Starting phenix.real_space_refine on Sun Dec 10 06:59:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/12_2023/8ixj_35793.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/12_2023/8ixj_35793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/12_2023/8ixj_35793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/12_2023/8ixj_35793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/12_2023/8ixj_35793.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixj_35793/12_2023/8ixj_35793.pdb" } resolution = 3.1 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= 0.000 sd= 0.004 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 40 5.16 5 C 9080 2.51 5 N 2160 2.21 5 O 2480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "L ASP 5": "OD1" <-> "OD2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 5": "OD1" <-> "OD2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "I ASP 5": "OD1" <-> "OD2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 5": "OD1" <-> "OD2" Residue "E ASP 5": "OD1" <-> "OD2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 5": "OD1" <-> "OD2" Residue "M TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 5": "OD1" <-> "OD2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "O ASP 5": "OD1" <-> "OD2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 5": "OD1" <-> "OD2" Residue "S ASP 5": "OD1" <-> "OD2" Residue "T GLU 20": "OE1" <-> "OE2" Residue "T TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 5": "OD1" <-> "OD2" Residue "V TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 5": "OD1" <-> "OD2" Residue "W GLU 20": "OE1" <-> "OE2" Residue "X ASP 5": "OD1" <-> "OD2" Residue "Z TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA ASP 5": "OD1" <-> "OD2" Residue "BA ASP 5": "OD1" <-> "OD2" Residue "CA GLU 20": "OE1" <-> "OE2" Residue "CA TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA ASP 5": "OD1" <-> "OD2" Residue "DA TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EA ASP 5": "OD1" <-> "OD2" Residue "EA GLU 20": "OE1" <-> "OE2" Residue "FA ASP 5": "OD1" <-> "OD2" Residue "HA TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IA ASP 5": "OD1" <-> "OD2" Residue "JA ASP 5": "OD1" <-> "OD2" Residue "KA GLU 20": "OE1" <-> "OE2" Residue "KA TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KA PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 5": "OD1" <-> "OD2" Residue "LA TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MA ASP 5": "OD1" <-> "OD2" Residue "MA GLU 20": "OE1" <-> "OE2" Residue "NA ASP 5": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13760 Number of models: 1 Model: "" Number of chains: 40 Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "F" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "H" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "J" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "D" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "K" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "R" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "S" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "T" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Y" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "FA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "GA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "HA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "IA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "JA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "KA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "LA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "MA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "NA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "OA" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 7.64, per 1000 atoms: 0.56 Number of scatterers: 13760 At special positions: 0 Unit cell: (78.57, 80.51, 194.97, 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 40 16.00 O 2480 8.00 N 2160 7.00 C 9080 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: 5.80 Conformation dependent library (CDL) restraints added in 2.3 seconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 97.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'B' and resid 5 through 50 Processing helix chain 'C' and resid 6 through 50 Processing helix chain 'L' and resid 6 through 50 Processing helix chain 'F' and resid 6 through 50 Processing helix chain 'G' and resid 6 through 50 Processing helix chain 'H' and resid 6 through 50 Processing helix chain 'I' and resid 6 through 50 Processing helix chain 'J' and resid 6 through 50 removed outlier: 3.940A pdb=" N VAL J 30 " --> pdb=" O TRP J 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL J 31 " --> pdb=" O ALA J 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 50 Processing helix chain 'D' and resid 6 through 50 Processing helix chain 'E' and resid 6 through 50 Processing helix chain 'K' and resid 6 through 50 Processing helix chain 'M' and resid 6 through 50 Processing helix chain 'N' and resid 6 through 50 Processing helix chain 'O' and resid 6 through 50 Processing helix chain 'P' and resid 6 through 50 removed outlier: 3.940A pdb=" N VAL P 30 " --> pdb=" O TRP P 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 50 Processing helix chain 'R' and resid 6 through 50 Processing helix chain 'S' and resid 6 through 50 Processing helix chain 'T' and resid 6 through 50 Processing helix chain 'V' and resid 6 through 50 Processing helix chain 'W' and resid 6 through 50 Processing helix chain 'X' and resid 6 through 50 Processing helix chain 'Y' and resid 6 through 50 removed outlier: 3.940A pdb=" N VAL Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 50 Processing helix chain 'AA' and resid 6 through 50 Processing helix chain 'BA' and resid 6 through 50 Processing helix chain 'CA' and resid 6 through 50 Processing helix chain 'DA' and resid 6 through 50 Processing helix chain 'EA' and resid 6 through 50 Processing helix chain 'FA' and resid 6 through 50 Processing helix chain 'GA' and resid 6 through 50 removed outlier: 3.940A pdb=" N VALGA 30 " --> pdb=" O TRPGA 26 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VALGA 31 " --> pdb=" O ALAGA 27 " (cutoff:3.500A) Processing helix chain 'HA' and resid 6 through 50 Processing helix chain 'IA' and resid 6 through 50 Processing helix chain 'JA' and resid 6 through 50 Processing helix chain 'KA' and resid 6 through 50 Processing helix chain 'LA' and resid 6 through 50 Processing helix chain 'MA' and resid 6 through 50 Processing helix chain 'NA' and resid 6 through 50 Processing helix chain 'OA' and resid 6 through 50 removed outlier: 3.940A pdb=" N VALOA 30 " --> pdb=" O TRPOA 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALOA 31 " --> pdb=" O ALAOA 27 " (cutoff:3.500A) 1631 hydrogen bonds defined for protein. 4893 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: 4.70 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2507 1.34 - 1.45: 3463 1.45 - 1.57: 7990 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 14040 Sorted by residual: bond pdb=" N VALIA 31 " pdb=" CA VALIA 31 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.96e+00 bond pdb=" N VALGA 29 " pdb=" CA VALGA 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.88e+00 bond pdb=" N VAL Y 29 " pdb=" CA VAL Y 29 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.87e+00 bond pdb=" N VAL C 31 " pdb=" CA VAL C 31 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.77e+00 bond pdb=" N VALOA 29 " pdb=" CA VALOA 29 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.72e+00 ... (remaining 14035 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.05: 280 107.05 - 113.88: 8032 113.88 - 120.70: 5864 120.70 - 127.52: 4739 127.52 - 134.34: 85 Bond angle restraints: 19000 Sorted by residual: angle pdb=" N PROMA 6 " pdb=" CA PROMA 6 " pdb=" C PROMA 6 " ideal model delta sigma weight residual 113.84 108.13 5.71 1.30e+00 5.92e-01 1.93e+01 angle pdb=" N PRO W 6 " pdb=" CA PRO W 6 " pdb=" C PRO W 6 " ideal model delta sigma weight residual 113.84 108.14 5.70 1.30e+00 5.92e-01 1.92e+01 angle pdb=" N PRO N 6 " pdb=" CA PRO N 6 " pdb=" C PRO N 6 " ideal model delta sigma weight residual 113.84 108.15 5.69 1.30e+00 5.92e-01 1.92e+01 angle pdb=" N PRO H 6 " pdb=" CA PRO H 6 " pdb=" C PRO H 6 " ideal model delta sigma weight residual 113.84 108.15 5.69 1.30e+00 5.92e-01 1.92e+01 angle pdb=" N PROEA 6 " pdb=" CA PROEA 6 " pdb=" C PROEA 6 " ideal model delta sigma weight residual 113.65 108.11 5.54 1.35e+00 5.49e-01 1.68e+01 ... (remaining 18995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.95: 7130 9.95 - 19.91: 702 19.91 - 29.86: 228 29.86 - 39.81: 115 39.81 - 49.77: 25 Dihedral angle restraints: 8200 sinusoidal: 2880 harmonic: 5320 Sorted by residual: dihedral pdb=" N LEUMA 14 " pdb=" CA LEUMA 14 " pdb=" CB LEUMA 14 " pdb=" CG LEUMA 14 " ideal model delta sinusoidal sigma weight residual -60.00 -109.77 49.77 3 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" N LEU W 14 " pdb=" CA LEU W 14 " pdb=" CB LEU W 14 " pdb=" CG LEU W 14 " ideal model delta sinusoidal sigma weight residual -60.00 -109.75 49.75 3 1.50e+01 4.44e-03 8.81e+00 dihedral pdb=" N LEU N 14 " pdb=" CA LEU N 14 " pdb=" CB LEU N 14 " pdb=" CG LEU N 14 " ideal model delta sinusoidal sigma weight residual -60.00 -109.75 49.75 3 1.50e+01 4.44e-03 8.81e+00 ... (remaining 8197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 530 0.040 - 0.080: 632 0.080 - 0.120: 661 0.120 - 0.160: 310 0.160 - 0.200: 107 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CB VALIA 31 " pdb=" CA VALIA 31 " pdb=" CG1 VALIA 31 " pdb=" CG2 VALIA 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.96e-01 chirality pdb=" CB VALAA 31 " pdb=" CA VALAA 31 " pdb=" CG1 VALAA 31 " pdb=" CG2 VALAA 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CB VAL D 31 " pdb=" CA VAL D 31 " pdb=" CG1 VAL D 31 " pdb=" CG2 VAL D 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.58e-01 ... (remaining 2237 not shown) Planarity restraints: 2280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 6 " 0.010 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C PRO Y 6 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO Y 6 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA Y 7 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROOA 6 " -0.010 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" C PROOA 6 " 0.038 2.00e-02 2.50e+03 pdb=" O PROOA 6 " -0.015 2.00e-02 2.50e+03 pdb=" N ALAOA 7 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO J 6 " -0.010 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C PRO J 6 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO J 6 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA J 7 " -0.013 2.00e-02 2.50e+03 ... (remaining 2277 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5230 2.91 - 3.41: 15533 3.41 - 3.90: 23177 3.90 - 4.40: 24320 4.40 - 4.90: 42826 Nonbonded interactions: 111086 Sorted by model distance: nonbonded pdb=" O PHEHA 42 " pdb=" OG1 THRHA 46 " model vdw 2.412 2.440 nonbonded pdb=" O PHE B 42 " pdb=" OG1 THR B 46 " model vdw 2.412 2.440 nonbonded pdb=" O PHE Z 42 " pdb=" OG1 THR Z 46 " model vdw 2.412 2.440 nonbonded pdb=" O PHE Q 42 " pdb=" OG1 THR Q 46 " model vdw 2.412 2.440 nonbonded pdb=" O PHE A 42 " pdb=" OG1 THR A 46 " model vdw 2.413 2.440 ... (remaining 111081 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 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'KA' selection = chain 'L' selection = chain 'LA' selection = chain 'M' selection = chain 'MA' selection = chain 'N' selection = chain 'NA' selection = chain 'O' selection = chain 'OA' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 3.710 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.810 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 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 : 0.012 0.038 14040 Z= 0.768 Angle : 1.449 5.711 19000 Z= 1.229 Chirality : 0.092 0.200 2240 Planarity : 0.004 0.022 2280 Dihedral : 10.466 49.766 4760 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 3.48 (0.16), residues: 1760 helix: 2.29 (0.10), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 26 PHE 0.012 0.002 PHEOA 11 TYR 0.012 0.002 TYR P 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.553 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.3405 time to fit residues: 96.5370 Evaluate side-chains 166 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN H 12 ASN K 12 ASN M 12 ASN N 12 ASN T 12 ASN V 12 ASN W 12 ASN CA 12 ASN DA 12 ASN EA 12 ASN HA 12 ASN KA 12 ASN LA 12 ASN MA 12 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 14040 Z= 0.150 Angle : 0.336 3.615 19000 Z= 0.201 Chirality : 0.031 0.106 2240 Planarity : 0.002 0.012 2280 Dihedral : 3.907 35.784 1920 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.44 % Allowed : 6.76 % Favored : 92.79 % 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: 6.73 (0.15), residues: 1760 helix: 4.30 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPBA 26 PHE 0.008 0.001 PHE E 11 TYR 0.030 0.002 TYR R 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 263 time to evaluate : 1.507 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 266 average time/residue: 0.3235 time to fit residues: 116.5158 Evaluate side-chains 216 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1132 time to fit residues: 2.1385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN HA 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14040 Z= 0.154 Angle : 0.317 3.546 19000 Z= 0.189 Chirality : 0.030 0.111 2240 Planarity : 0.002 0.015 2280 Dihedral : 3.225 29.945 1920 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 9.71 % Favored : 89.34 % 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: 7.22 (0.14), residues: 1760 helix: 4.60 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 26 PHE 0.006 0.001 PHE B 45 TYR 0.020 0.001 TYRIA 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 254 time to evaluate : 1.404 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 256 average time/residue: 0.3079 time to fit residues: 107.8693 Evaluate side-chains 247 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1187 time to fit residues: 4.2267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.0870 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN DA 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14040 Z= 0.130 Angle : 0.297 3.375 19000 Z= 0.176 Chirality : 0.030 0.115 2240 Planarity : 0.002 0.014 2280 Dihedral : 2.965 28.660 1920 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.59 % Allowed : 10.59 % Favored : 88.82 % 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: 7.40 (0.14), residues: 1760 helix: 4.71 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 26 PHE 0.006 0.001 PHE A 45 TYR 0.014 0.001 TYR Z 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 251 time to evaluate : 1.603 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 251 average time/residue: 0.3342 time to fit residues: 114.9904 Evaluate side-chains 246 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 1.456 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3162 time to fit residues: 4.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14040 Z= 0.146 Angle : 0.300 3.431 19000 Z= 0.179 Chirality : 0.030 0.120 2240 Planarity : 0.002 0.014 2280 Dihedral : 2.956 29.824 1920 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.74 % Allowed : 12.28 % Favored : 86.99 % 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: 7.29 (0.14), residues: 1760 helix: 4.65 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 26 PHE 0.008 0.001 PHELA 42 TYR 0.021 0.001 TYRIA 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 1.500 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 248 average time/residue: 0.3023 time to fit residues: 103.0424 Evaluate side-chains 250 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2279 time to fit residues: 4.7005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14040 Z= 0.167 Angle : 0.311 3.467 19000 Z= 0.186 Chirality : 0.030 0.110 2240 Planarity : 0.002 0.014 2280 Dihedral : 3.085 33.540 1920 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.07 % Allowed : 12.79 % Favored : 87.13 % 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: 7.18 (0.14), residues: 1760 helix: 4.58 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 26 PHE 0.007 0.001 PHE E 45 TYR 0.019 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 260 time to evaluate : 1.473 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.3066 time to fit residues: 110.2670 Evaluate side-chains 250 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14040 Z= 0.211 Angle : 0.333 3.543 19000 Z= 0.200 Chirality : 0.031 0.126 2240 Planarity : 0.002 0.016 2280 Dihedral : 3.355 37.385 1920 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.51 % Allowed : 13.75 % Favored : 85.74 % 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: 6.94 (0.14), residues: 1760 helix: 4.43 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 26 PHE 0.008 0.001 PHE E 45 TYR 0.022 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 256 time to evaluate : 1.450 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 258 average time/residue: 0.2979 time to fit residues: 107.1134 Evaluate side-chains 255 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 250 time to evaluate : 1.484 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1129 time to fit residues: 3.0757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN Q 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14040 Z= 0.135 Angle : 0.296 3.435 19000 Z= 0.179 Chirality : 0.030 0.124 2240 Planarity : 0.002 0.024 2280 Dihedral : 2.940 29.840 1920 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.37 % Allowed : 13.75 % Favored : 85.88 % 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: 7.24 (0.14), residues: 1760 helix: 4.62 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP V 26 PHE 0.006 0.001 PHE E 45 TYR 0.022 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 253 time to evaluate : 1.477 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 253 average time/residue: 0.3038 time to fit residues: 105.5349 Evaluate side-chains 250 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 246 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2694 time to fit residues: 3.5154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 143 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14040 Z= 0.156 Angle : 0.310 3.478 19000 Z= 0.187 Chirality : 0.031 0.123 2240 Planarity : 0.002 0.022 2280 Dihedral : 2.925 27.068 1920 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.44 % Allowed : 14.56 % Favored : 85.00 % 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: 7.13 (0.14), residues: 1760 helix: 4.55 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 26 PHE 0.006 0.001 PHE E 45 TYR 0.023 0.001 TYRHA 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 1.506 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 247 average time/residue: 0.2945 time to fit residues: 101.0967 Evaluate side-chains 249 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 244 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1266 time to fit residues: 3.2422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14040 Z= 0.140 Angle : 0.309 4.605 19000 Z= 0.189 Chirality : 0.031 0.141 2240 Planarity : 0.002 0.021 2280 Dihedral : 2.836 26.443 1920 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.07 % Allowed : 14.85 % Favored : 85.07 % 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: 7.15 (0.14), residues: 1760 helix: 4.56 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 26 PHE 0.006 0.001 PHE E 45 TYR 0.023 0.001 TYRHA 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.455 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.3072 time to fit residues: 105.0557 Evaluate side-chains 245 residues out of total 1360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.591 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.118125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.089717 restraints weight = 16280.267| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.55 r_work: 0.3046 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14040 Z= 0.169 Angle : 0.321 4.111 19000 Z= 0.195 Chirality : 0.031 0.132 2240 Planarity : 0.002 0.021 2280 Dihedral : 2.953 29.486 1920 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.22 % Allowed : 15.00 % Favored : 84.78 % 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: 6.99 (0.15), residues: 1760 helix: 4.46 (0.09), residues: 1760 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 26 PHE 0.007 0.001 PHE E 45 TYR 0.023 0.001 TYRHA 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.34 seconds wall clock time: 52 minutes 28.15 seconds (3148.15 seconds total)