Starting phenix.real_space_refine (version: dev) on Mon Apr 4 14:39:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/04_2022/5oh0_3809_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/04_2022/5oh0_3809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/04_2022/5oh0_3809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/04_2022/5oh0_3809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/04_2022/5oh0_3809_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/04_2022/5oh0_3809_neut.pdb" } resolution = 4.2 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= 0.001 sd= 0.005 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 ARG 136": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 6588 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "B" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "C" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "D" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "E" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain: "F" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1098 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 2, 'TRANS': 154} Time building chain proxies: 4.17, per 1000 atoms: 0.63 Number of scatterers: 6588 At special positions: 0 Unit cell: (87.01, 84.75, 84.75, 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 12 16.00 O 1386 8.00 N 1158 7.00 C 4032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 21 " - pdb=" SG CYS F 61 " distance=2.03 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: 2.28 Conformation dependent library (CDL) restraints added in 1.3 seconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 5.2% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 38 through 42 Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'F' and resid 25 through 28 removed outlier: 4.033A pdb=" N VAL F 28 " --> pdb=" O ALA F 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 25 through 28' Processing helix chain 'F' and resid 38 through 42 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR A 48 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA A 139 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER A 50 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR A 137 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.967A pdb=" N GLN A 30 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS B 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 32 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU B 15 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE A 154 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR B 9 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 152 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 33 removed outlier: 6.967A pdb=" N GLN A 30 " --> pdb=" O HIS B 11 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS B 13 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A 32 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N GLU B 15 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 148 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 16 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR B 48 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 139 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 50 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR B 137 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.970A pdb=" N GLN B 30 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LYS C 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 32 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLU C 15 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE B 154 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR C 9 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ALA B 152 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.970A pdb=" N GLN B 30 " --> pdb=" O HIS C 11 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LYS C 13 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 32 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N GLU C 15 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 148 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL C 16 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR C 48 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA C 139 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER C 50 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR C 137 " --> pdb=" O SER C 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 35 removed outlier: 3.788A pdb=" N GLN C 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 32 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU D 15 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE C 154 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR D 9 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA C 152 " --> pdb=" O THR D 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 35 removed outlier: 3.788A pdb=" N GLN C 30 " --> pdb=" O THR D 9 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 32 " --> pdb=" O HIS D 11 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU D 15 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA C 148 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL D 16 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 22 through 23 removed outlier: 6.518A pdb=" N THR D 48 " --> pdb=" O ALA D 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA D 139 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER D 50 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR D 137 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.940A pdb=" N GLN D 30 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS E 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 32 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU E 15 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N PHE D 154 " --> pdb=" O GLY E 7 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR E 9 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA D 152 " --> pdb=" O THR E 9 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.940A pdb=" N GLN D 30 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LYS E 13 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL D 32 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU E 15 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 148 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 16 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 22 through 23 removed outlier: 6.518A pdb=" N THR E 48 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA E 139 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER E 50 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR E 137 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 35 removed outlier: 3.720A pdb=" N GLN E 30 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 32 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU F 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE E 154 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR F 9 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA E 152 " --> pdb=" O THR F 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 29 through 35 removed outlier: 3.720A pdb=" N GLN E 30 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL E 32 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLU F 15 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 148 " --> pdb=" O GLY F 14 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 16 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 22 through 23 removed outlier: 6.519A pdb=" N THR F 48 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA F 139 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER F 50 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR F 137 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 70 through 74 145 hydrogen bonds defined for protein. 312 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: 1.74 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2328 1.34 - 1.46: 1473 1.46 - 1.58: 2847 1.58 - 1.70: 0 1.70 - 1.82: 12 Bond restraints: 6660 Sorted by residual: bond pdb=" N GLY A 53 " pdb=" CA GLY A 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.24e+00 bond pdb=" N GLY F 53 " pdb=" CA GLY F 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.18e+00 bond pdb=" N GLY E 53 " pdb=" CA GLY E 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" N GLY D 53 " pdb=" CA GLY D 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.14e+00 bond pdb=" N GLY B 53 " pdb=" CA GLY B 53 " ideal model delta sigma weight residual 1.444 1.455 -0.011 1.02e-02 9.61e+03 1.11e+00 ... (remaining 6655 not shown) Histogram of bond angle deviations from ideal: 102.56 - 108.30: 211 108.30 - 114.04: 3831 114.04 - 119.79: 1535 119.79 - 125.53: 3489 125.53 - 131.27: 36 Bond angle restraints: 9102 Sorted by residual: angle pdb=" N ASP A 114 " pdb=" CA ASP A 114 " pdb=" C ASP A 114 " ideal model delta sigma weight residual 114.56 110.82 3.74 1.27e+00 6.20e-01 8.70e+00 angle pdb=" N ASP D 114 " pdb=" CA ASP D 114 " pdb=" C ASP D 114 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.59e+00 angle pdb=" N ASP C 114 " pdb=" CA ASP C 114 " pdb=" C ASP C 114 " ideal model delta sigma weight residual 114.56 110.84 3.72 1.27e+00 6.20e-01 8.58e+00 angle pdb=" N ASP F 114 " pdb=" CA ASP F 114 " pdb=" C ASP F 114 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.48e+00 angle pdb=" N ASP B 114 " pdb=" CA ASP B 114 " pdb=" C ASP B 114 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.47e+00 ... (remaining 9097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 3710 14.28 - 28.57: 136 28.57 - 42.85: 30 42.85 - 57.13: 0 57.13 - 71.42: 6 Dihedral angle restraints: 3882 sinusoidal: 1242 harmonic: 2640 Sorted by residual: dihedral pdb=" CA PHE E 154 " pdb=" C PHE E 154 " pdb=" N LYS E 155 " pdb=" CA LYS E 155 " ideal model delta harmonic sigma weight residual 180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE D 154 " pdb=" C PHE D 154 " pdb=" N LYS D 155 " pdb=" CA LYS D 155 " ideal model delta harmonic sigma weight residual -180.00 -164.14 -15.86 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA PHE C 154 " pdb=" C PHE C 154 " pdb=" N LYS C 155 " pdb=" CA LYS C 155 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 614 0.030 - 0.059: 322 0.059 - 0.089: 113 0.089 - 0.119: 60 0.119 - 0.148: 31 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA VAL C 5 " pdb=" N VAL C 5 " pdb=" C VAL C 5 " pdb=" CB VAL C 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL F 5 " pdb=" N VAL F 5 " pdb=" C VAL F 5 " pdb=" CB VAL F 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1137 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 131 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 132 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 132 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 131 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 132 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 132 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 132 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 131 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO C 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 132 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 132 " 0.022 5.00e-02 4.00e+02 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2071 2.82 - 3.34: 4982 3.34 - 3.86: 10156 3.86 - 4.38: 10347 4.38 - 4.90: 19483 Nonbonded interactions: 47039 Sorted by model distance: nonbonded pdb=" OD1 ASN A 98 " pdb=" OG1 THR A 140 " model vdw 2.295 2.440 nonbonded pdb=" OD1 ASN D 98 " pdb=" OG1 THR D 140 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASN E 98 " pdb=" OG1 THR E 140 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG1 THR B 140 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASN C 98 " pdb=" OG1 THR C 140 " model vdw 2.296 2.440 ... (remaining 47034 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' } 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 12 5.16 5 C 4032 2.51 5 N 1158 2.21 5 O 1386 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.310 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.050 Process input model: 21.160 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.003 0.023 6660 Z= 0.212 Angle : 0.750 5.312 9102 Z= 0.463 Chirality : 0.047 0.148 1140 Planarity : 0.004 0.039 1218 Dihedral : 8.942 71.416 2172 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.00 % 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: -3.74 (0.24), residues: 930 helix: None (None), residues: 0 sheet: -1.38 (0.38), residues: 216 loop : -3.13 (0.19), residues: 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.755 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2024 time to fit residues: 21.8708 Evaluate side-chains 22 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 9.9990 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 6660 Z= 0.149 Angle : 0.441 3.790 9102 Z= 0.245 Chirality : 0.038 0.122 1140 Planarity : 0.003 0.032 1218 Dihedral : 3.826 12.638 966 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % 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: -3.03 (0.25), residues: 930 helix: None (None), residues: 0 sheet: -0.99 (0.35), residues: 240 loop : -2.61 (0.20), residues: 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.782 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1421 time to fit residues: 8.0555 Evaluate side-chains 18 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 6660 Z= 0.360 Angle : 0.575 7.435 9102 Z= 0.310 Chirality : 0.038 0.117 1140 Planarity : 0.003 0.027 1218 Dihedral : 4.638 14.172 966 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer Outliers : 0.00 % 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: -2.76 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.47 (0.37), residues: 240 loop : -2.56 (0.21), residues: 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.733 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1342 time to fit residues: 6.0492 Evaluate side-chains 15 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 0.0170 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 6660 Z= 0.212 Angle : 0.466 4.478 9102 Z= 0.253 Chirality : 0.037 0.119 1140 Planarity : 0.002 0.023 1218 Dihedral : 4.051 13.013 966 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.00 % 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: -2.50 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.26 (0.36), residues: 240 loop : -2.39 (0.21), residues: 690 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.780 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1494 time to fit residues: 5.9313 Evaluate side-chains 16 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 35 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.017 6660 Z= 0.142 Angle : 0.416 4.049 9102 Z= 0.227 Chirality : 0.037 0.118 1140 Planarity : 0.002 0.021 1218 Dihedral : 3.517 11.506 966 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.00 % 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: -2.39 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.13 (0.37), residues: 216 loop : -2.37 (0.21), residues: 714 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.702 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1292 time to fit residues: 6.0030 Evaluate side-chains 16 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 83 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.032 6660 Z= 0.382 Angle : 0.575 7.402 9102 Z= 0.308 Chirality : 0.038 0.117 1140 Planarity : 0.003 0.023 1218 Dihedral : 4.638 16.083 966 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 0.00 % 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: -2.47 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.06 (0.36), residues: 216 loop : -2.37 (0.21), residues: 714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.687 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1241 time to fit residues: 5.0911 Evaluate side-chains 17 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 6660 Z= 0.195 Angle : 0.451 5.005 9102 Z= 0.247 Chirality : 0.037 0.120 1140 Planarity : 0.002 0.020 1218 Dihedral : 3.981 14.797 966 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.00 % 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: -2.31 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.12 (0.36), residues: 216 loop : -2.28 (0.21), residues: 714 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.747 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1219 time to fit residues: 4.9822 Evaluate side-chains 17 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.782 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 42 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 83 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 6660 Z= 0.105 Angle : 0.404 5.074 9102 Z= 0.220 Chirality : 0.038 0.124 1140 Planarity : 0.002 0.017 1218 Dihedral : 3.254 12.893 966 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.00 % 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: -2.11 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.29 (0.36), residues: 216 loop : -2.15 (0.22), residues: 714 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.788 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1371 time to fit residues: 6.7136 Evaluate side-chains 17 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 0.0050 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6660 Z= 0.170 Angle : 0.430 4.765 9102 Z= 0.233 Chirality : 0.037 0.122 1140 Planarity : 0.002 0.019 1218 Dihedral : 3.518 12.111 966 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % 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: -2.09 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.31 (0.35), residues: 216 loop : -2.13 (0.22), residues: 714 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.763 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1197 time to fit residues: 4.8987 Evaluate side-chains 17 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 82 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN E 64 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 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 6660 Z= 0.232 Angle : 0.465 4.750 9102 Z= 0.251 Chirality : 0.037 0.119 1140 Planarity : 0.002 0.020 1218 Dihedral : 3.851 12.448 966 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.00 % 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: -2.13 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.23 (0.35), residues: 216 loop : -2.14 (0.22), residues: 714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.759 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.1523 time to fit residues: 5.7257 Evaluate side-chains 17 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.044196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.038744 restraints weight = 38680.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.039848 restraints weight = 22497.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.040575 restraints weight = 15015.187| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 6660 Z= 0.158 Angle : 0.425 4.724 9102 Z= 0.231 Chirality : 0.038 0.119 1140 Planarity : 0.002 0.019 1218 Dihedral : 3.607 13.830 966 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.00 % 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: -2.07 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.25 (0.35), residues: 216 loop : -2.10 (0.22), residues: 714 =============================================================================== Job complete usr+sys time: 1156.93 seconds wall clock time: 22 minutes 1.98 seconds (1321.98 seconds total)