Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:57:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knu_22963/11_2022/7knu_22963.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knu_22963/11_2022/7knu_22963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knu_22963/11_2022/7knu_22963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knu_22963/11_2022/7knu_22963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knu_22963/11_2022/7knu_22963.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7knu_22963/11_2022/7knu_22963.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3809 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 931 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 108} Chain: "P" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2796 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 9, 'TRANS': 331} Chain breaks: 4 Time building chain proxies: 2.70, per 1000 atoms: 0.71 Number of scatterers: 3809 At special positions: 0 Unit cell: (63.08, 105.41, 82.17, 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 31 16.00 O 643 8.00 N 631 7.00 C 2504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 74 " distance=2.03 Simple disulfide: pdb=" SG CYS R 65 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 88 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 282 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 669.6 milliseconds 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 68.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.547A pdb=" N LEU E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 removed outlier: 3.676A pdb=" N GLN E 45 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL E 46 " --> pdb=" O THR E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 80 removed outlier: 5.458A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER E 65 " --> pdb=" O ARG E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.759A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 143 removed outlier: 4.031A pdb=" N PHE E 122 " --> pdb=" O ILE E 118 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 3.911A pdb=" N LEU E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.082A pdb=" N ALA R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN R 50 " --> pdb=" O TYR R 46 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS R 51 " --> pdb=" O GLU R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 167 removed outlier: 3.719A pdb=" N PHE R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE R 147 " --> pdb=" O TYR R 143 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE R 153 " --> pdb=" O HIS R 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER R 159 " --> pdb=" O SER R 155 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE R 162 " --> pdb=" O ILE R 158 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 166 " --> pdb=" O ILE R 162 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS R 167 " --> pdb=" O PHE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 192 removed outlier: 4.146A pdb=" N ASN R 179 " --> pdb=" O THR R 175 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE R 182 " --> pdb=" O LYS R 178 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE R 192 " --> pdb=" O SER R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 208 Processing helix chain 'R' and resid 209 through 242 removed outlier: 3.678A pdb=" N LYS R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY R 224 " --> pdb=" O LEU R 220 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 261 Processing helix chain 'R' and resid 263 through 278 removed outlier: 3.734A pdb=" N SER R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR R 277 " --> pdb=" O ALA R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 removed outlier: 3.535A pdb=" N TRP R 283 " --> pdb=" O ASP R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 319 Proline residue: R 297 - end of helix removed outlier: 3.505A pdb=" N LEU R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 317 " --> pdb=" O VAL R 313 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR R 318 " --> pdb=" O ARG R 314 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 351 removed outlier: 3.668A pdb=" N VAL R 335 " --> pdb=" O TYR R 331 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 337 " --> pdb=" O LYS R 333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU R 341 " --> pdb=" O ALA R 337 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 5.650A pdb=" N GLU R 348 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE R 349 " --> pdb=" O LEU R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 375 removed outlier: 3.596A pdb=" N HIS R 374 " --> pdb=" O HIS R 370 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 388 through 402 Processing sheet with id=AA1, first strand: chain 'R' and resid 83 through 87 removed outlier: 3.507A pdb=" N GLN R 86 " --> pdb=" O VAL R 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 113 through 114 199 hydrogen bonds defined for protein. 591 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: 0.86 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1162 1.34 - 1.46: 1033 1.46 - 1.58: 1681 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 3918 Sorted by residual: bond pdb=" C TYR E 120 " pdb=" N PRO E 121 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.13e+00 bond pdb=" CA MET R 253 " pdb=" C MET R 253 " ideal model delta sigma weight residual 1.524 1.506 0.018 1.29e-02 6.01e+03 1.85e+00 bond pdb=" N LEU R 252 " pdb=" CA LEU R 252 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.42e+00 bond pdb=" CA TRP R 254 " pdb=" C TRP R 254 " ideal model delta sigma weight residual 1.523 1.509 0.015 1.30e-02 5.92e+03 1.28e+00 bond pdb=" N ARG R 173 " pdb=" CA ARG R 173 " ideal model delta sigma weight residual 1.459 1.445 0.014 1.21e-02 6.83e+03 1.27e+00 ... (remaining 3913 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 106 106.67 - 113.50: 2114 113.50 - 120.34: 1506 120.34 - 127.17: 1547 127.17 - 134.01: 61 Bond angle restraints: 5334 Sorted by residual: angle pdb=" N ALA R 247 " pdb=" CA ALA R 247 " pdb=" C ALA R 247 " ideal model delta sigma weight residual 110.10 103.85 6.25 1.49e+00 4.50e-01 1.76e+01 angle pdb=" N MET R 253 " pdb=" CA MET R 253 " pdb=" C MET R 253 " ideal model delta sigma weight residual 111.36 107.96 3.40 1.09e+00 8.42e-01 9.72e+00 angle pdb=" N LYS R 249 " pdb=" CA LYS R 249 " pdb=" C LYS R 249 " ideal model delta sigma weight residual 108.90 113.91 -5.01 1.63e+00 3.76e-01 9.44e+00 angle pdb=" N LEU R 252 " pdb=" CA LEU R 252 " pdb=" C LEU R 252 " ideal model delta sigma weight residual 110.80 116.79 -5.99 2.13e+00 2.20e-01 7.91e+00 angle pdb=" C GLU R 248 " pdb=" N LYS R 249 " pdb=" CA LYS R 249 " ideal model delta sigma weight residual 122.99 119.22 3.77 1.41e+00 5.03e-01 7.16e+00 ... (remaining 5329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2015 17.76 - 35.52: 205 35.52 - 53.28: 36 53.28 - 71.04: 5 71.04 - 88.80: 3 Dihedral angle restraints: 2264 sinusoidal: 891 harmonic: 1373 Sorted by residual: dihedral pdb=" CB CYS R 212 " pdb=" SG CYS R 212 " pdb=" SG CYS R 282 " pdb=" CB CYS R 282 " ideal model delta sinusoidal sigma weight residual 93.00 43.74 49.26 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 52.64 40.36 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -121.81 35.81 1 1.00e+01 1.00e-02 1.81e+01 ... (remaining 2261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 563 0.077 - 0.153: 30 0.153 - 0.230: 4 0.230 - 0.307: 1 0.307 - 0.383: 1 Chirality restraints: 599 Sorted by residual: chirality pdb=" CA PHE R 246 " pdb=" N PHE R 246 " pdb=" C PHE R 246 " pdb=" CB PHE R 246 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA LEU R 252 " pdb=" N LEU R 252 " pdb=" C LEU R 252 " pdb=" CB LEU R 252 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLU R 248 " pdb=" N GLU R 248 " pdb=" C GLU R 248 " pdb=" CB GLU R 248 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 596 not shown) Planarity restraints: 653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 96 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO R 97 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO R 97 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO R 97 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 296 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.62e+00 pdb=" N PRO R 297 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 297 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 297 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 96 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C ASP R 96 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP R 96 " -0.007 2.00e-02 2.50e+03 pdb=" N PRO R 97 " -0.007 2.00e-02 2.50e+03 ... (remaining 650 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 72 2.69 - 3.24: 4048 3.24 - 3.80: 6093 3.80 - 4.35: 8134 4.35 - 4.90: 12421 Nonbonded interactions: 30768 Sorted by model distance: nonbonded pdb=" OG SER R 285 " pdb=" OD1 ASP R 287 " model vdw 2.141 2.440 nonbonded pdb=" O GLY E 33 " pdb=" NH1 ARG E 37 " model vdw 2.197 2.520 nonbonded pdb=" O SER R 170 " pdb=" OG SER R 170 " model vdw 2.296 2.440 nonbonded pdb=" OG SER R 155 " pdb=" OG SER R 381 " model vdw 2.319 2.440 nonbonded pdb=" OE2 GLU E 29 " pdb=" ND2 ASN E 31 " model vdw 2.352 2.520 ... (remaining 30763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 31 5.16 5 C 2504 2.51 5 N 631 2.21 5 O 643 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 3.030 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 15.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3918 Z= 0.174 Angle : 0.643 7.242 5334 Z= 0.371 Chirality : 0.045 0.383 599 Planarity : 0.005 0.110 653 Dihedral : 14.107 88.802 1356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.39), residues: 453 helix: -0.62 (0.30), residues: 298 sheet: -1.73 (1.17), residues: 12 loop : -1.67 (0.50), residues: 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.469 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1776 time to fit residues: 15.6383 Evaluate side-chains 44 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 39 ASN R 219 HIS R 250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 3918 Z= 0.217 Angle : 0.618 5.774 5334 Z= 0.324 Chirality : 0.040 0.135 599 Planarity : 0.005 0.080 653 Dihedral : 4.538 17.265 503 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.39), residues: 453 helix: -0.20 (0.30), residues: 305 sheet: -1.54 (1.22), residues: 12 loop : -2.00 (0.51), residues: 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.490 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.1443 time to fit residues: 10.2228 Evaluate side-chains 48 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0356 time to fit residues: 0.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3918 Z= 0.212 Angle : 0.592 6.509 5334 Z= 0.304 Chirality : 0.040 0.245 599 Planarity : 0.004 0.068 653 Dihedral : 4.536 15.152 503 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.40), residues: 453 helix: 0.02 (0.31), residues: 304 sheet: -1.12 (1.25), residues: 12 loop : -2.03 (0.51), residues: 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.466 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1633 time to fit residues: 11.0113 Evaluate side-chains 49 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0371 time to fit residues: 0.7344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 3918 Z= 0.220 Angle : 0.609 6.864 5334 Z= 0.306 Chirality : 0.040 0.198 599 Planarity : 0.004 0.060 653 Dihedral : 4.557 14.715 503 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.90 (0.39), residues: 453 helix: 0.13 (0.31), residues: 295 sheet: -0.74 (1.38), residues: 12 loop : -1.99 (0.49), residues: 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 57 average time/residue: 0.1402 time to fit residues: 10.3622 Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0379 time to fit residues: 0.7197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3918 Z= 0.178 Angle : 0.594 8.230 5334 Z= 0.296 Chirality : 0.039 0.194 599 Planarity : 0.004 0.056 653 Dihedral : 4.477 14.527 503 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.70 (0.40), residues: 453 helix: 0.28 (0.31), residues: 300 sheet: -0.53 (1.44), residues: 12 loop : -1.97 (0.50), residues: 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.471 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.1286 time to fit residues: 9.6226 Evaluate side-chains 53 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0370 time to fit residues: 0.6842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3918 Z= 0.168 Angle : 0.611 8.771 5334 Z= 0.300 Chirality : 0.040 0.166 599 Planarity : 0.004 0.051 653 Dihedral : 4.410 13.396 503 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.67 (0.40), residues: 453 helix: 0.32 (0.31), residues: 295 sheet: -0.48 (1.43), residues: 12 loop : -1.95 (0.50), residues: 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 63 average time/residue: 0.1528 time to fit residues: 12.2705 Evaluate side-chains 62 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1180 time to fit residues: 1.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 30.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 3918 Z= 0.233 Angle : 0.634 8.523 5334 Z= 0.319 Chirality : 0.040 0.172 599 Planarity : 0.004 0.048 653 Dihedral : 4.488 13.981 503 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.67 (0.40), residues: 453 helix: 0.26 (0.31), residues: 302 sheet: -0.66 (1.39), residues: 12 loop : -1.87 (0.52), residues: 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1383 time to fit residues: 10.4230 Evaluate side-chains 55 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.502 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0379 time to fit residues: 0.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.003 0.038 3918 Z= 0.201 Angle : 0.647 8.023 5334 Z= 0.318 Chirality : 0.041 0.205 599 Planarity : 0.004 0.047 653 Dihedral : 4.526 18.642 503 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.58 (0.41), residues: 453 helix: 0.34 (0.31), residues: 302 sheet: -0.67 (1.39), residues: 12 loop : -1.86 (0.51), residues: 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.1393 time to fit residues: 9.7169 Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0333 time to fit residues: 0.5364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 0.0270 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3918 Z= 0.173 Angle : 0.638 9.142 5334 Z= 0.313 Chirality : 0.039 0.174 599 Planarity : 0.004 0.052 653 Dihedral : 4.414 16.036 503 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.48 (0.41), residues: 453 helix: 0.42 (0.32), residues: 301 sheet: -0.55 (1.42), residues: 12 loop : -1.83 (0.51), residues: 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 58 average time/residue: 0.1323 time to fit residues: 10.1419 Evaluate side-chains 52 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 GLN ** R 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3918 Z= 0.181 Angle : 0.667 8.833 5334 Z= 0.323 Chirality : 0.040 0.215 599 Planarity : 0.004 0.052 653 Dihedral : 4.386 18.754 503 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.39 (0.41), residues: 453 helix: 0.49 (0.32), residues: 301 sheet: -0.56 (1.39), residues: 12 loop : -1.77 (0.52), residues: 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 906 Ramachandran restraints generated. 453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1392 time to fit residues: 10.7682 Evaluate side-chains 52 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.094027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.076501 restraints weight = 15333.624| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 4.78 r_work: 0.3563 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work: 0.3547 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work: 0.3539 rms_B_bonded: 4.55 restraints_weight: 0.0625 r_work: 0.3532 rms_B_bonded: 4.61 restraints_weight: 0.0312 r_work: 0.3524 rms_B_bonded: 4.70 restraints_weight: 0.0156 r_work: 0.3516 rms_B_bonded: 4.80 restraints_weight: 0.0078 r_work: 0.3507 rms_B_bonded: 4.91 restraints_weight: 0.0039 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3918 Z= 0.194 Angle : 0.657 9.301 5334 Z= 0.323 Chirality : 0.040 0.167 599 Planarity : 0.004 0.052 653 Dihedral : 4.379 15.861 503 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.39 (0.41), residues: 453 helix: 0.47 (0.32), residues: 301 sheet: -0.55 (1.38), residues: 12 loop : -1.73 (0.52), residues: 140 =============================================================================== Job complete usr+sys time: 1045.07 seconds wall clock time: 19 minutes 43.26 seconds (1183.26 seconds total)