Starting phenix.real_space_refine on Mon Mar 11 02:06:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/03_2024/5oh0_3809_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/03_2024/5oh0_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_3809/03_2024/5oh0_3809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/03_2024/5oh0_3809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/03_2024/5oh0_3809_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5oh0_3809/03_2024/5oh0_3809_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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-5265/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: 4.05, per 1000 atoms: 0.61 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: 2.39 Conformation dependent library (CDL) restraints added in 1.9 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: 0.72 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: 1.54 Time building geometry restraints manager: 2.66 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 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: 1.750 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: 3.210 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 % Allowed : 2.70 % Favored : 97.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 11 PHE 0.020 0.002 PHE E 154 TYR 0.002 0.001 TYR F 158 ARG 0.001 0.000 ARG A 106 *********************** 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 : 0.731 Fit side-chains REVERT: F 29 ASP cc_start: 0.8339 (t70) cc_final: 0.8054 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2047 time to fit residues: 22.0028 Evaluate side-chains 23 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 2.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 overall best weight: 1.2164 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.1800 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= 0.139 Angle : 0.435 3.804 9102 Z= 0.242 Chirality : 0.038 0.121 1140 Planarity : 0.003 0.032 1218 Dihedral : 3.806 12.629 966 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % 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: -1.00 (0.35), residues: 240 loop : -2.61 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 11 PHE 0.007 0.001 PHE F 118 TYR 0.002 0.000 TYR B 137 ARG 0.001 0.000 ARG A 136 *********************** 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 38 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.779 Fit side-chains REVERT: A 114 ASP cc_start: 0.8604 (p0) cc_final: 0.8281 (p0) REVERT: A 124 LEU cc_start: 0.8600 (mt) cc_final: 0.8362 (mt) REVERT: C 105 ASP cc_start: 0.8061 (t70) cc_final: 0.7714 (p0) REVERT: F 29 ASP cc_start: 0.8538 (t70) cc_final: 0.8314 (t0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1534 time to fit residues: 9.0648 Evaluate side-chains 21 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 0.0060 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.9002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 6660 Z= 0.184 Angle : 0.444 4.772 9102 Z= 0.243 Chirality : 0.037 0.116 1140 Planarity : 0.002 0.025 1218 Dihedral : 3.716 11.375 966 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -2.64 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.38 (0.37), residues: 240 loop : -2.48 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 11 PHE 0.007 0.001 PHE E 154 TYR 0.003 0.000 TYR E 158 ARG 0.002 0.000 ARG A 136 *********************** 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 35 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.822 Fit side-chains REVERT: A 114 ASP cc_start: 0.8532 (p0) cc_final: 0.8314 (p0) REVERT: D 114 ASP cc_start: 0.8865 (p0) cc_final: 0.8660 (p0) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1498 time to fit residues: 8.7815 Evaluate side-chains 18 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 0.0060 chunk 77 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2670 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= 0.105 Angle : 0.401 3.851 9102 Z= 0.219 Chirality : 0.037 0.121 1140 Planarity : 0.002 0.022 1218 Dihedral : 3.255 12.327 966 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: -2.36 (0.26), residues: 930 helix: None (None), residues: 0 sheet: -0.13 (0.36), residues: 240 loop : -2.31 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 11 PHE 0.005 0.001 PHE E 154 TYR 0.001 0.000 TYR E 158 ARG 0.001 0.000 ARG A 136 *********************** 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 30 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.763 Fit side-chains REVERT: A 114 ASP cc_start: 0.8431 (p0) cc_final: 0.8205 (p0) REVERT: A 124 LEU cc_start: 0.8689 (mt) cc_final: 0.8385 (mt) REVERT: D 114 ASP cc_start: 0.8789 (p0) cc_final: 0.8588 (p0) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1514 time to fit residues: 7.2777 Evaluate side-chains 20 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.3562 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6660 Z= 0.141 Angle : 0.407 3.918 9102 Z= 0.222 Chirality : 0.037 0.120 1140 Planarity : 0.002 0.022 1218 Dihedral : 3.289 11.151 966 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -2.10 (0.26), residues: 930 helix: None (None), residues: 0 sheet: 0.10 (0.36), residues: 240 loop : -2.14 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 11 PHE 0.005 0.001 PHE B 133 TYR 0.002 0.000 TYR F 158 ARG 0.002 0.000 ARG A 136 *********************** 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 28 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.962 Fit side-chains REVERT: A 114 ASP cc_start: 0.8303 (p0) cc_final: 0.8095 (p0) REVERT: D 114 ASP cc_start: 0.8815 (p0) cc_final: 0.8595 (p0) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1729 time to fit residues: 7.5048 Evaluate side-chains 19 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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: 7.9990 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.0030 overall best weight: 1.6192 ------------------------------------------------------------------------------- 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 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: 0.8478 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6660 Z= 0.160 Angle : 0.411 4.032 9102 Z= 0.225 Chirality : 0.037 0.117 1140 Planarity : 0.002 0.021 1218 Dihedral : 3.352 11.004 966 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -1.98 (0.27), residues: 930 helix: None (None), residues: 0 sheet: 0.16 (0.36), residues: 240 loop : -2.04 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 11 PHE 0.006 0.001 PHE B 133 TYR 0.002 0.000 TYR B 137 ARG 0.002 0.000 ARG A 136 *********************** 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 26 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.756 Fit side-chains REVERT: D 114 ASP cc_start: 0.8780 (p0) cc_final: 0.8577 (p0) REVERT: F 74 LEU cc_start: 0.9192 (tp) cc_final: 0.8957 (tp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1322 time to fit residues: 5.9715 Evaluate side-chains 18 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 0.0070 chunk 73 optimal weight: 0.0040 chunk 48 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 overall best weight: 1.2212 ------------------------------------------------------------------------------- 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 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: 0.8465 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6660 Z= 0.128 Angle : 0.394 3.914 9102 Z= 0.215 Chirality : 0.037 0.118 1140 Planarity : 0.002 0.021 1218 Dihedral : 3.146 9.917 966 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.83 (0.27), residues: 930 helix: None (None), residues: 0 sheet: 0.22 (0.36), residues: 240 loop : -1.91 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 11 PHE 0.005 0.001 PHE E 154 TYR 0.002 0.000 TYR E 158 ARG 0.001 0.000 ARG A 136 *********************** 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 29 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.814 Fit side-chains REVERT: B 89 GLN cc_start: 0.7190 (tp-100) cc_final: 0.6532 (tm-30) REVERT: D 29 ASP cc_start: 0.8687 (t70) cc_final: 0.8480 (t0) REVERT: F 74 LEU cc_start: 0.9193 (tp) cc_final: 0.8974 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1493 time to fit residues: 7.1664 Evaluate side-chains 19 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 0.0370 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.0020 chunk 59 optimal weight: 0.0570 chunk 42 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 0.0570 overall best weight: 0.0502 ------------------------------------------------------------------------------- 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 ** 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** E 102 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.019 6660 Z= 0.081 Angle : 0.372 3.977 9102 Z= 0.202 Chirality : 0.038 0.122 1140 Planarity : 0.002 0.020 1218 Dihedral : 2.679 9.036 966 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.72 (0.27), residues: 930 helix: None (None), residues: 0 sheet: -0.06 (0.34), residues: 258 loop : -1.71 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 11 PHE 0.005 0.001 PHE E 154 TYR 0.002 0.000 TYR F 158 ARG 0.001 0.000 ARG A 106 *********************** 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 34 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.701 Fit side-chains REVERT: A 124 LEU cc_start: 0.8634 (mt) cc_final: 0.8311 (mt) REVERT: B 89 GLN cc_start: 0.7110 (tp-100) cc_final: 0.6427 (tm-30) REVERT: D 29 ASP cc_start: 0.8651 (t70) cc_final: 0.8344 (t0) REVERT: D 114 ASP cc_start: 0.8659 (p0) cc_final: 0.8425 (p0) REVERT: F 74 LEU cc_start: 0.9110 (tp) cc_final: 0.8888 (tp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1380 time to fit residues: 7.4514 Evaluate side-chains 21 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** 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: 0.8505 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6660 Z= 0.257 Angle : 0.478 5.837 9102 Z= 0.257 Chirality : 0.037 0.138 1140 Planarity : 0.002 0.021 1218 Dihedral : 3.707 12.259 966 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.75 (0.27), residues: 930 helix: None (None), residues: 0 sheet: 0.24 (0.35), residues: 240 loop : -1.84 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 82 PHE 0.009 0.001 PHE A 133 TYR 0.005 0.001 TYR F 158 ARG 0.004 0.001 ARG A 136 *********************** 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 29 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.664 Fit side-chains REVERT: B 89 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6546 (tm-30) REVERT: C 15 GLU cc_start: 0.7617 (pp20) cc_final: 0.7254 (pp20) REVERT: D 29 ASP cc_start: 0.8757 (t70) cc_final: 0.8539 (t0) REVERT: D 114 ASP cc_start: 0.8772 (p0) cc_final: 0.8520 (p0) REVERT: F 74 LEU cc_start: 0.9230 (tp) cc_final: 0.9017 (tp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1411 time to fit residues: 6.5839 Evaluate side-chains 21 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 0.0170 chunk 56 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 overall best weight: 3.5022 ------------------------------------------------------------------------------- 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 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** E 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 6660 Z= 0.307 Angle : 0.517 5.590 9102 Z= 0.279 Chirality : 0.037 0.115 1140 Planarity : 0.002 0.024 1218 Dihedral : 4.215 14.657 966 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.87 (0.27), residues: 930 helix: None (None), residues: 0 sheet: 0.09 (0.34), residues: 240 loop : -1.90 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 82 PHE 0.008 0.001 PHE A 133 TYR 0.004 0.001 TYR F 158 ARG 0.003 0.001 ARG D 136 ********************** 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 30 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.724 Fit side-chains REVERT: B 89 GLN cc_start: 0.7078 (tp-100) cc_final: 0.6511 (tm-30) REVERT: C 15 GLU cc_start: 0.8111 (pp20) cc_final: 0.7819 (pp20) REVERT: C 24 ASP cc_start: 0.9068 (t70) cc_final: 0.8773 (p0) REVERT: F 74 LEU cc_start: 0.9249 (tp) cc_final: 0.9009 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1237 time to fit residues: 6.3006 Evaluate side-chains 22 residues out of total 666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0770 chunk 71 optimal weight: 9.9990 chunk 29 optimal weight: 0.0000 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.7146 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.045003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.039311 restraints weight = 37940.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.040453 restraints weight = 21769.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.041261 restraints weight = 14438.869| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.020 6660 Z= 0.102 Angle : 0.402 4.378 9102 Z= 0.220 Chirality : 0.038 0.124 1140 Planarity : 0.002 0.020 1218 Dihedral : 3.214 10.256 966 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.27), residues: 930 helix: None (None), residues: 0 sheet: 0.23 (0.34), residues: 240 loop : -1.80 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 11 PHE 0.005 0.001 PHE B 133 TYR 0.002 0.000 TYR E 158 ARG 0.001 0.000 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.58 seconds wall clock time: 25 minutes 41.15 seconds (1541.15 seconds total)