Starting phenix.real_space_refine (version: dev) on Mon Dec 12 05:50:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/12_2022/6mhu_9118_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F ARG 33": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G ARG 270": "NH1" <-> "NH2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8810 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2393 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2643 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 2 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "G" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 200 Unusual residues: {'JSG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.58 Number of scatterers: 8810 At special positions: 0 Unit cell: (92.25, 95.94, 145.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 4 15.00 O 1624 8.00 N 1482 7.00 C 5658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 10 sheets defined 45.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'F' and resid 7 through 39 removed outlier: 3.742A pdb=" N LEU F 12 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 13 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU F 24 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 26 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU F 31 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 39 " --> pdb=" O GLY F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.715A pdb=" N GLY F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.762A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Proline residue: F 65 - end of helix removed outlier: 3.978A pdb=" N THR F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 95 through 119 removed outlier: 3.778A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 265 through 283 removed outlier: 4.379A pdb=" N ILE F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 317 removed outlier: 3.683A pdb=" N LEU F 308 " --> pdb=" O LEU F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 346 Processing helix chain 'G' and resid 8 through 40 removed outlier: 3.683A pdb=" N SER G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 65 removed outlier: 4.650A pdb=" N LEU G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Proline residue: G 61 - end of helix removed outlier: 3.665A pdb=" N GLN G 65 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 85 removed outlier: 4.098A pdb=" N LEU G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 95 Processing helix chain 'G' and resid 99 through 123 removed outlier: 4.120A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 4.009A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 137 removed outlier: 4.382A pdb=" N ALA G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 251 through 254 No H-bonds generated for 'chain 'G' and resid 251 through 254' Processing helix chain 'G' and resid 270 through 279 removed outlier: 3.667A pdb=" N ILE G 279 " --> pdb=" O MET G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 305 through 326 Processing helix chain 'G' and resid 337 through 342 Processing helix chain 'G' and resid 346 through 356 removed outlier: 4.242A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.646A pdb=" N GLU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.763A pdb=" N ALA A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.853A pdb=" N PHE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 95 through 105 removed outlier: 5.026A pdb=" N ILE B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.552A pdb=" N ALA B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.758A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 221 through 226 Processing sheet with id= A, first strand: chain 'F' and resid 187 through 189 Processing sheet with id= B, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.577A pdb=" N PHE G 160 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 162 " --> pdb=" O SER G 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 210 through 212 Processing sheet with id= D, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= E, first strand: chain 'A' and resid 214 through 219 removed outlier: 7.231A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS A 218 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA A 207 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 206 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 190 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU A 34 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 192 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 193 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 83 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 9 through 11 removed outlier: 7.920A pdb=" N LYS A 11 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= H, first strand: chain 'B' and resid 31 through 34 removed outlier: 5.956A pdb=" N VAL B 190 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 34 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 192 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 9 through 11 removed outlier: 7.899A pdb=" N LYS B 11 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU B 20 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.587A pdb=" N ALA B 217 " --> pdb=" O ILE B 209 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 927 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: 2.49 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2785 1.34 - 1.46: 1431 1.46 - 1.57: 4662 1.57 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 8963 Sorted by residual: bond pdb=" C7 JSG G 401 " pdb=" N2 JSG G 401 " ideal model delta sigma weight residual 1.551 1.344 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CDO JSG G 401 " pdb=" NAO JSG G 401 " ideal model delta sigma weight residual 1.505 1.343 0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" CFK JSG G 401 " pdb=" O3 JSG G 401 " ideal model delta sigma weight residual 1.509 1.362 0.147 2.00e-02 2.50e+03 5.41e+01 bond pdb=" CBV JSG G 401 " pdb=" OBW JSG G 401 " ideal model delta sigma weight residual 1.554 1.423 0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" CEE JSG G 401 " pdb=" OAQ JSG G 401 " ideal model delta sigma weight residual 1.469 1.356 0.113 2.00e-02 2.50e+03 3.18e+01 ... (remaining 8958 not shown) Histogram of bond angle deviations from ideal: 96.27 - 104.01: 144 104.01 - 111.76: 4109 111.76 - 119.50: 3605 119.50 - 127.25: 4196 127.25 - 135.00: 87 Bond angle restraints: 12141 Sorted by residual: angle pdb=" CA ASP G 198 " pdb=" C ASP G 198 " pdb=" N PRO G 199 " ideal model delta sigma weight residual 117.68 121.17 -3.49 7.10e-01 1.98e+00 2.42e+01 angle pdb=" N GLY G 173 " pdb=" CA GLY G 173 " pdb=" C GLY G 173 " ideal model delta sigma weight residual 113.18 102.23 10.95 2.37e+00 1.78e-01 2.13e+01 angle pdb=" C GLU B 228 " pdb=" N HIS B 229 " pdb=" CA HIS B 229 " ideal model delta sigma weight residual 121.56 128.22 -6.66 1.56e+00 4.11e-01 1.82e+01 angle pdb=" C PHE F 173 " pdb=" N LEU F 174 " pdb=" CA LEU F 174 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C MET G 140 " pdb=" N TYR G 141 " pdb=" CA TYR G 141 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 ... (remaining 12136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4973 16.92 - 33.84: 276 33.84 - 50.76: 72 50.76 - 67.69: 7 67.69 - 84.61: 6 Dihedral angle restraints: 5334 sinusoidal: 2151 harmonic: 3183 Sorted by residual: dihedral pdb=" CA GLU B 228 " pdb=" C GLU B 228 " pdb=" N HIS B 229 " pdb=" CA HIS B 229 " ideal model delta harmonic sigma weight residual -180.00 -145.60 -34.40 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA GLY G 173 " pdb=" C GLY G 173 " pdb=" N GLY G 174 " pdb=" CA GLY G 174 " ideal model delta harmonic sigma weight residual -180.00 -146.76 -33.24 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA VAL F 288 " pdb=" C VAL F 288 " pdb=" N VAL F 289 " pdb=" CA VAL F 289 " ideal model delta harmonic sigma weight residual -180.00 -146.88 -33.12 0 5.00e+00 4.00e-02 4.39e+01 ... (remaining 5331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.067: 1443 1.067 - 2.134: 0 2.134 - 3.201: 0 3.201 - 4.268: 0 4.268 - 5.335: 3 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CBP JSG G 401 " pdb=" CBM JSG G 401 " pdb=" CBQ JSG G 401 " pdb=" OBW JSG G 401 " both_signs ideal model delta sigma weight residual False 2.51 -2.82 5.33 2.00e-01 2.50e+01 7.11e+02 chirality pdb=" CBA JSG G 401 " pdb=" CAX JSG G 401 " pdb=" CBB JSG G 401 " pdb=" OBH JSG G 401 " both_signs ideal model delta sigma weight residual False 2.57 -2.48 5.05 2.00e-01 2.50e+01 6.38e+02 chirality pdb=" CCB JSG G 401 " pdb=" CCC JSG G 401 " pdb=" OBF JSG G 401 " pdb=" OCL JSG G 401 " both_signs ideal model delta sigma weight residual False 2.44 -2.23 4.67 2.00e-01 2.50e+01 5.46e+02 ... (remaining 1443 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 68 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO G 69 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 69 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 69 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 245 " -0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO G 246 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 246 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 246 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 268 " 0.017 2.00e-02 2.50e+03 1.54e-02 5.89e+00 pdb=" CG TRP F 268 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 268 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 268 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 268 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 268 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 268 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 268 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 268 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 268 " 0.000 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2084 2.79 - 3.32: 8277 3.32 - 3.85: 14446 3.85 - 4.37: 16343 4.37 - 4.90: 27247 Nonbonded interactions: 68397 Sorted by model distance: nonbonded pdb=" OD2 ASP G 37 " pdb=" OAS JSG G 401 " model vdw 2.267 2.440 nonbonded pdb=" O ALA B 2 " pdb=" OG SER B 28 " model vdw 2.282 2.440 nonbonded pdb=" O LEU F 272 " pdb=" OG1 THR F 275 " model vdw 2.293 2.440 nonbonded pdb=" O THR B 25 " pdb=" OH TYR B 208 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR A 47 " pdb=" OD2 ASP A 162 " model vdw 2.330 2.440 ... (remaining 68392 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' } 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 42 5.16 5 C 5658 2.51 5 N 1482 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 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: 2.470 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 26.150 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 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 : 0.010 0.207 8963 Z= 0.651 Angle : 1.240 11.652 12141 Z= 0.616 Chirality : 0.237 5.335 1446 Planarity : 0.008 0.065 1513 Dihedral : 12.045 84.607 3282 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -4.84 (0.19), residues: 1094 helix: -2.92 (0.16), residues: 523 sheet: -2.77 (0.41), residues: 99 loop : -3.59 (0.23), residues: 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 382 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 385 average time/residue: 0.2252 time to fit residues: 114.3115 Evaluate side-chains 239 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 235 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0784 time to fit residues: 2.0575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 40.0000 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 ASN F 148 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 216 ASN G 281 GLN A 38 ASN A 104 GLN A 119 ASN B 113 GLN B 212 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 8963 Z= 0.349 Angle : 0.994 23.801 12141 Z= 0.456 Chirality : 0.101 2.407 1446 Planarity : 0.006 0.055 1513 Dihedral : 9.364 88.415 1264 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 5.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.75 (0.21), residues: 1094 helix: -1.82 (0.19), residues: 528 sheet: -2.75 (0.42), residues: 99 loop : -3.17 (0.25), residues: 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 241 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 35 residues processed: 275 average time/residue: 0.1904 time to fit residues: 72.9197 Evaluate side-chains 243 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.0998 time to fit residues: 7.2412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 ASN F 228 GLN A 38 ASN B 27 ASN B 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8963 Z= 0.258 Angle : 0.917 24.963 12141 Z= 0.408 Chirality : 0.099 2.367 1446 Planarity : 0.005 0.055 1513 Dihedral : 8.839 84.153 1264 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.94 (0.23), residues: 1094 helix: -1.01 (0.22), residues: 513 sheet: -2.51 (0.43), residues: 97 loop : -2.88 (0.25), residues: 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 264 average time/residue: 0.1931 time to fit residues: 70.9814 Evaluate side-chains 231 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0841 time to fit residues: 3.4988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN F 150 GLN G 93 GLN B 27 ASN B 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8963 Z= 0.243 Angle : 0.903 24.893 12141 Z= 0.399 Chirality : 0.098 2.365 1446 Planarity : 0.005 0.052 1513 Dihedral : 8.624 84.115 1264 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.59 (0.24), residues: 1094 helix: -0.68 (0.22), residues: 521 sheet: -2.30 (0.46), residues: 97 loop : -2.79 (0.26), residues: 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 259 average time/residue: 0.1859 time to fit residues: 67.4005 Evaluate side-chains 236 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0819 time to fit residues: 4.9810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8963 Z= 0.223 Angle : 0.882 25.017 12141 Z= 0.388 Chirality : 0.097 2.356 1446 Planarity : 0.005 0.044 1513 Dihedral : 8.398 81.934 1264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.30 (0.24), residues: 1094 helix: -0.44 (0.23), residues: 519 sheet: -2.19 (0.46), residues: 97 loop : -2.63 (0.26), residues: 478 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 244 average time/residue: 0.1910 time to fit residues: 65.2361 Evaluate side-chains 230 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1043 time to fit residues: 3.7191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 0.0970 chunk 49 optimal weight: 0.0270 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN F 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8963 Z= 0.193 Angle : 0.870 25.110 12141 Z= 0.378 Chirality : 0.096 2.352 1446 Planarity : 0.004 0.041 1513 Dihedral : 8.095 81.830 1264 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.12 (0.25), residues: 1094 helix: -0.30 (0.23), residues: 519 sheet: -2.11 (0.47), residues: 97 loop : -2.51 (0.27), residues: 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 244 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 251 average time/residue: 0.1878 time to fit residues: 66.0056 Evaluate side-chains 228 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0858 time to fit residues: 3.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 ASN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8963 Z= 0.195 Angle : 0.864 24.943 12141 Z= 0.377 Chirality : 0.096 2.353 1446 Planarity : 0.004 0.041 1513 Dihedral : 8.001 81.347 1264 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 1.94 % 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: -1.97 (0.25), residues: 1094 helix: -0.20 (0.23), residues: 522 sheet: -2.01 (0.48), residues: 97 loop : -2.42 (0.27), residues: 475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 238 average time/residue: 0.1863 time to fit residues: 62.3532 Evaluate side-chains 227 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 219 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0908 time to fit residues: 2.7874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8963 Z= 0.172 Angle : 0.867 25.115 12141 Z= 0.373 Chirality : 0.095 2.344 1446 Planarity : 0.004 0.045 1513 Dihedral : 7.672 84.210 1264 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.74 (0.25), residues: 1094 helix: -0.02 (0.23), residues: 525 sheet: -1.82 (0.48), residues: 97 loop : -2.33 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 237 average time/residue: 0.1955 time to fit residues: 64.6410 Evaluate side-chains 227 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0941 time to fit residues: 2.7683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 208 ASN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8963 Z= 0.281 Angle : 0.917 24.743 12141 Z= 0.408 Chirality : 0.098 2.360 1446 Planarity : 0.005 0.041 1513 Dihedral : 7.958 75.072 1264 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.97 (0.25), residues: 1094 helix: -0.26 (0.23), residues: 524 sheet: -1.88 (0.49), residues: 88 loop : -2.39 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 220 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 225 average time/residue: 0.1809 time to fit residues: 58.4146 Evaluate side-chains 230 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 221 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0804 time to fit residues: 2.7892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8963 Z= 0.178 Angle : 0.889 24.916 12141 Z= 0.384 Chirality : 0.096 2.354 1446 Planarity : 0.004 0.045 1513 Dihedral : 7.637 79.279 1264 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1094 helix: 0.00 (0.23), residues: 525 sheet: -1.74 (0.49), residues: 88 loop : -2.26 (0.28), residues: 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 241 average time/residue: 0.1880 time to fit residues: 63.7477 Evaluate side-chains 232 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0817 time to fit residues: 1.7901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.159832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132432 restraints weight = 17198.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134894 restraints weight = 10169.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136526 restraints weight = 7004.969| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8963 Z= 0.187 Angle : 0.899 24.960 12141 Z= 0.392 Chirality : 0.096 2.348 1446 Planarity : 0.005 0.041 1513 Dihedral : 7.319 81.720 1264 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer Outliers : 0.54 % 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: -1.56 (0.26), residues: 1094 helix: 0.05 (0.23), residues: 528 sheet: -1.46 (0.50), residues: 88 loop : -2.22 (0.28), residues: 478 =============================================================================== Job complete usr+sys time: 1968.59 seconds wall clock time: 36 minutes 14.94 seconds (2174.94 seconds total)