369 Chirality : 0.039 0.138 4920 Planarity : 0.006 0.056 5880 Dihedral : 4.520 14.153 4464 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.69 % Allowed : 6.94 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.12), residues: 4032 helix: 1.89 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : -0.31 (0.26), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 89 HIS 0.004 0.001 HIS U 124 PHE 0.025 0.003 PHE Q 50 TYR 0.027 0.002 TYR D 28 ARG 0.011 0.001 ARG P 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7728 Ramachandran restraints generated. 3864 Oldfield, 0 Emsley, 3864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLN cc_start: 0.8551 (pt0) cc_final: 0.8102 (tp40) REVERT: B 6 GLN cc_start: 0.8456 (tt0) cc_final: 0.7498 (tm-30) REVERT: B 7 ASN cc_start: 0.8267 (t0) cc_final: 0.8024 (t0) REVERT: B 22 LEU cc_start: 0.9323 (mm) cc_final: 0.9096 (mm) REVERT: B 64 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8087 (mmm-85) REVERT: B 65 LEU cc_start: 0.9227 (mt) cc_final: 0.8879 (mt) REVERT: B 67 LYS cc_start: 0.9418 (tptt) cc_final: 0.9155 (tppt) REVERT: B 71 GLN cc_start: 0.9656 (mt0) cc_final: 0.9454 (mt0) REVERT: B 83 LYS cc_start: 0.8705 (pttt) cc_final: 0.8364 (mmtt) REVERT: B 86 GLN cc_start: 0.9214 (mt0) cc_final: 0.8970 (mt0) REVERT: B 104 LYS cc_start: 0.9383 (mmmt) cc_final: 0.9070 (mmmt) REVERT: B 120 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7626 (mm-40) REVERT: B 132 HIS cc_start: 0.8699 (m90) cc_final: 0.8250 (m90) REVERT: B 133 PHE cc_start: 0.9271 (m-80) cc_final: 0.8732 (m-80) REVERT: B 141 ILE cc_start: 0.9009 (mt) cc_final: 0.8675 (mt) REVERT: B 142 LYS cc_start: 0.9203 (tptp) cc_final: 0.8649 (tppt) REVERT: B 146 ASP cc_start: 0.9254 (m-30) cc_final: 0.8841 (m-30) REVERT: B 168 ARG cc_start: 0.8779 (tpm170) cc_final: 0.7270 (tpt-90) outliers start: 1 outliers final: 0 residues processed: 109 average time/residue: 0.1847 time to fit residues: 21.5893 Evaluate side-chains 75 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 368 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33264 Z= 0.287 Angle : 0.693 5.991 44784 Z= 0.363 Chirality : 0.043 0.156 4920 Planarity : 0.008 0.103 5880 Dihedral : 4.281 14.102 4464 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.69 % Allowed : 8.33 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.13), residues: 4032 helix: 2.42 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.21 (0.27), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP J 89 HIS 0.003 0.001 HIS M 124 PHE 0.013 0.002 PHE R 128 TYR 0.018 0.003 TYR P 23 ARG 0.010 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 3 GLN cc_start: 0.8340 (pt0) cc_final: 0.8097 (tt0) REVERT: R 6 GLN cc_start: 0.8540 (tt0) cc_final: 0.8038 (tt0) REVERT: R 7 ASN cc_start: 0.8327 (t0) cc_final: 0.7923 (t0) REVERT: R 18 ARG cc_start: 0.8179 (tpp-160) cc_final: 0.7906 (mmp80) REVERT: R 64 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8241 (mmm-85) REVERT: R 67 LYS cc_start: 0.9492 (tptt) cc_final: 0.9136 (tppt) REVERT: R 82 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8161 (tp40) REVERT: R 83 LYS cc_start: 0.8613 (pttt) cc_final: 0.8246 (mmtt) REVERT: R 96 MET cc_start: 0.8492 (mmm) cc_final: 0.8190 (mmm) REVERT: R 104 LYS cc_start: 0.9282 (mmmt) cc_final: 0.8958 (mmmt) REVERT: R 106 LEU cc_start: 0.9573 (mt) cc_final: 0.9337 (mt) REVERT: R 132 HIS cc_start: 0.8831 (m90) cc_final: 0.8249 (m90) REVERT: R 141 ILE cc_start: 0.8722 (mt) cc_final: 0.8507 (mt) REVERT: R 142 LYS cc_start: 0.9269 (tptp) cc_final: 0.8813 (tttt) REVERT: R 146 ASP cc_start: 0.9094 (m-30) cc_final: 0.8855 (m-30) REVERT: R 150 ASN cc_start: 0.8933 (m110) cc_final: 0.8512 (m110) REVERT: R 153 ARG cc_start: 0.8803 (ptm160) cc_final: 0.7073 (tmt170) REVERT: R 168 ARG cc_start: 0.8731 (tpm170) cc_final: 0.7420 (tpt-90) REVERT: R 170 THR cc_start: 0.8538 (p) cc_final: 0.8297 (p) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1816 time to fit residues: 20.7437 Evaluate side-chains 83 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 0.0020 chunk 249 optimal weight: 0.0370 chunk 372 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 353 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 1.1668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 17 ASN ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33264 Z= 0.172 Angle : 0.622 6.864 44784 Z= 0.332 Chirality : 0.038 0.137 4920 Planarity : 0.003 0.028 5880 Dihedral : 4.353 15.775 4464 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.69 % Allowed : 4.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.13), residues: 4032 helix: 2.52 (0.09), residues: 3288 sheet: None (None), residues: 0 loop : -0.22 (0.28), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 89 HIS 0.002 0.001 HIS D 114 PHE 0.020 0.003 PHE J 35 TYR 0.022 0.002 TYR G 164 ARG 0.012 0.001 ARG J 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 3 GLN cc_start: 0.8280 (pt0) cc_final: 0.8075 (tt0) REVERT: R 5 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7726 (ttp80) REVERT: R 6 GLN cc_start: 0.8084 (tt0) cc_final: 0.7705 (tt0) REVERT: R 7 ASN cc_start: 0.8202 (t0) cc_final: 0.7876 (t0) REVERT: R 44 LEU cc_start: 0.9384 (mp) cc_final: 0.9115 (mm) REVERT: R 67 LYS cc_start: 0.9485 (tptt) cc_final: 0.9150 (tppt) REVERT: R 82 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8005 (tp-100) REVERT: R 83 LYS cc_start: 0.8529 (pttt) cc_final: 0.8221 (mmtt) REVERT: R 96 MET cc_start: 0.8516 (mmm) cc_final: 0.8217 (mmm) REVERT: R 104 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9053 (mmmt) REVERT: R 106 LEU cc_start: 0.9539 (mt) cc_final: 0.9337 (mt) REVERT: R 142 LYS cc_start: 0.9420 (tptp) cc_final: 0.8894 (tptt) REVERT: R 146 ASP cc_start: 0.9013 (m-30) cc_final: 0.8691 (m-30) REVERT: R 149 THR cc_start: 0.8126 (m) cc_final: 0.7328 (m) REVERT: R 153 ARG cc_start: 0.8827 (ptm160) cc_final: 0.8254 (ptp-170) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1810 time to fit residues: 20.3537 Evaluate side-chains 80 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 336 optimal weight: 0.0060 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 353 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 71 GLN R 108 GLN R 132 HIS R 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.7957 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= 0.206 Angle : 0.628 6.769 44784 Z= 0.326 Chirality : 0.040 0.147 4920 Planarity : 0.005 0.063 5880 Dihedral : 4.556 19.781 4464 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.14), residues: 4032 helix: 2.45 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -0.35 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 89 HIS 0.003 0.001 HIS D 124 PHE 0.014 0.002 PHE X 35 TYR 0.021 0.003 TYR J 28 ARG 0.009 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 3 GLN cc_start: 0.8427 (pt0) cc_final: 0.8156 (tt0) REVERT: R 5 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7380 (ttp80) REVERT: R 6 GLN cc_start: 0.8010 (tt0) cc_final: 0.7608 (tt0) REVERT: R 7 ASN cc_start: 0.8255 (t0) cc_final: 0.7933 (t0) REVERT: R 60 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8309 (tm-30) REVERT: R 67 LYS cc_start: 0.9548 (tptt) cc_final: 0.9150 (tppt) REVERT: R 69 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8596 (tp-100) REVERT: R 82 GLN cc_start: 0.8492 (tp-100) cc_final: 0.7990 (tp-100) REVERT: R 83 LYS cc_start: 0.8483 (pttt) cc_final: 0.8202 (mmtt) REVERT: R 104 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9100 (mmmt) REVERT: R 106 LEU cc_start: 0.9573 (mt) cc_final: 0.9366 (mt) REVERT: R 124 HIS cc_start: 0.9065 (t-90) cc_final: 0.8737 (t-90) REVERT: R 127 ASP cc_start: 0.8768 (t70) cc_final: 0.8532 (p0) REVERT: R 141 ILE cc_start: 0.9085 (pt) cc_final: 0.8620 (pt) REVERT: R 142 LYS cc_start: 0.9363 (tptp) cc_final: 0.8915 (tptt) REVERT: R 149 THR cc_start: 0.8106 (m) cc_final: 0.7817 (m) REVERT: R 168 ARG cc_start: 0.8756 (tpm170) cc_final: 0.7134 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1629 time to fit residues: 18.0649 Evaluate side-chains 79 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.4980 chunk 355 optimal weight: 0.0050 chunk 77 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 327 optimal weight: 0.0980 chunk 182 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33264 Z= 0.177 Angle : 0.639 6.704 44784 Z= 0.330 Chirality : 0.038 0.139 4920 Planarity : 0.003 0.019 5880 Dihedral : 4.809 23.616 4464 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.00 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.14), residues: 4032 helix: 2.12 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.56 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP O 89 HIS 0.003 0.001 HIS E 132 PHE 0.014 0.002 PHE U 166 TYR 0.019 0.002 TYR R 164 ARG 0.005 0.001 ARG I 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7392 Ramachandran restraints generated. 3696 Oldfield, 0 Emsley, 3696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 5 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7496 (ttp80) REVERT: R 6 GLN cc_start: 0.8091 (tt0) cc_final: 0.7624 (tt0) REVERT: R 7 ASN cc_start: 0.7701 (t0) cc_final: 0.7367 (t0) REVERT: R 60 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8512 (tm-30) REVERT: R 67 LYS cc_start: 0.9547 (tptt) cc_final: 0.9243 (tppt) REVERT: R 82 GLN cc_start: 0.8414 (tp-100) cc_final: 0.8074 (tp40) REVERT: R 83 LYS cc_start: 0.8448 (pttt) cc_final: 0.8162 (mmtt) REVERT: R 104 LYS cc_start: 0.9453 (mmmt) cc_final: 0.9154 (mmmt) REVERT: R 124 HIS cc_start: 0.9019 (t-90) cc_final: 0.8658 (t-90) REVERT: R 127 ASP cc_start: 0.8697 (t70) cc_final: 0.8457 (p0) REVERT: R 142 LYS cc_start: 0.9301 (tptp) cc_final: 0.8860 (tppt) REVERT: R 144 MET cc_start: 0.9403 (ptm) cc_final: 0.9159 (ptm) REVERT: R 147 HIS cc_start: 0.8936 (m-70) cc_final: 0.8504 (m-70) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1660 time to fit residues: 19.0488 Evaluate side-chains 88 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 220 optimal weight: 0.0970 chunk 393 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 0.2980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 17 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 33264 Z= 0.183 Angle : 0.682 6.553 44784 Z= 0.349 Chirality : 0.039 0.131 4920 Planarity : 0.005 0.043 5880 Dihedral : 4.781 22.943 4464 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.14), residues: 4032 helix: 2.13 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -0.53 (0.25), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP O 89 HIS 0.001 0.001 HIS X 114 PHE 0.014 0.002 PHE I 35 TYR 0.022 0.003 TYR J 23 ARG 0.006 0.001 ARG U 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 ASN cc_start: 0.7459 (t0) cc_final: 0.7218 (t0) REVERT: K 45 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8599 (tm-30) REVERT: K 60 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8413 (tm-30) REVERT: K 82 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7753 (tp40) REVERT: K 83 LYS cc_start: 0.8541 (pttt) cc_final: 0.8150 (mmtt) REVERT: K 104 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9072 (mmmt) REVERT: K 106 LEU cc_start: 0.9556 (mt) cc_final: 0.9354 (mt) REVERT: K 127 ASP cc_start: 0.8704 (t70) cc_final: 0.8481 (p0) REVERT: K 129 LEU cc_start: 0.9285 (mt) cc_final: 0.8961 (tt) REVERT: K 142 LYS cc_start: 0.9308 (tptp) cc_final: 0.8846 (tppt) REVERT: K 144 MET cc_start: 0.9236 (ptm) cc_final: 0.8975 (ptm) REVERT: K 147 HIS cc_start: 0.8921 (m-70) cc_final: 0.8508 (m-70) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1769 time to fit residues: 20.6533 Evaluate side-chains 85 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 0.0670 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.8777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 33264 Z= 0.191 Angle : 0.661 6.007 44784 Z= 0.341 Chirality : 0.038 0.133 4920 Planarity : 0.004 0.035 5880 Dihedral : 4.728 21.254 4464 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 19.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.13), residues: 4032 helix: 2.01 (0.09), residues: 3240 sheet: None (None), residues: 0 loop : -0.60 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP I 89 HIS 0.002 0.001 HIS X 147 PHE 0.015 0.002 PHE M 35 TYR 0.022 0.003 TYR U 164 ARG 0.005 0.001 ARG U 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8224 (tt0) cc_final: 0.7298 (tp40) REVERT: H 18 ARG cc_start: 0.7895 (mmp80) cc_final: 0.7663 (mmp80) REVERT: H 45 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8618 (tm-30) REVERT: H 60 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8291 (tm-30) REVERT: H 82 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7711 (tp40) REVERT: H 83 LYS cc_start: 0.8535 (pttt) cc_final: 0.8088 (mmtt) REVERT: H 104 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9178 (mmmt) REVERT: H 127 ASP cc_start: 0.8687 (t70) cc_final: 0.8465 (p0) REVERT: H 142 LYS cc_start: 0.9274 (tptp) cc_final: 0.8894 (tppt) REVERT: H 144 MET cc_start: 0.9335 (ptm) cc_final: 0.8698 (ptm) REVERT: H 147 HIS cc_start: 0.8903 (m-70) cc_final: 0.8329 (m-70) REVERT: H 168 ARG cc_start: 0.8801 (tpm170) cc_final: 0.7018 (tpt170) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1489 time to fit residues: 16.6723 Evaluate side-chains 77 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 343 optimal weight: 10.0000 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 0.0970 chunk 159 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 365 optimal weight: 0.1980 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 17 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.9055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33264 Z= 0.210 Angle : 0.729 8.388 44784 Z= 0.370 Chirality : 0.041 0.127 4920 Planarity : 0.005 0.041 5880 Dihedral : 4.869 22.762 4464 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.69 % Allowed : 0.00 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.13), residues: 4032 helix: 1.50 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : -0.74 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 89 HIS 0.002 0.001 HIS M 124 PHE 0.015 0.002 PHE U 35 TYR 0.033 0.003 TYR U 23 ARG 0.005 0.001 ARG M 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 5 ARG cc_start: 0.7705 (ttp80) cc_final: 0.7487 (ttp80) REVERT: K 6 GLN cc_start: 0.8184 (tt0) cc_final: 0.7238 (tp40) REVERT: K 18 ARG cc_start: 0.7876 (mmp80) cc_final: 0.7665 (mmp80) REVERT: K 45 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8554 (tm-30) REVERT: K 60 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8256 (tm-30) REVERT: K 82 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7774 (tp40) REVERT: K 83 LYS cc_start: 0.8481 (pttt) cc_final: 0.8060 (mmtt) REVERT: K 104 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9179 (mmmt) REVERT: K 127 ASP cc_start: 0.8781 (t70) cc_final: 0.8456 (p0) REVERT: K 142 LYS cc_start: 0.9331 (tptp) cc_final: 0.8950 (tppt) REVERT: K 147 HIS cc_start: 0.8860 (m-70) cc_final: 0.8537 (m-70) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.1548 time to fit residues: 18.0568 Evaluate side-chains 81 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 7.9990 chunk 387 optimal weight: 0.7980 chunk 236 optimal weight: 0.1980 chunk 183 optimal weight: 7.9990 chunk 269 optimal weight: 0.0770 chunk 406 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 323 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 chunk 198 optimal weight: 6.9990 overall best weight: 1.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.9154 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= 0.181 Angle : 0.705 8.893 44784 Z= 0.353 Chirality : 0.039 0.123 4920 Planarity : 0.004 0.038 5880 Dihedral : 4.661 20.902 4464 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.13), residues: 4032 helix: 1.77 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.92 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 89 HIS 0.002 0.000 HIS U 114 PHE 0.011 0.002 PHE O 166 TYR 0.025 0.003 TYR P 164 ARG 0.006 0.001 ARG J 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6720 Ramachandran restraints generated. 3360 Oldfield, 0 Emsley, 3360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 59 ARG cc_start: 0.8895 (ttt-90) cc_final: 0.8573 (tpp80) REVERT: R 60 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8251 (tm-30) REVERT: R 82 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7750 (tp40) REVERT: R 104 LYS cc_start: 0.9364 (mmmt) cc_final: 0.9104 (mmmt) REVERT: R 124 HIS cc_start: 0.8950 (t-90) cc_final: 0.8591 (t-90) REVERT: R 127 ASP cc_start: 0.8661 (t70) cc_final: 0.8422 (p0) REVERT: R 142 LYS cc_start: 0.9329 (tptp) cc_final: 0.8936 (tppt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1352 time to fit residues: 14.8532 Evaluate side-chains 81 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 5.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 0.0570 chunk 298 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 324 optimal weight: 0.0070 chunk 135 optimal weight: 2.9990 chunk 332 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.9118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 17 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.100738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091534 restraints weight = 3944.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094142 restraints weight = 2258.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095730 restraints weight = 1434.901| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.9483 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= 0.190 Angle : 0.744 8.518 44784 Z= 0.368 Chirality : 0.039 0.119 4920 Planarity : 0.004 0.036 5880 Dihedral : 5.097 21.089 4464 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.69 % Allowed : 0.00 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.13), residues: 4032 helix: 1.96 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -1.56 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 89 HIS 0.002 0.000 HIS H 114 PHE 0.014 0.002 PHE U 35 TYR 0.011 0.002 TYR F 23 ARG 0.004 0.001 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3705.40 seconds wall clock time: 69 minutes 37.21 seconds (4177.21 seconds total)