Starting phenix.real_space_refine (version: dev) on Thu May 12 16:07:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtu_24689/05_2022/7rtu_24689.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtu_24689/05_2022/7rtu_24689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtu_24689/05_2022/7rtu_24689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtu_24689/05_2022/7rtu_24689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtu_24689/05_2022/7rtu_24689.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtu_24689/05_2022/7rtu_24689.pdb" } resolution = 3.89 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= 1.000 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 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "B ASP 278": "OD1" <-> "OD2" Residue "B ASP 366": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 5962 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3053 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 9, 'TRANS': 385} Chain breaks: 1 Chain: "B" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2755 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 6, 'TRANS': 352} Chain breaks: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.04, per 1000 atoms: 0.68 Number of scatterers: 5962 At special positions: 0 Unit cell: (74.705, 60.21, 223, 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 48 16.00 O 1126 8.00 N 959 7.00 C 3829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.02 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG C 1 " - " ASN A 129 " " NAG D 1 " - " ASN A 352 " " NAG E 1 " - " ASN B 129 " " NAG F 1 " - " ASN B 352 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 89.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 Processing helix chain 'A' and resid 38 through 73 removed outlier: 3.727A pdb=" N LEU A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 162 removed outlier: 4.419A pdb=" N LEU A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 187 removed outlier: 4.423A pdb=" N THR A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 236 Processing helix chain 'A' and resid 245 through 276 removed outlier: 3.766A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 removed outlier: 3.553A pdb=" N THR A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.530A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 333 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 365 removed outlier: 4.179A pdb=" N GLY A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.486A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 Proline residue: A 411 - end of helix removed outlier: 3.860A pdb=" N TRP A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 71 removed outlier: 4.519A pdb=" N SER B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 45 " --> pdb=" O TYR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 162 removed outlier: 3.556A pdb=" N ILE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 150 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.711A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 236 removed outlier: 3.658A pdb=" N THR B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 245 through 276 removed outlier: 4.081A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.718A pdb=" N THR B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 333 Processing helix chain 'B' and resid 338 through 365 removed outlier: 3.849A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 346 " --> pdb=" O LYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 414 removed outlier: 4.394A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Proline residue: B 411 - end of helix 547 hydrogen bonds defined for protein. 1641 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: 1.64 Time building geometry restraints manager: 2.96 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: 1866 1.34 - 1.46: 1093 1.46 - 1.58: 3048 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6073 Sorted by residual: bond pdb=" CB MET A 322 " pdb=" CG MET A 322 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" SD MET A 322 " pdb=" CE MET A 322 " ideal model delta sigma weight residual 1.791 1.770 0.021 2.50e-02 1.60e+03 7.17e-01 bond pdb=" CG MET A 322 " pdb=" SD MET A 322 " ideal model delta sigma weight residual 1.803 1.783 0.020 2.50e-02 1.60e+03 6.62e-01 bond pdb=" CB MET A 174 " pdb=" CG MET A 174 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.51e-01 bond pdb=" CB ASP B 384 " pdb=" CG ASP B 384 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 5.74e-01 ... (remaining 6068 not shown) Histogram of bond angle deviations from ideal: 97.84 - 105.07: 61 105.07 - 112.29: 3318 112.29 - 119.52: 1891 119.52 - 126.74: 2920 126.74 - 133.97: 79 Bond angle restraints: 8269 Sorted by residual: angle pdb=" N VAL B 194 " pdb=" CA VAL B 194 " pdb=" C VAL B 194 " ideal model delta sigma weight residual 112.96 109.08 3.88 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 104.26 8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" C LYS B 147 " pdb=" N VAL B 148 " pdb=" CA VAL B 148 " ideal model delta sigma weight residual 122.97 120.53 2.44 9.80e-01 1.04e+00 6.20e+00 angle pdb=" C MET A 174 " pdb=" CA MET A 174 " pdb=" CB MET A 174 " ideal model delta sigma weight residual 109.99 114.49 -4.50 2.09e+00 2.29e-01 4.64e+00 angle pdb=" CA LEU A 67 " pdb=" CB LEU A 67 " pdb=" CG LEU A 67 " ideal model delta sigma weight residual 116.30 123.25 -6.95 3.50e+00 8.16e-02 3.94e+00 ... (remaining 8264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 3270 21.55 - 43.09: 262 43.09 - 64.64: 26 64.64 - 86.18: 6 86.18 - 107.73: 2 Dihedral angle restraints: 3566 sinusoidal: 1383 harmonic: 2183 Sorted by residual: dihedral pdb=" C1 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C4 NAG D 2 " ideal model delta sinusoidal sigma weight residual -50.00 57.73 -107.73 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" C1 NAG F 2 " pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " ideal model delta sinusoidal sigma weight residual -50.00 56.95 -106.95 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual 93.00 46.08 46.92 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 3563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 907 0.052 - 0.104: 118 0.104 - 0.156: 9 0.156 - 0.208: 0 0.208 - 0.260: 3 Chirality restraints: 1037 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 352 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 129 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 352 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1034 not shown) Planarity restraints: 1009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 381 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" C ILE B 381 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE B 381 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS B 382 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 337 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO A 338 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 379 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C THR A 379 " 0.024 2.00e-02 2.50e+03 pdb=" O THR A 379 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 380 " -0.008 2.00e-02 2.50e+03 ... (remaining 1006 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 179 2.72 - 3.26: 6387 3.26 - 3.81: 10502 3.81 - 4.35: 10390 4.35 - 4.90: 18898 Nonbonded interactions: 46356 Sorted by model distance: nonbonded pdb=" O TYR A 280 " pdb=" ND2 ASN A 284 " model vdw 2.175 2.520 nonbonded pdb=" O ILE A 9 " pdb=" OH TYR A 383 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 212 " model vdw 2.253 2.520 nonbonded pdb=" OD1 ASN B 111 " pdb=" NH1 ARG B 212 " model vdw 2.257 2.520 nonbonded pdb=" OD1 ASP A 223 " pdb=" OG1 THR A 252 " model vdw 2.293 2.440 ... (remaining 46351 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' and (resid 39 through 71 or resid 89 through 414)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'D' selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'F' } 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 48 5.16 5 C 3829 2.51 5 N 959 2.21 5 O 1126 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.870 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 20.700 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 0.033 6073 Z= 0.180 Angle : 0.507 8.436 8269 Z= 0.260 Chirality : 0.036 0.260 1037 Planarity : 0.003 0.035 1005 Dihedral : 14.840 107.728 2150 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.32 (0.31), residues: 746 helix: 3.15 (0.20), residues: 662 sheet: None (None), residues: 0 loop : 0.02 (0.73), residues: 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.703 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1743 time to fit residues: 19.5185 Evaluate side-chains 70 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 6073 Z= 0.284 Angle : 0.567 6.738 8269 Z= 0.294 Chirality : 0.040 0.278 1037 Planarity : 0.004 0.055 1005 Dihedral : 8.421 108.245 890 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.41 % 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: 3.92 (0.30), residues: 746 helix: 2.86 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -0.08 (0.73), residues: 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.638 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.1719 time to fit residues: 18.0229 Evaluate side-chains 75 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.708 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0643 time to fit residues: 1.6565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 6073 Z= 0.202 Angle : 0.476 6.799 8269 Z= 0.248 Chirality : 0.037 0.261 1037 Planarity : 0.004 0.071 1005 Dihedral : 8.349 107.832 890 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.30), residues: 746 helix: 3.00 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.21 (0.73), residues: 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.568 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 74 average time/residue: 0.1703 time to fit residues: 17.1061 Evaluate side-chains 67 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 0.0270 chunk 34 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 6073 Z= 0.184 Angle : 0.471 7.138 8269 Z= 0.242 Chirality : 0.036 0.259 1037 Planarity : 0.004 0.076 1005 Dihedral : 8.293 107.585 890 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.30), residues: 746 helix: 3.10 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.19 (0.72), residues: 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.683 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 80 average time/residue: 0.1659 time to fit residues: 18.1227 Evaluate side-chains 76 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0580 time to fit residues: 1.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 6073 Z= 0.245 Angle : 0.515 6.848 8269 Z= 0.267 Chirality : 0.039 0.273 1037 Planarity : 0.004 0.078 1005 Dihedral : 8.352 108.058 890 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.30), residues: 746 helix: 2.99 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.27 (0.72), residues: 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.644 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 84 average time/residue: 0.1614 time to fit residues: 18.5577 Evaluate side-chains 74 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0569 time to fit residues: 1.5379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 6073 Z= 0.249 Angle : 0.538 7.068 8269 Z= 0.273 Chirality : 0.039 0.272 1037 Planarity : 0.004 0.082 1005 Dihedral : 8.371 108.188 890 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.57 % 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: 3.98 (0.30), residues: 746 helix: 2.92 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.28 (0.72), residues: 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.665 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.1683 time to fit residues: 17.0901 Evaluate side-chains 72 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0573 time to fit residues: 1.4406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 6073 Z= 0.210 Angle : 0.523 8.052 8269 Z= 0.261 Chirality : 0.037 0.261 1037 Planarity : 0.004 0.087 1005 Dihedral : 8.331 107.876 890 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.30), residues: 746 helix: 3.01 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.27 (0.72), residues: 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.710 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 77 average time/residue: 0.1745 time to fit residues: 18.1179 Evaluate side-chains 70 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0559 time to fit residues: 1.1951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 6073 Z= 0.240 Angle : 0.547 8.072 8269 Z= 0.272 Chirality : 0.038 0.270 1037 Planarity : 0.004 0.095 1005 Dihedral : 8.339 107.879 890 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.10 (0.30), residues: 746 helix: 3.01 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.32 (0.70), residues: 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.649 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.1712 time to fit residues: 16.7066 Evaluate side-chains 72 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0580 time to fit residues: 1.2125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 0.0470 chunk 52 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 6073 Z= 0.227 Angle : 0.541 8.311 8269 Z= 0.270 Chirality : 0.038 0.269 1037 Planarity : 0.005 0.104 1005 Dihedral : 8.322 107.726 890 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.17 (0.30), residues: 746 helix: 3.05 (0.19), residues: 667 sheet: None (None), residues: 0 loop : -0.25 (0.71), residues: 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.647 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 74 average time/residue: 0.1710 time to fit residues: 17.3187 Evaluate side-chains 69 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0616 time to fit residues: 1.0656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 0.0770 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.114 6073 Z= 0.248 Angle : 0.552 8.484 8269 Z= 0.279 Chirality : 0.038 0.274 1037 Planarity : 0.005 0.113 1005 Dihedral : 8.337 107.817 890 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.30), residues: 746 helix: 3.01 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.36 (0.70), residues: 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.668 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.1695 time to fit residues: 16.6799 Evaluate side-chains 71 residues out of total 637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0568 time to fit residues: 1.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 24 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 42 optimal weight: 0.0770 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.218512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.209156 restraints weight = 6438.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.205273 restraints weight = 12380.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.200741 restraints weight = 13098.851| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.119 6073 Z= 0.195 Angle : 0.508 9.064 8269 Z= 0.257 Chirality : 0.036 0.259 1037 Planarity : 0.005 0.114 1005 Dihedral : 8.241 107.061 890 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.30), residues: 746 helix: 3.21 (0.20), residues: 667 sheet: None (None), residues: 0 loop : -0.42 (0.69), residues: 79 =============================================================================== Job complete usr+sys time: 1239.65 seconds wall clock time: 23 minutes 24.78 seconds (1404.78 seconds total)