Starting phenix.real_space_refine (version: dev) on Sun Dec 11 17:09:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/12_2022/6qnt_4608.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/12_2022/6qnt_4608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/12_2022/6qnt_4608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/12_2022/6qnt_4608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/12_2022/6qnt_4608.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/12_2022/6qnt_4608.pdb" } resolution = 3.5 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 5774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 2 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1409 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Time building chain proxies: 4.00, per 1000 atoms: 0.69 Number of scatterers: 5774 At special positions: 0 Unit cell: (93.896, 100.298, 91.762, 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 20 16.00 O 1117 8.00 N 928 7.00 C 3709 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: 2.03 Conformation dependent library (CDL) restraints added in 840.5 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 16 sheets defined 3.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.524A pdb=" N ASN B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.671A pdb=" N LYS C 185 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 182 through 186' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.754A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.562A pdb=" N LEU A 160 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.687A pdb=" N THR A 172 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 197 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 197 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 154 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 197 removed outlier: 3.731A pdb=" N TYR B 284 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 215 through 216 removed outlier: 3.990A pdb=" N VAL C 161 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.653A pdb=" N LEU C 292 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.653A pdb=" N LEU C 292 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.733A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.855A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 230 through 231 removed outlier: 6.641A pdb=" N GLY D 230 " --> pdb=" O LYS D 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 245 removed outlier: 6.839A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 285 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 282 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 262 through 265 removed outlier: 7.010A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 387 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 2.24 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: 1788 1.34 - 1.46: 1082 1.46 - 1.57: 2995 1.57 - 1.69: 0 1.69 - 1.80: 34 Bond restraints: 5899 Sorted by residual: bond pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.53e+00 bond pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.57e+00 bond pdb=" CA LYS A 275 " pdb=" C LYS A 275 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.19e+00 bond pdb=" CA LYS C 275 " pdb=" C LYS C 275 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.16e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.95e+00 ... (remaining 5894 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.02: 198 107.02 - 113.78: 3264 113.78 - 120.54: 2175 120.54 - 127.30: 2319 127.30 - 134.07: 62 Bond angle restraints: 8018 Sorted by residual: angle pdb=" C GLU D 234 " pdb=" N ASN D 235 " pdb=" CA ASN D 235 " ideal model delta sigma weight residual 122.82 132.08 -9.26 1.42e+00 4.96e-01 4.25e+01 angle pdb=" N THR B 135 " pdb=" CA THR B 135 " pdb=" C THR B 135 " ideal model delta sigma weight residual 113.89 106.62 7.27 1.58e+00 4.01e-01 2.12e+01 angle pdb=" C ASN A 274 " pdb=" N LYS A 275 " pdb=" CA LYS A 275 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.03e+01 angle pdb=" N ASN D 235 " pdb=" CA ASN D 235 " pdb=" C ASN D 235 " ideal model delta sigma weight residual 111.17 116.92 -5.75 1.41e+00 5.03e-01 1.66e+01 angle pdb=" CA TYR D 158 " pdb=" CB TYR D 158 " pdb=" CG TYR D 158 " ideal model delta sigma weight residual 113.90 121.08 -7.18 1.80e+00 3.09e-01 1.59e+01 ... (remaining 8013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3116 16.52 - 33.03: 316 33.03 - 49.55: 65 49.55 - 66.07: 9 66.07 - 82.59: 5 Dihedral angle restraints: 3511 sinusoidal: 1368 harmonic: 2143 Sorted by residual: dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual -180.00 -132.74 -47.26 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -136.92 -43.08 0 5.00e+00 4.00e-02 7.42e+01 dihedral pdb=" CA LEU C 273 " pdb=" C LEU C 273 " pdb=" N ASN C 274 " pdb=" CA ASN C 274 " ideal model delta harmonic sigma weight residual -180.00 -139.58 -40.42 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 3508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 689 0.053 - 0.107: 182 0.107 - 0.160: 48 0.160 - 0.213: 4 0.213 - 0.267: 4 Chirality restraints: 927 Sorted by residual: chirality pdb=" CA ASN D 235 " pdb=" N ASN D 235 " pdb=" C ASN D 235 " pdb=" CB ASN D 235 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA TYR D 158 " pdb=" N TYR D 158 " pdb=" C TYR D 158 " pdb=" CB TYR D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE B 145 " pdb=" CA ILE B 145 " pdb=" CG1 ILE B 145 " pdb=" CG2 ILE B 145 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 924 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C LYS B 275 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 276 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 308 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.73e+00 pdb=" N PRO C 309 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 273 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C LEU B 273 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU B 273 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 274 " -0.014 2.00e-02 2.50e+03 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1875 2.84 - 3.36: 4172 3.36 - 3.87: 9369 3.87 - 4.39: 9650 4.39 - 4.90: 18278 Nonbonded interactions: 43344 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.329 2.440 nonbonded pdb=" O LEU B 204 " pdb=" OG SER B 208 " model vdw 2.345 2.440 nonbonded pdb=" OE1 GLU A 194 " pdb=" OH TYR A 196 " model vdw 2.348 2.440 nonbonded pdb=" O VAL D 305 " pdb=" OH TYR D 319 " model vdw 2.349 2.440 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.366 2.440 ... (remaining 43339 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' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ ugh 318)) selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318)) } 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 20 5.16 5 C 3709 2.51 5 N 928 2.21 5 O 1117 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: 0.300 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: 2.280 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.060 Process input model: 19.270 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 0.040 5899 Z= 0.279 Angle : 0.852 12.128 8018 Z= 0.460 Chirality : 0.054 0.267 927 Planarity : 0.007 0.065 1013 Dihedral : 13.952 82.587 2127 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -4.25 (0.25), residues: 705 helix: -4.46 (0.22), residues: 32 sheet: -2.09 (0.28), residues: 284 loop : -3.34 (0.23), residues: 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.738 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.2166 time to fit residues: 41.0811 Evaluate side-chains 111 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0501 time to fit residues: 0.9774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 188 ASN A 246 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN D 217 ASN D 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 5899 Z= 0.437 Angle : 0.690 8.701 8018 Z= 0.356 Chirality : 0.048 0.154 927 Planarity : 0.005 0.041 1013 Dihedral : 5.938 38.703 777 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.65 % Favored : 91.21 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.88 % 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: -3.67 (0.27), residues: 705 helix: -4.01 (0.31), residues: 32 sheet: -1.74 (0.29), residues: 286 loop : -2.91 (0.26), residues: 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.657 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.1810 time to fit residues: 25.7780 Evaluate side-chains 101 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0592 time to fit residues: 1.6597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 5899 Z= 0.158 Angle : 0.546 7.603 8018 Z= 0.278 Chirality : 0.043 0.136 927 Planarity : 0.003 0.031 1013 Dihedral : 5.194 34.493 777 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.18 (0.28), residues: 705 helix: -3.61 (0.38), residues: 32 sheet: -1.41 (0.30), residues: 286 loop : -2.59 (0.26), residues: 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.733 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 117 average time/residue: 0.1789 time to fit residues: 27.2892 Evaluate side-chains 109 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0545 time to fit residues: 1.5722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 5899 Z= 0.330 Angle : 0.613 7.930 8018 Z= 0.312 Chirality : 0.045 0.137 927 Planarity : 0.004 0.033 1013 Dihedral : 5.433 36.592 777 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -2.90 (0.29), residues: 705 helix: -2.98 (0.54), residues: 26 sheet: -1.25 (0.31), residues: 275 loop : -2.40 (0.27), residues: 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 0.1916 time to fit residues: 27.2237 Evaluate side-chains 104 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0619 time to fit residues: 1.6942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.0870 chunk 47 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 5899 Z= 0.135 Angle : 0.527 8.843 8018 Z= 0.262 Chirality : 0.043 0.137 927 Planarity : 0.003 0.027 1013 Dihedral : 4.810 35.165 777 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.29), residues: 705 helix: -3.04 (0.52), residues: 32 sheet: -1.08 (0.31), residues: 274 loop : -2.18 (0.27), residues: 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 114 average time/residue: 0.1940 time to fit residues: 28.6179 Evaluate side-chains 104 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0696 time to fit residues: 1.6891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.0980 chunk 68 optimal weight: 0.0470 chunk 57 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 66 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5899 Z= 0.290 Angle : 0.586 7.982 8018 Z= 0.295 Chirality : 0.045 0.139 927 Planarity : 0.003 0.030 1013 Dihedral : 5.119 36.176 777 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.48 (0.29), residues: 705 helix: -2.42 (0.67), residues: 26 sheet: -1.00 (0.31), residues: 273 loop : -2.11 (0.27), residues: 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.1900 time to fit residues: 24.6423 Evaluate side-chains 98 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0635 time to fit residues: 1.4554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.0370 chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 5899 Z= 0.141 Angle : 0.520 7.108 8018 Z= 0.260 Chirality : 0.043 0.139 927 Planarity : 0.003 0.027 1013 Dihedral : 4.575 33.878 777 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.30), residues: 705 helix: -2.16 (0.72), residues: 26 sheet: -0.92 (0.31), residues: 278 loop : -1.98 (0.28), residues: 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 111 average time/residue: 0.1792 time to fit residues: 26.2149 Evaluate side-chains 98 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0618 time to fit residues: 1.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 5899 Z= 0.449 Angle : 0.694 9.762 8018 Z= 0.347 Chirality : 0.047 0.168 927 Planarity : 0.004 0.031 1013 Dihedral : 5.495 37.089 777 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.30), residues: 705 helix: -2.14 (0.75), residues: 26 sheet: -0.95 (0.31), residues: 275 loop : -2.10 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.696 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 101 average time/residue: 0.1950 time to fit residues: 25.6082 Evaluate side-chains 98 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0646 time to fit residues: 1.6845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 5899 Z= 0.223 Angle : 0.602 9.322 8018 Z= 0.301 Chirality : 0.045 0.136 927 Planarity : 0.003 0.029 1013 Dihedral : 5.197 37.334 777 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.32 (0.30), residues: 705 helix: -2.00 (0.79), residues: 26 sheet: -0.89 (0.31), residues: 275 loop : -2.02 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.761 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 101 average time/residue: 0.1816 time to fit residues: 24.1618 Evaluate side-chains 97 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0652 time to fit residues: 1.2889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 5899 Z= 0.193 Angle : 0.592 9.419 8018 Z= 0.297 Chirality : 0.044 0.133 927 Planarity : 0.003 0.031 1013 Dihedral : 5.012 36.540 777 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.30), residues: 705 helix: -2.45 (0.69), residues: 32 sheet: -0.86 (0.31), residues: 276 loop : -1.97 (0.29), residues: 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.776 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1736 time to fit residues: 22.9619 Evaluate side-chains 97 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115926 restraints weight = 7918.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118844 restraints weight = 4410.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120969 restraints weight = 2953.977| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 5899 Z= 0.208 Angle : 0.592 9.389 8018 Z= 0.298 Chirality : 0.044 0.131 927 Planarity : 0.003 0.030 1013 Dihedral : 4.976 36.522 777 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.30), residues: 705 helix: -1.18 (0.94), residues: 20 sheet: -0.82 (0.31), residues: 276 loop : -1.88 (0.28), residues: 409 =============================================================================== Job complete usr+sys time: 1356.36 seconds wall clock time: 25 minutes 23.75 seconds (1523.75 seconds total)