Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 06:47:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/04_2023/8gyx_34379_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/04_2023/8gyx_34379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/04_2023/8gyx_34379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/04_2023/8gyx_34379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/04_2023/8gyx_34379_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyx_34379/04_2023/8gyx_34379_updated.pdb" } resolution = 3.7 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= 0.004 sd= 0.108 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 4050 2.51 5 N 978 2.21 5 O 1036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 313": "OE1" <-> "OE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6118 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.85, per 1000 atoms: 0.63 Number of scatterers: 6118 At special positions: 0 Unit cell: (108.07, 90.95, 72.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 2 15.00 Mg 4 11.99 O 1036 8.00 N 978 7.00 C 4050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 78 removed outlier: 3.966A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 Processing helix chain 'B' and resid 116 through 142 removed outlier: 3.600A pdb=" N ILE B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 172 removed outlier: 3.595A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 179 through 203 Processing helix chain 'B' and resid 213 through 236 removed outlier: 3.540A pdb=" N LEU B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 246 through 271 Proline residue: B 250 - end of helix removed outlier: 3.702A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 306 removed outlier: 4.200A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 316 through 339 Processing helix chain 'B' and resid 349 through 362 removed outlier: 4.007A pdb=" N GLY B 353 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Proline residue: B 354 - end of helix removed outlier: 3.601A pdb=" N LEU B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 361 " --> pdb=" O PHE B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 399 Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.967A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 Processing helix chain 'A' and resid 116 through 142 removed outlier: 3.600A pdb=" N ILE A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.596A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 179 through 203 Processing helix chain 'A' and resid 213 through 236 removed outlier: 3.540A pdb=" N LEU A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 246 through 271 Proline residue: A 250 - end of helix removed outlier: 3.703A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 306 removed outlier: 4.200A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 316 through 339 Processing helix chain 'A' and resid 349 through 362 removed outlier: 4.006A pdb=" N GLY A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix removed outlier: 3.600A pdb=" N LEU A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 361 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 399 376 hydrogen bonds defined for protein. 1104 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: 1.59 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 898 1.32 - 1.44: 1812 1.44 - 1.57: 3498 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6286 Sorted by residual: bond pdb=" O12 POV A 501 " pdb=" P POV A 501 " ideal model delta sigma weight residual 1.657 1.601 0.056 2.00e-02 2.50e+03 7.96e+00 bond pdb=" O12 POV B 501 " pdb=" P POV B 501 " ideal model delta sigma weight residual 1.657 1.601 0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CB ASN B 144 " pdb=" CG ASN B 144 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.80e+00 bond pdb=" CB ASN A 144 " pdb=" CG ASN A 144 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.77e+00 bond pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta sigma weight residual 1.529 1.567 -0.038 1.62e-02 3.81e+03 5.49e+00 ... (remaining 6281 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 172 105.83 - 112.90: 3084 112.90 - 119.97: 2448 119.97 - 127.04: 2740 127.04 - 134.11: 100 Bond angle restraints: 8544 Sorted by residual: angle pdb=" CB MET A 339 " pdb=" CG MET A 339 " pdb=" SD MET A 339 " ideal model delta sigma weight residual 112.70 130.88 -18.18 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CB MET B 339 " pdb=" CG MET B 339 " pdb=" SD MET B 339 " ideal model delta sigma weight residual 112.70 130.87 -18.17 3.00e+00 1.11e-01 3.67e+01 angle pdb=" CA PRO B 148 " pdb=" N PRO B 148 " pdb=" CD PRO B 148 " ideal model delta sigma weight residual 112.00 104.61 7.39 1.40e+00 5.10e-01 2.79e+01 angle pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" CD PRO A 148 " ideal model delta sigma weight residual 112.00 104.64 7.36 1.40e+00 5.10e-01 2.76e+01 angle pdb=" CA ASN B 144 " pdb=" CB ASN B 144 " pdb=" CG ASN B 144 " ideal model delta sigma weight residual 112.60 117.61 -5.01 1.00e+00 1.00e+00 2.51e+01 ... (remaining 8539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 3223 18.09 - 36.17: 305 36.17 - 54.26: 90 54.26 - 72.34: 18 72.34 - 90.43: 6 Dihedral angle restraints: 3642 sinusoidal: 1434 harmonic: 2208 Sorted by residual: dihedral pdb=" C ASN B 144 " pdb=" N ASN B 144 " pdb=" CA ASN B 144 " pdb=" CB ASN B 144 " ideal model delta harmonic sigma weight residual -122.60 -131.96 9.36 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" C ASN A 144 " pdb=" N ASN A 144 " pdb=" CA ASN A 144 " pdb=" CB ASN A 144 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA ASP B 348 " pdb=" CB ASP B 348 " pdb=" CG ASP B 348 " pdb=" OD1 ASP B 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.29 59.29 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 3639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 796 0.082 - 0.164: 142 0.164 - 0.245: 34 0.245 - 0.327: 2 0.327 - 0.409: 4 Chirality restraints: 978 Sorted by residual: chirality pdb=" CB ILE A 222 " pdb=" CA ILE A 222 " pdb=" CG1 ILE A 222 " pdb=" CG2 ILE A 222 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CB ILE B 222 " pdb=" CA ILE B 222 " pdb=" CG1 ILE B 222 " pdb=" CG2 ILE B 222 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA PRO A 148 " pdb=" N PRO A 148 " pdb=" C PRO A 148 " pdb=" CB PRO A 148 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 975 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 501 " -0.096 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C29 POV B 501 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV B 501 " -0.325 2.00e-02 2.50e+03 pdb="C211 POV B 501 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 501 " 0.096 2.00e-02 2.50e+03 2.38e-01 5.66e+02 pdb=" C29 POV A 501 " -0.317 2.00e-02 2.50e+03 pdb="C210 POV A 501 " 0.325 2.00e-02 2.50e+03 pdb="C211 POV A 501 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 147 " -0.071 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 148 " 0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 148 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 148 " -0.057 5.00e-02 4.00e+02 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 322 2.75 - 3.28: 6541 3.28 - 3.82: 10137 3.82 - 4.36: 11820 4.36 - 4.90: 20133 Nonbonded interactions: 48953 Sorted by model distance: nonbonded pdb=" OD1 ASP A 133 " pdb="MG MG A 502 " model vdw 2.208 2.170 nonbonded pdb=" OD1 ASP B 133 " pdb="MG MG B 502 " model vdw 2.208 2.170 nonbonded pdb=" OD2 ASP B 158 " pdb="MG MG B 503 " model vdw 2.234 2.170 nonbonded pdb=" OD2 ASP A 158 " pdb="MG MG A 503 " model vdw 2.235 2.170 nonbonded pdb=" OG1 THR A 143 " pdb=" OG SER A 145 " model vdw 2.261 2.440 ... (remaining 48948 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.240 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.007 0.060 6286 Z= 0.439 Angle : 1.358 18.179 8544 Z= 0.780 Chirality : 0.072 0.409 978 Planarity : 0.014 0.238 1040 Dihedral : 15.990 90.426 2218 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.28), residues: 756 helix: 0.85 (0.20), residues: 548 sheet: None (None), residues: 0 loop : 0.67 (0.45), residues: 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.721 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 164 average time/residue: 0.2104 time to fit residues: 43.6102 Evaluate side-chains 158 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.556 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0623 time to fit residues: 1.2790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN B 197 HIS ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 57 GLN A 130 GLN A 197 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6286 Z= 0.185 Angle : 0.598 10.446 8544 Z= 0.307 Chirality : 0.042 0.163 978 Planarity : 0.005 0.058 1040 Dihedral : 9.915 83.256 882 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.29), residues: 756 helix: 2.06 (0.20), residues: 566 sheet: None (None), residues: 0 loop : 1.30 (0.50), residues: 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 193 average time/residue: 0.2073 time to fit residues: 50.7679 Evaluate side-chains 184 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0605 time to fit residues: 2.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 224 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 224 HIS ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 6286 Z= 0.416 Angle : 0.689 8.417 8544 Z= 0.362 Chirality : 0.048 0.156 978 Planarity : 0.005 0.047 1040 Dihedral : 9.851 81.361 882 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.29), residues: 756 helix: 1.86 (0.20), residues: 562 sheet: None (None), residues: 0 loop : 1.01 (0.48), residues: 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 227 time to evaluate : 0.686 Fit side-chains outliers start: 30 outliers final: 22 residues processed: 239 average time/residue: 0.1720 time to fit residues: 53.7480 Evaluate side-chains 234 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0594 time to fit residues: 3.4712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 GLN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 6286 Z= 0.193 Angle : 0.566 8.394 8544 Z= 0.294 Chirality : 0.042 0.157 978 Planarity : 0.005 0.033 1040 Dihedral : 9.285 71.811 882 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 2.57 % 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: 2.68 (0.29), residues: 756 helix: 2.08 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.06 (0.48), residues: 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 202 time to evaluate : 0.869 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 213 average time/residue: 0.2064 time to fit residues: 55.8008 Evaluate side-chains 202 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0585 time to fit residues: 2.0107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6286 Z= 0.213 Angle : 0.566 8.310 8544 Z= 0.295 Chirality : 0.042 0.181 978 Planarity : 0.004 0.032 1040 Dihedral : 8.881 67.626 882 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.30), residues: 756 helix: 2.06 (0.20), residues: 562 sheet: None (None), residues: 0 loop : 1.17 (0.49), residues: 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 0.715 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 204 average time/residue: 0.1787 time to fit residues: 47.6832 Evaluate side-chains 208 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0708 time to fit residues: 2.1221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 HIS A 86 ASN A 174 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6286 Z= 0.166 Angle : 0.556 7.299 8544 Z= 0.290 Chirality : 0.041 0.177 978 Planarity : 0.004 0.032 1040 Dihedral : 8.551 62.186 882 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.30), residues: 756 helix: 2.01 (0.20), residues: 564 sheet: None (None), residues: 0 loop : 1.13 (0.49), residues: 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 203 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 206 average time/residue: 0.2108 time to fit residues: 54.8074 Evaluate side-chains 194 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0649 time to fit residues: 2.2420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN A 174 GLN A 197 HIS ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6286 Z= 0.174 Angle : 0.581 9.077 8544 Z= 0.295 Chirality : 0.042 0.198 978 Planarity : 0.004 0.033 1040 Dihedral : 8.239 59.003 882 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.30), residues: 756 helix: 2.13 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 1.03 (0.48), residues: 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 0.757 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 199 average time/residue: 0.1893 time to fit residues: 48.5788 Evaluate side-chains 195 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0615 time to fit residues: 1.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 HIS ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 6286 Z= 0.229 Angle : 0.628 9.913 8544 Z= 0.314 Chirality : 0.043 0.202 978 Planarity : 0.004 0.030 1040 Dihedral : 8.095 59.618 882 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.30), residues: 756 helix: 1.99 (0.20), residues: 562 sheet: None (None), residues: 0 loop : 1.07 (0.50), residues: 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 0.669 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 185 average time/residue: 0.1841 time to fit residues: 44.3803 Evaluate side-chains 190 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0593 time to fit residues: 1.5310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 245 GLN A 174 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6286 Z= 0.185 Angle : 0.625 10.786 8544 Z= 0.308 Chirality : 0.042 0.195 978 Planarity : 0.004 0.031 1040 Dihedral : 7.845 56.895 882 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.30), residues: 756 helix: 2.05 (0.20), residues: 562 sheet: None (None), residues: 0 loop : 1.10 (0.50), residues: 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 0.674 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 192 average time/residue: 0.2185 time to fit residues: 53.2747 Evaluate side-chains 185 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0689 time to fit residues: 2.0388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.0270 chunk 16 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 245 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6286 Z= 0.187 Angle : 0.637 11.108 8544 Z= 0.312 Chirality : 0.042 0.201 978 Planarity : 0.005 0.031 1040 Dihedral : 7.638 52.775 882 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.30), residues: 756 helix: 2.10 (0.20), residues: 562 sheet: None (None), residues: 0 loop : 1.00 (0.50), residues: 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 0.717 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 182 average time/residue: 0.1786 time to fit residues: 42.5873 Evaluate side-chains 175 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 171 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0593 time to fit residues: 1.4011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN A 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128975 restraints weight = 7765.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134699 restraints weight = 3915.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138334 restraints weight = 2597.109| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6286 Z= 0.228 Angle : 0.634 9.093 8544 Z= 0.316 Chirality : 0.042 0.197 978 Planarity : 0.005 0.038 1040 Dihedral : 7.644 55.698 882 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.30), residues: 756 helix: 2.14 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 1.15 (0.50), residues: 198 =============================================================================== Job complete usr+sys time: 1508.80 seconds wall clock time: 27 minutes 58.73 seconds (1678.73 seconds total)