Starting phenix.real_space_refine (version: dev) on Sun Dec 11 20:27:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/12_2022/6qnu_4609.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/12_2022/6qnu_4609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/12_2022/6qnu_4609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/12_2022/6qnu_4609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/12_2022/6qnu_4609.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnu_4609/12_2022/6qnu_4609.pdb" } resolution = 3.8 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= 0.008 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 PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E GLU 191": "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: 7250 Number of models: 1 Model: "" Number of chains: 5 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 Chain: "E" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1476 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 7, 'TRANS': 179} Chain breaks: 5 Time building chain proxies: 4.71, per 1000 atoms: 0.65 Number of scatterers: 7250 At special positions: 0 Unit cell: (94.963, 105.633, 93.896, 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 22 16.00 O 1404 8.00 N 1169 7.00 C 4655 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: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 17 sheets defined 2.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.583A pdb=" N ASN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.153A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.424A pdb=" N GLY E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL A 269 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 188 through 196 removed outlier: 3.734A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.175A pdb=" N LEU C 305 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 132 through 133 removed outlier: 3.652A pdb=" N PHE C 312 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 188 through 197 removed outlier: 5.542A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.401A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 191 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 151 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG D 193 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR D 149 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.854A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 170 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 222 through 223 removed outlier: 3.722A pdb=" N VAL D 222 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 259 through 263 removed outlier: 3.753A pdb=" N VAL D 303 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 324 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 120 removed outlier: 6.511A pdb=" N PHE E 115 " --> pdb=" O GLN E 210 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ARG E 212 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY E 117 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU E 214 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL E 119 " --> pdb=" O LEU E 214 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 190 " --> pdb=" O ALA E 207 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR E 187 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU E 154 " --> pdb=" O THR E 187 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR E 189 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.724A pdb=" N ILE E 171 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 222 through 223 removed outlier: 3.521A pdb=" N VAL E 222 " --> pdb=" O PHE E 247 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 229 through 232 removed outlier: 6.681A pdb=" N GLY E 230 " --> pdb=" O LYS E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AB8, first strand: chain 'E' and resid 272 through 277 188 hydrogen bonds defined for protein. 507 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: 1.75 Time building geometry restraints manager: 2.99 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: 2260 1.34 - 1.46: 1349 1.46 - 1.57: 3752 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 7399 Sorted by residual: bond pdb=" C GLU E 155 " pdb=" N PRO E 156 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 bond pdb=" CA THR A 304 " pdb=" CB THR A 304 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.95e+00 bond pdb=" CA TYR D 158 " pdb=" C TYR D 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.64e+00 bond pdb=" CA TYR E 158 " pdb=" C TYR E 158 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.26e-02 6.30e+03 1.63e+00 ... (remaining 7394 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 231 106.78 - 113.59: 4100 113.59 - 120.40: 2620 120.40 - 127.20: 3032 127.20 - 134.01: 67 Bond angle restraints: 10050 Sorted by residual: angle pdb=" C ALA A 303 " pdb=" N THR A 304 " pdb=" CA THR A 304 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.88e+01 angle pdb=" C ASN D 219 " pdb=" N ILE D 220 " pdb=" CA ILE D 220 " ideal model delta sigma weight residual 122.13 130.06 -7.93 1.85e+00 2.92e-01 1.84e+01 angle pdb=" N ILE D 315 " pdb=" CA ILE D 315 " pdb=" C ILE D 315 " ideal model delta sigma weight residual 113.71 109.68 4.03 9.50e-01 1.11e+00 1.80e+01 angle pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N TRP D 257 " pdb=" CA TRP D 257 " pdb=" C TRP D 257 " ideal model delta sigma weight residual 114.04 109.06 4.98 1.24e+00 6.50e-01 1.62e+01 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 3940 16.84 - 33.69: 390 33.69 - 50.53: 66 50.53 - 67.37: 11 67.37 - 84.22: 6 Dihedral angle restraints: 4413 sinusoidal: 1724 harmonic: 2689 Sorted by residual: 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 -138.37 -41.63 0 5.00e+00 4.00e-02 6.93e+01 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 -145.15 -34.85 0 5.00e+00 4.00e-02 4.86e+01 dihedral pdb=" CA ASP D 218 " pdb=" C ASP D 218 " pdb=" N ASN D 219 " pdb=" CA ASN D 219 " ideal model delta harmonic sigma weight residual 180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 845 0.053 - 0.106: 236 0.106 - 0.159: 77 0.159 - 0.211: 7 0.211 - 0.264: 5 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA TYR E 158 " pdb=" N TYR E 158 " pdb=" C TYR E 158 " pdb=" CB TYR E 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+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 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE C 306 " pdb=" CA ILE C 306 " pdb=" CG1 ILE C 306 " pdb=" CG2 ILE C 306 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 1167 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C LYS B 275 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.016 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=" CA ASN E 219 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASN E 219 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN E 219 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE E 220 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 308 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO A 309 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " -0.030 5.00e-02 4.00e+02 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2300 2.84 - 3.35: 5486 3.35 - 3.87: 11611 3.87 - 4.38: 12135 4.38 - 4.90: 22568 Nonbonded interactions: 54100 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.324 2.440 nonbonded pdb=" OE1 GLU C 194 " pdb=" OH TYR C 196 " model vdw 2.328 2.440 nonbonded pdb=" OG1 THR C 135 " pdb=" O LEU C 158 " model vdw 2.349 2.440 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.351 2.440 nonbonded pdb=" OE1 GLU E 170 " pdb=" OH TYR E 172 " model vdw 2.392 2.440 ... (remaining 54095 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)) } ncs_group { reference = (chain 'D' and (resid 108 through 134 or resid 146 through 193 or resid 206 thro \ ugh 233 or resid 238 through 291 or resid 299 through 331)) selection = chain 'E' } 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 22 5.16 5 C 4655 2.51 5 N 1169 2.21 5 O 1404 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.530 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 23.440 Find NCS groups from input model: 0.520 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.045 7399 Z= 0.286 Angle : 0.909 10.852 10050 Z= 0.494 Chirality : 0.057 0.264 1170 Planarity : 0.006 0.054 1269 Dihedral : 13.913 84.215 2671 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -4.05 (0.24), residues: 880 helix: -4.32 (0.26), residues: 24 sheet: -1.61 (0.27), residues: 323 loop : -3.50 (0.21), residues: 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 0.920 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 187 average time/residue: 0.2601 time to fit residues: 60.6820 Evaluate side-chains 123 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0631 time to fit residues: 1.5451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 151 ASN A 168 ASN A 246 HIS ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN D 210 GLN D 236 GLN E 126 HIS E 183 HIS E 208 GLN E 217 ASN E 312 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 7399 Z= 0.314 Angle : 0.660 6.789 10050 Z= 0.342 Chirality : 0.046 0.180 1170 Planarity : 0.004 0.038 1269 Dihedral : 6.068 30.963 971 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.48 (0.25), residues: 880 helix: -2.80 (0.75), residues: 18 sheet: -1.54 (0.27), residues: 334 loop : -2.96 (0.24), residues: 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.810 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 140 average time/residue: 0.2059 time to fit residues: 38.0675 Evaluate side-chains 123 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0677 time to fit residues: 2.8176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 249 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN B 246 HIS C 151 ASN E 208 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 7399 Z= 0.331 Angle : 0.664 8.791 10050 Z= 0.342 Chirality : 0.047 0.166 1170 Planarity : 0.004 0.033 1269 Dihedral : 5.992 29.872 971 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.26), residues: 880 helix: -1.82 (1.01), residues: 18 sheet: -1.30 (0.27), residues: 333 loop : -2.80 (0.24), residues: 529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.997 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 135 average time/residue: 0.2007 time to fit residues: 35.9550 Evaluate side-chains 118 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0697 time to fit residues: 2.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 151 ASN E 208 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 7399 Z= 0.381 Angle : 0.690 7.611 10050 Z= 0.356 Chirality : 0.048 0.163 1170 Planarity : 0.004 0.032 1269 Dihedral : 6.122 31.502 971 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -3.11 (0.27), residues: 880 helix: -1.25 (1.16), residues: 18 sheet: -1.32 (0.28), residues: 328 loop : -2.71 (0.25), residues: 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.912 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 129 average time/residue: 0.1845 time to fit residues: 32.4624 Evaluate side-chains 121 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0619 time to fit residues: 3.5194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN C 151 ASN E 208 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7399 Z= 0.281 Angle : 0.629 6.914 10050 Z= 0.324 Chirality : 0.046 0.158 1170 Planarity : 0.004 0.031 1269 Dihedral : 5.796 28.357 971 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.27), residues: 880 helix: -0.61 (1.22), residues: 19 sheet: -1.42 (0.27), residues: 339 loop : -2.51 (0.26), residues: 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.893 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 119 average time/residue: 0.1921 time to fit residues: 31.2311 Evaluate side-chains 112 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0672 time to fit residues: 2.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 302 GLN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7399 Z= 0.271 Angle : 0.618 6.876 10050 Z= 0.317 Chirality : 0.046 0.156 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.642 27.900 971 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.27), residues: 880 helix: -0.59 (1.20), residues: 19 sheet: -1.24 (0.28), residues: 329 loop : -2.48 (0.26), residues: 532 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.954 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.1963 time to fit residues: 31.7151 Evaluate side-chains 117 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0670 time to fit residues: 2.7116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.044 7399 Z= 0.523 Angle : 0.776 7.521 10050 Z= 0.399 Chirality : 0.051 0.169 1170 Planarity : 0.005 0.039 1269 Dihedral : 6.353 33.635 971 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.18 % Favored : 86.70 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -3.10 (0.26), residues: 880 helix: -1.02 (1.11), residues: 18 sheet: -1.55 (0.27), residues: 329 loop : -2.52 (0.25), residues: 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.858 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.1911 time to fit residues: 28.4441 Evaluate side-chains 111 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0899 time to fit residues: 2.9799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 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: 0.8129 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7399 Z= 0.165 Angle : 0.586 7.336 10050 Z= 0.300 Chirality : 0.046 0.154 1170 Planarity : 0.004 0.031 1269 Dihedral : 5.360 26.069 971 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.27), residues: 880 helix: -1.95 (0.90), residues: 26 sheet: -1.43 (0.27), residues: 348 loop : -2.24 (0.27), residues: 506 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.893 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 105 average time/residue: 0.1880 time to fit residues: 27.1338 Evaluate side-chains 97 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS E 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7399 Z= 0.182 Angle : 0.582 6.952 10050 Z= 0.297 Chirality : 0.045 0.151 1170 Planarity : 0.004 0.030 1269 Dihedral : 5.120 23.924 971 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.27), residues: 880 helix: -1.79 (0.90), residues: 25 sheet: -1.16 (0.28), residues: 339 loop : -2.24 (0.27), residues: 516 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.874 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 112 average time/residue: 0.1776 time to fit residues: 27.7456 Evaluate side-chains 106 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0690 time to fit residues: 1.8853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 7 optimal weight: 0.0570 chunk 54 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS B 130 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 7399 Z= 0.143 Angle : 0.553 7.342 10050 Z= 0.281 Chirality : 0.044 0.147 1170 Planarity : 0.004 0.029 1269 Dihedral : 4.676 20.461 971 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.28), residues: 880 helix: -1.84 (0.88), residues: 25 sheet: -1.00 (0.28), residues: 353 loop : -2.03 (0.27), residues: 502 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 0.959 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 126 average time/residue: 0.1901 time to fit residues: 32.7432 Evaluate side-chains 119 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0801 time to fit residues: 1.4751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 80 optimal weight: 0.0370 chunk 47 optimal weight: 10.0000 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** C 130 ASN ** 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 = 0.4020 r_free = 0.4020 target = 0.158602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138948 restraints weight = 10763.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141787 restraints weight = 6502.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.143708 restraints weight = 4540.267| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7399 Z= 0.187 Angle : 0.595 9.753 10050 Z= 0.301 Chirality : 0.045 0.187 1170 Planarity : 0.004 0.032 1269 Dihedral : 4.740 23.630 971 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.28), residues: 880 helix: -1.77 (0.90), residues: 25 sheet: -0.89 (0.28), residues: 348 loop : -2.05 (0.27), residues: 507 =============================================================================== Job complete usr+sys time: 1524.97 seconds wall clock time: 28 minutes 34.07 seconds (1714.07 seconds total)