Starting phenix.real_space_refine (version: dev) on Fri May 13 15:43:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/05_2022/6xzc_10658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/05_2022/6xzc_10658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/05_2022/6xzc_10658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/05_2022/6xzc_10658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/05_2022/6xzc_10658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xzc_10658/05_2022/6xzc_10658.pdb" } resolution = 3.37 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= 0.100 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 None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 13279 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "F" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1897 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 20, 'TRANS': 221} Chain breaks: 1 Time building chain proxies: 7.73, per 1000 atoms: 0.58 Number of scatterers: 13279 At special positions: 0 Unit cell: (111.09, 110.032, 112.148, 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 49 16.00 O 2569 8.00 N 2359 7.00 C 8302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.04 Conformation dependent library (CDL) restraints added in 2.1 seconds 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 75.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.676A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 160 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 246 through 268 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 160 " --> pdb=" O TRP B 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 161 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 246 through 268 Processing helix chain 'C' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 155 " --> pdb=" O HIS C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 160 " --> pdb=" O TRP C 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 161 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.841A pdb=" N ASN C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 246 through 268 Processing helix chain 'D' and resid 10 through 22 removed outlier: 3.676A pdb=" N ILE D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 82 removed outlier: 4.024A pdb=" N TYR D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 155 " --> pdb=" O HIS D 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 160 " --> pdb=" O TRP D 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 Processing helix chain 'D' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.841A pdb=" N ASN D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 246 through 268 Processing helix chain 'E' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU E 133 " --> pdb=" O ASN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY E 155 " --> pdb=" O HIS E 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN E 160 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 Processing helix chain 'E' and resid 179 through 223 removed outlier: 3.834A pdb=" N ALA E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 246 through 268 Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.673A pdb=" N LEU F 133 " --> pdb=" O ASN F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 166 removed outlier: 3.635A pdb=" N ASP F 154 " --> pdb=" O ALA F 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 155 " --> pdb=" O HIS F 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 160 " --> pdb=" O TRP F 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 161 " --> pdb=" O ASN F 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 Processing helix chain 'F' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA F 183 " --> pdb=" O ASP F 179 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 243 Processing helix chain 'F' and resid 246 through 268 Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.675A pdb=" N ILE G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 82 removed outlier: 4.025A pdb=" N TYR G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 142 removed outlier: 3.672A pdb=" N LEU G 133 " --> pdb=" O ASN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 166 removed outlier: 3.636A pdb=" N ASP G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY G 155 " --> pdb=" O HIS G 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN G 160 " --> pdb=" O TRP G 156 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU G 161 " --> pdb=" O ASN G 157 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP G 166 " --> pdb=" O THR G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 Processing helix chain 'G' and resid 179 through 223 removed outlier: 3.833A pdb=" N ALA G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS G 223 " --> pdb=" O ALA G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 239 removed outlier: 3.840A pdb=" N ASN G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 243 Processing helix chain 'G' and resid 246 through 268 952 hydrogen bonds defined for protein. 2793 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: 3.41 Time building geometry restraints manager: 5.43 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: 4566 1.34 - 1.46: 1663 1.46 - 1.57: 7267 1.57 - 1.69: 0 1.69 - 1.80: 84 Bond restraints: 13580 Sorted by residual: bond pdb=" CA GLU B 127 " pdb=" C GLU B 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.38e+00 bond pdb=" CA GLU G 127 " pdb=" C GLU G 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.36e+00 bond pdb=" CA GLU D 127 " pdb=" C GLU D 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.29e+00 bond pdb=" CA GLU C 127 " pdb=" C GLU C 127 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.26e+00 bond pdb=" CA GLU E 127 " pdb=" C GLU E 127 " ideal model delta sigma weight residual 1.525 1.556 -0.031 2.10e-02 2.27e+03 2.22e+00 ... (remaining 13575 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.00: 658 107.00 - 113.76: 7326 113.76 - 120.52: 5959 120.52 - 127.28: 4355 127.28 - 134.04: 196 Bond angle restraints: 18494 Sorted by residual: angle pdb=" CA GLU B 127 " pdb=" C GLU B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 7.02e+00 angle pdb=" CA GLU G 127 " pdb=" C GLU G 127 " pdb=" N PRO G 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 6.99e+00 angle pdb=" CA GLU F 127 " pdb=" C GLU F 127 " pdb=" N PRO F 128 " ideal model delta sigma weight residual 116.90 120.87 -3.97 1.50e+00 4.44e-01 6.99e+00 angle pdb=" CA GLU D 127 " pdb=" C GLU D 127 " pdb=" N PRO D 128 " ideal model delta sigma weight residual 116.90 120.86 -3.96 1.50e+00 4.44e-01 6.96e+00 angle pdb=" CA GLU C 127 " pdb=" C GLU C 127 " pdb=" N PRO C 128 " ideal model delta sigma weight residual 116.90 120.83 -3.93 1.50e+00 4.44e-01 6.86e+00 ... (remaining 18489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.87: 7559 13.87 - 27.74: 575 27.74 - 41.62: 203 41.62 - 55.49: 42 55.49 - 69.36: 28 Dihedral angle restraints: 8407 sinusoidal: 3409 harmonic: 4998 Sorted by residual: dihedral pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " pdb=" CG ASP A 228 " pdb=" OD1 ASP A 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.83 57.83 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP G 228 " pdb=" CB ASP G 228 " pdb=" CG ASP G 228 " pdb=" OD1 ASP G 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " pdb=" CG ASP C 228 " pdb=" OD1 ASP C 228 " ideal model delta sinusoidal sigma weight residual -30.00 -87.81 57.81 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 8404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1128 0.026 - 0.051: 558 0.051 - 0.077: 162 0.077 - 0.103: 99 0.103 - 0.129: 41 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CB ILE B 282 " pdb=" CA ILE B 282 " pdb=" CG1 ILE B 282 " pdb=" CG2 ILE B 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CB ILE C 282 " pdb=" CA ILE C 282 " pdb=" CG1 ILE C 282 " pdb=" CG2 ILE C 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CB ILE E 282 " pdb=" CA ILE E 282 " pdb=" CG1 ILE E 282 " pdb=" CG2 ILE E 282 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 1985 not shown) Planarity restraints: 2513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 247 " 0.040 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO E 248 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 248 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 248 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 247 " 0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO F 248 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 248 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 248 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 247 " -0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 248 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " -0.034 5.00e-02 4.00e+02 ... (remaining 2510 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4243 2.84 - 3.35: 12529 3.35 - 3.87: 21661 3.87 - 4.38: 23214 4.38 - 4.90: 40794 Nonbonded interactions: 102441 Sorted by model distance: nonbonded pdb=" OD1 ASN B 129 " pdb=" OH TYR B 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN E 129 " pdb=" OH TYR E 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN D 129 " pdb=" OH TYR D 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN A 129 " pdb=" OH TYR A 250 " model vdw 2.323 2.440 nonbonded pdb=" OD1 ASN F 129 " pdb=" OH TYR F 250 " model vdw 2.323 2.440 ... (remaining 102436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 49 5.16 5 C 8302 2.51 5 N 2359 2.21 5 O 2569 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.010 Extract box with map and model: 14.360 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 36.070 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 0.004 0.041 13580 Z= 0.280 Angle : 0.628 5.872 18494 Z= 0.372 Chirality : 0.038 0.129 1988 Planarity : 0.007 0.059 2513 Dihedral : 12.496 69.359 5145 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 3.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 1666 helix: -1.20 (0.11), residues: 1176 sheet: None (None), residues: 0 loop : -0.98 (0.29), residues: 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 334 time to evaluate : 1.527 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 1 residues processed: 357 average time/residue: 0.2652 time to fit residues: 132.8459 Evaluate side-chains 172 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1105 time to fit residues: 2.3929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 216 HIS B 48 GLN B 216 HIS C 216 HIS ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN E 48 GLN E 216 HIS F 48 GLN F 175 ASN F 216 HIS G 216 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 13580 Z= 0.265 Angle : 0.671 13.438 18494 Z= 0.344 Chirality : 0.035 0.243 1988 Planarity : 0.006 0.080 2513 Dihedral : 3.622 11.856 1834 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 2.04 % 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: 1.67 (0.19), residues: 1666 helix: 1.64 (0.13), residues: 1204 sheet: None (None), residues: 0 loop : -0.19 (0.31), residues: 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.651 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 206 average time/residue: 0.2358 time to fit residues: 72.1109 Evaluate side-chains 154 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1225 time to fit residues: 5.0634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN E 129 ASN F 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.138 13580 Z= 0.260 Angle : 0.542 8.088 18494 Z= 0.279 Chirality : 0.034 0.182 1988 Planarity : 0.007 0.106 2513 Dihedral : 3.481 20.753 1834 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 0.73 % 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: 3.17 (0.20), residues: 1666 helix: 2.69 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : 0.48 (0.32), residues: 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 160 time to evaluate : 1.735 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 169 average time/residue: 0.2608 time to fit residues: 64.3416 Evaluate side-chains 143 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1205 time to fit residues: 4.1984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS E 245 GLN ** F 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN G 245 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 13580 Z= 0.242 Angle : 0.561 12.635 18494 Z= 0.280 Chirality : 0.035 0.214 1988 Planarity : 0.005 0.098 2513 Dihedral : 3.352 13.517 1834 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 1.17 % 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: 4.06 (0.21), residues: 1666 helix: 3.35 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 0.97 (0.34), residues: 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 158 time to evaluate : 1.537 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 171 average time/residue: 0.2470 time to fit residues: 62.2492 Evaluate side-chains 144 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.682 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1112 time to fit residues: 3.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 16 ASN C 48 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 13580 Z= 0.209 Angle : 0.552 16.226 18494 Z= 0.270 Chirality : 0.034 0.191 1988 Planarity : 0.004 0.090 2513 Dihedral : 3.215 12.035 1834 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 1.46 % 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: 4.48 (0.21), residues: 1666 helix: 3.64 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.18 (0.34), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.679 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 162 average time/residue: 0.2506 time to fit residues: 61.0509 Evaluate side-chains 133 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1206 time to fit residues: 4.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.0050 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 0.0370 chunk 40 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 13580 Z= 0.212 Angle : 0.527 15.638 18494 Z= 0.265 Chirality : 0.034 0.211 1988 Planarity : 0.005 0.110 2513 Dihedral : 3.186 17.041 1834 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer Outliers : 0.95 % 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: 4.71 (0.21), residues: 1666 helix: 3.82 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.25 (0.34), residues: 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.703 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 148 average time/residue: 0.2462 time to fit residues: 54.5045 Evaluate side-chains 134 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1154 time to fit residues: 2.8726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 136 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 74 optimal weight: 0.0020 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN D 12 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 254 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.119 13580 Z= 0.202 Angle : 0.480 9.152 18494 Z= 0.238 Chirality : 0.034 0.199 1988 Planarity : 0.005 0.130 2513 Dihedral : 3.164 11.938 1834 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer Outliers : 0.51 % 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: 4.79 (0.21), residues: 1666 helix: 3.88 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.26 (0.34), residues: 476 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.689 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 139 average time/residue: 0.2360 time to fit residues: 49.4385 Evaluate side-chains 128 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1115 time to fit residues: 2.5993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN B 274 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN G 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.331 13580 Z= 0.372 Angle : 0.637 32.447 18494 Z= 0.333 Chirality : 0.036 0.234 1988 Planarity : 0.004 0.097 2513 Dihedral : 3.214 12.467 1834 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 0.87 % 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: 4.77 (0.21), residues: 1666 helix: 3.86 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.26 (0.34), residues: 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.762 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 143 average time/residue: 0.2542 time to fit residues: 53.9518 Evaluate side-chains 128 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1152 time to fit residues: 3.1007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.3980 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 0.0170 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN G 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.375 13580 Z= 0.344 Angle : 0.659 30.239 18494 Z= 0.353 Chirality : 0.034 0.219 1988 Planarity : 0.005 0.139 2513 Dihedral : 3.150 12.621 1834 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer Outliers : 0.58 % 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: 4.96 (0.21), residues: 1666 helix: 4.01 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.34 (0.34), residues: 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.852 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 134 average time/residue: 0.2616 time to fit residues: 52.1917 Evaluate side-chains 121 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1207 time to fit residues: 2.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 167 optimal weight: 0.0670 chunk 154 optimal weight: 0.6980 chunk 133 optimal weight: 0.0000 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.221 13580 Z= 0.253 Angle : 0.626 30.916 18494 Z= 0.338 Chirality : 0.034 0.246 1988 Planarity : 0.006 0.186 2513 Dihedral : 3.143 13.465 1834 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.02 (0.21), residues: 1666 helix: 4.06 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.33 (0.34), residues: 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3332 Ramachandran restraints generated. 1666 Oldfield, 0 Emsley, 1666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.591 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 121 average time/residue: 0.2548 time to fit residues: 46.1567 Evaluate side-chains 113 residues out of total 1372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1155 time to fit residues: 2.4448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 0.0070 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN C 245 GLN C 274 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.106768 restraints weight = 16024.427| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.51 r_work: 0.2890 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 1.34 restraints_weight: 0.2500 r_work: 0.2867 rms_B_bonded: 1.38 restraints_weight: 0.1250 r_work: 0.2854 rms_B_bonded: 1.46 restraints_weight: 0.0625 r_work: 0.2839 rms_B_bonded: 1.58 restraints_weight: 0.0312 r_work: 0.2823 rms_B_bonded: 1.73 restraints_weight: 0.0156 r_work: 0.2805 rms_B_bonded: 1.93 restraints_weight: 0.0078 r_work: 0.2785 rms_B_bonded: 2.17 restraints_weight: 0.0039 r_work: 0.2762 rms_B_bonded: 2.46 restraints_weight: 0.0020 r_work: 0.2737 rms_B_bonded: 2.81 restraints_weight: 0.0010 r_work: 0.2708 rms_B_bonded: 3.23 restraints_weight: 0.0005 r_work: 0.2675 rms_B_bonded: 3.72 restraints_weight: 0.0002 r_work: 0.2638 rms_B_bonded: 4.30 restraints_weight: 0.0001 r_work: 0.2596 rms_B_bonded: 4.99 restraints_weight: 0.0001 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.135 13580 Z= 0.230 Angle : 0.583 28.922 18494 Z= 0.315 Chirality : 0.034 0.218 1988 Planarity : 0.006 0.183 2513 Dihedral : 3.127 12.956 1834 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.10 (0.21), residues: 1666 helix: 4.13 (0.14), residues: 1190 sheet: None (None), residues: 0 loop : 1.31 (0.34), residues: 476 =============================================================================== Job complete usr+sys time: 2377.50 seconds wall clock time: 44 minutes 15.84 seconds (2655.84 seconds total)