Starting phenix.real_space_refine (version: dev) on Tue Apr 5 14:39:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/04_2022/6bze_7314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/04_2022/6bze_7314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/04_2022/6bze_7314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/04_2022/6bze_7314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/04_2022/6bze_7314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bze_7314/04_2022/6bze_7314.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 sd= 0.020 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7072 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "B" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "C" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "D" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "F" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "G" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "H" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 104} Time building chain proxies: 4.49, per 1000 atoms: 0.63 Number of scatterers: 7072 At special positions: 0 Unit cell: (105.7, 105.7, 87.58, 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 16 16.00 O 1352 8.00 N 1296 7.00 C 4408 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: 3.10 Conformation dependent library (CDL) restraints added in 955.5 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.778A pdb=" N VAL A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 18 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.213A pdb=" N ARG A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.834A pdb=" N GLU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.709A pdb=" N LEU A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.521A pdb=" N VAL A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 115 removed outlier: 3.568A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.691A pdb=" N VAL B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 38 through 44 removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 44 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.922A pdb=" N GLU B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.927A pdb=" N LEU B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 95 through 115 removed outlier: 3.808A pdb=" N LEU B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 25 removed outlier: 3.634A pdb=" N VAL C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS C 18 " --> pdb=" O THR C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.216A pdb=" N ARG C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 44 " --> pdb=" O HIS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.844A pdb=" N GLU C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 73 removed outlier: 3.891A pdb=" N LEU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.502A pdb=" N VAL C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 115 removed outlier: 3.649A pdb=" N LEU C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.810A pdb=" N VAL D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 18 " --> pdb=" O THR D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 38 through 44 removed outlier: 4.478A pdb=" N ARG D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS D 44 " --> pdb=" O HIS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.530A pdb=" N GLU D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 75 removed outlier: 4.003A pdb=" N LEU D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 75 " --> pdb=" O TYR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 95 through 115 removed outlier: 3.684A pdb=" N LEU D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 25 removed outlier: 3.736A pdb=" N VAL E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS E 18 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 38 through 44 removed outlier: 4.343A pdb=" N ARG E 42 " --> pdb=" O PHE E 38 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS E 44 " --> pdb=" O HIS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.862A pdb=" N GLU E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 72 removed outlier: 4.102A pdb=" N LEU E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 95 through 115 removed outlier: 3.658A pdb=" N LEU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 38 through 44 removed outlier: 4.390A pdb=" N ARG F 42 " --> pdb=" O PHE F 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 44 " --> pdb=" O HIS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.881A pdb=" N GLU F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG F 58 " --> pdb=" O GLU F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.089A pdb=" N LEU F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 95 through 115 removed outlier: 3.702A pdb=" N LEU F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 25 removed outlier: 3.914A pdb=" N VAL G 16 " --> pdb=" O ASP G 12 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 38 through 44 removed outlier: 4.369A pdb=" N ARG G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 44 " --> pdb=" O HIS G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.820A pdb=" N GLU G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG G 58 " --> pdb=" O GLU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 72 removed outlier: 4.103A pdb=" N LEU G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 87 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.580A pdb=" N LEU G 114 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 115 " --> pdb=" O LEU G 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 25 removed outlier: 3.699A pdb=" N VAL H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 Processing helix chain 'H' and resid 38 through 44 removed outlier: 4.412A pdb=" N ARG H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 44 " --> pdb=" O HIS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 58 removed outlier: 3.790A pdb=" N GLU H 53 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 58 " --> pdb=" O GLU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 72 removed outlier: 3.856A pdb=" N LEU H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 87 Processing helix chain 'H' and resid 95 through 115 removed outlier: 3.778A pdb=" N LEU H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 963 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: 1.59 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1247 1.28 - 1.41: 1457 1.41 - 1.54: 4361 1.54 - 1.68: 47 1.68 - 1.81: 16 Bond restraints: 7128 Sorted by residual: bond pdb=" C GLU B 74 " pdb=" O GLU B 74 " ideal model delta sigma weight residual 1.235 1.145 0.091 1.26e-02 6.30e+03 5.18e+01 bond pdb=" C GLU D 74 " pdb=" O GLU D 74 " ideal model delta sigma weight residual 1.235 1.151 0.084 1.26e-02 6.30e+03 4.49e+01 bond pdb=" C GLU A 74 " pdb=" O GLU A 74 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.46e+01 bond pdb=" C GLU C 74 " pdb=" O GLU C 74 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.26e-02 6.30e+03 3.19e+01 bond pdb=" ND1 HIS G 40 " pdb=" CE1 HIS G 40 " ideal model delta sigma weight residual 1.321 1.359 -0.038 1.00e-02 1.00e+04 1.46e+01 ... (remaining 7123 not shown) Histogram of bond angle deviations from ideal: 101.89 - 108.29: 242 108.29 - 114.69: 4360 114.69 - 121.09: 2852 121.09 - 127.49: 2040 127.49 - 133.89: 26 Bond angle restraints: 9520 Sorted by residual: angle pdb=" N THR F 100 " pdb=" CA THR F 100 " pdb=" C THR F 100 " ideal model delta sigma weight residual 111.36 101.89 9.47 1.09e+00 8.42e-01 7.55e+01 angle pdb=" N THR H 100 " pdb=" CA THR H 100 " pdb=" C THR H 100 " ideal model delta sigma weight residual 111.82 101.98 9.84 1.16e+00 7.43e-01 7.20e+01 angle pdb=" N THR G 100 " pdb=" CA THR G 100 " pdb=" C THR G 100 " ideal model delta sigma weight residual 111.36 102.22 9.14 1.09e+00 8.42e-01 7.03e+01 angle pdb=" N THR A 100 " pdb=" CA THR A 100 " pdb=" C THR A 100 " ideal model delta sigma weight residual 111.36 102.30 9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N THR C 100 " pdb=" CA THR C 100 " pdb=" C THR C 100 " ideal model delta sigma weight residual 111.36 102.68 8.68 1.09e+00 8.42e-01 6.35e+01 ... (remaining 9515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 3971 17.56 - 35.13: 430 35.13 - 52.69: 124 52.69 - 70.25: 42 70.25 - 87.81: 17 Dihedral angle restraints: 4584 sinusoidal: 2064 harmonic: 2520 Sorted by residual: dihedral pdb=" CA SER A 56 " pdb=" C SER A 56 " pdb=" N CYS A 57 " pdb=" CA CYS A 57 " ideal model delta harmonic sigma weight residual -180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C PHE B 38 " pdb=" N PHE B 38 " pdb=" CA PHE B 38 " pdb=" CB PHE B 38 " ideal model delta harmonic sigma weight residual -122.60 -131.30 8.70 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CG ARG D 49 " pdb=" CD ARG D 49 " pdb=" NE ARG D 49 " pdb=" CZ ARG D 49 " ideal model delta sinusoidal sigma weight residual 90.00 41.95 48.05 2 1.50e+01 4.44e-03 1.18e+01 ... (remaining 4581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 756 0.079 - 0.157: 286 0.157 - 0.236: 54 0.236 - 0.315: 5 0.315 - 0.394: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA PHE B 38 " pdb=" N PHE B 38 " pdb=" C PHE B 38 " pdb=" CB PHE B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA PHE D 38 " pdb=" N PHE D 38 " pdb=" C PHE D 38 " pdb=" CB PHE D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA PHE A 38 " pdb=" N PHE A 38 " pdb=" C PHE A 38 " pdb=" CB PHE A 38 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1101 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.036 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE F 94 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 92 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C GLN B 92 " -0.058 2.00e-02 2.50e+03 pdb=" O GLN B 92 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN B 93 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 37 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C HIS F 37 " -0.053 2.00e-02 2.50e+03 pdb=" O HIS F 37 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE F 38 " 0.018 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 87 2.30 - 2.95: 4208 2.95 - 3.60: 11653 3.60 - 4.25: 17484 4.25 - 4.90: 26284 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" OG SER D 48 " pdb=" NE2 HIS H 37 " model vdw 1.648 2.520 nonbonded pdb=" OD2 ASP A 70 " pdb=" NH2 ARG D 49 " model vdw 1.789 2.520 nonbonded pdb=" OG SER A 48 " pdb=" NE2 HIS E 37 " model vdw 1.793 2.520 nonbonded pdb=" O ARG F 49 " pdb=" NH1 ARG F 49 " model vdw 1.879 2.520 nonbonded pdb=" O ARG C 49 " pdb=" NH1 ARG C 49 " model vdw 1.883 2.520 ... (remaining 59711 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 4408 2.51 5 N 1296 2.21 5 O 1352 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.050 Process input model: 21.720 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4770 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 : 0.009 0.091 7128 Z= 0.563 Angle : 1.421 10.371 9520 Z= 1.027 Chirality : 0.082 0.394 1104 Planarity : 0.005 0.033 1216 Dihedral : 17.335 87.814 2920 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 79.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.22 % Favored : 86.42 % Rotamer Outliers : 9.00 % 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: -5.34 (0.22), residues: 832 helix: -4.12 (0.14), residues: 528 sheet: None (None), residues: 0 loop : -1.99 (0.32), residues: 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 426 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 18 residues processed: 470 average time/residue: 0.2663 time to fit residues: 152.3509 Evaluate side-chains 298 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 280 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2065 time to fit residues: 5.9934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 97 GLN B 37 HIS B 92 GLN B 97 GLN B 113 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN C 97 GLN D 37 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 113 HIS F 23 ASN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN F 113 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 HIS ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4857 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 7128 Z= 0.295 Angle : 0.944 8.569 9520 Z= 0.508 Chirality : 0.053 0.398 1104 Planarity : 0.006 0.048 1216 Dihedral : 6.139 18.227 944 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 34.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 7.25 % 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: -3.73 (0.26), residues: 832 helix: -2.16 (0.19), residues: 584 sheet: None (None), residues: 0 loop : -2.82 (0.39), residues: 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 366 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 30 residues processed: 395 average time/residue: 0.2747 time to fit residues: 131.9435 Evaluate side-chains 299 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 269 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.0798 time to fit residues: 5.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 50.0000 chunk 22 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 49 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN F 23 ASN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN G 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4938 moved from start: 0.8917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 7128 Z= 0.299 Angle : 0.900 12.039 9520 Z= 0.475 Chirality : 0.050 0.325 1104 Planarity : 0.006 0.101 1216 Dihedral : 6.552 57.897 944 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 34.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 5.75 % 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: -2.62 (0.28), residues: 832 helix: -1.14 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -2.93 (0.37), residues: 248 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 327 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 355 average time/residue: 0.2586 time to fit residues: 111.6645 Evaluate side-chains 284 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0901 time to fit residues: 4.5503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 0.0020 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 108 ASN C 113 HIS D 37 HIS D 73 GLN F 23 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4929 moved from start: 0.9875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 7128 Z= 0.255 Angle : 0.820 10.993 9520 Z= 0.435 Chirality : 0.048 0.281 1104 Planarity : 0.005 0.038 1216 Dihedral : 6.522 59.100 944 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer Outliers : 4.12 % 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: -2.33 (0.28), residues: 832 helix: -0.86 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -3.07 (0.38), residues: 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 306 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 319 average time/residue: 0.2647 time to fit residues: 103.4114 Evaluate side-chains 256 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 242 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1051 time to fit residues: 3.5422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 53 optimal weight: 0.0770 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 108 ASN D 73 GLN F 23 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4933 moved from start: 1.0479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7128 Z= 0.265 Angle : 0.814 8.755 9520 Z= 0.430 Chirality : 0.048 0.250 1104 Planarity : 0.005 0.093 1216 Dihedral : 6.543 59.845 944 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 30.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer Outliers : 4.62 % 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: -2.53 (0.28), residues: 832 helix: -0.85 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -3.82 (0.33), residues: 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 275 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 290 average time/residue: 0.2520 time to fit residues: 90.3515 Evaluate side-chains 269 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 248 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0819 time to fit residues: 4.1673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 40 optimal weight: 50.0000 chunk 74 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN D 40 HIS D 73 GLN F 37 HIS ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 moved from start: 1.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7128 Z= 0.232 Angle : 0.807 13.991 9520 Z= 0.420 Chirality : 0.047 0.178 1104 Planarity : 0.005 0.063 1216 Dihedral : 6.373 58.045 944 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 2.50 % 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: -2.37 (0.29), residues: 832 helix: -0.75 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.71 (0.35), residues: 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 284 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 293 average time/residue: 0.2508 time to fit residues: 91.2775 Evaluate side-chains 260 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 253 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0739 time to fit residues: 2.2236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 40.0000 chunk 46 optimal weight: 0.1980 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN H 23 ASN ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4949 moved from start: 1.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 7128 Z= 0.231 Angle : 0.854 14.153 9520 Z= 0.436 Chirality : 0.047 0.179 1104 Planarity : 0.005 0.046 1216 Dihedral : 6.283 57.847 944 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer Outliers : 3.12 % 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: -2.28 (0.29), residues: 832 helix: -0.69 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -3.67 (0.35), residues: 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 287 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 295 average time/residue: 0.2609 time to fit residues: 95.0876 Evaluate side-chains 270 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0705 time to fit residues: 2.9222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 40.0000 chunk 70 optimal weight: 40.0000 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS F 37 HIS ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4959 moved from start: 1.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 7128 Z= 0.250 Angle : 0.870 12.716 9520 Z= 0.447 Chirality : 0.047 0.184 1104 Planarity : 0.005 0.044 1216 Dihedral : 6.301 58.775 944 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 28.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer Outliers : 2.00 % 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: -2.26 (0.29), residues: 832 helix: -0.64 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -3.66 (0.35), residues: 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 283 average time/residue: 0.2590 time to fit residues: 90.2687 Evaluate side-chains 255 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 248 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0669 time to fit residues: 2.1320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 47 optimal weight: 0.0870 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS C 37 HIS D 37 HIS F 37 HIS ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4956 moved from start: 1.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 7128 Z= 0.245 Angle : 0.909 15.349 9520 Z= 0.462 Chirality : 0.048 0.275 1104 Planarity : 0.005 0.041 1216 Dihedral : 6.342 57.535 944 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 27.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer Outliers : 1.62 % 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: -1.96 (0.29), residues: 832 helix: -0.26 (0.23), residues: 544 sheet: None (None), residues: 0 loop : -3.36 (0.33), residues: 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 266 average time/residue: 0.2645 time to fit residues: 86.8121 Evaluate side-chains 253 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 248 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1283 time to fit residues: 2.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 50 optimal weight: 40.0000 chunk 67 optimal weight: 40.0000 chunk 19 optimal weight: 0.5980 overall best weight: 3.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 113 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4975 moved from start: 1.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7128 Z= 0.241 Angle : 0.937 15.020 9520 Z= 0.476 Chirality : 0.048 0.264 1104 Planarity : 0.005 0.043 1216 Dihedral : 6.362 57.818 944 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 28.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.38 % Favored : 87.50 % Rotamer Outliers : 1.38 % 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: -2.06 (0.29), residues: 832 helix: -0.39 (0.23), residues: 552 sheet: None (None), residues: 0 loop : -3.36 (0.33), residues: 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 253 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 256 average time/residue: 0.2532 time to fit residues: 80.4424 Evaluate side-chains 245 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 238 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0703 time to fit residues: 2.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.134468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120577 restraints weight = 21170.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123160 restraints weight = 14176.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.124999 restraints weight = 10301.417| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 1.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7128 Z= 0.237 Angle : 0.935 15.187 9520 Z= 0.471 Chirality : 0.049 0.243 1104 Planarity : 0.005 0.041 1216 Dihedral : 6.337 58.046 944 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 28.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.18 % Favored : 88.58 % Rotamer Outliers : 1.00 % 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: -2.42 (0.29), residues: 832 helix: -0.81 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -3.55 (0.36), residues: 232 =============================================================================== Job complete usr+sys time: 2006.19 seconds wall clock time: 37 minutes 3.57 seconds (2223.57 seconds total)