Starting phenix.real_space_refine on Fri Dec 8 03:16:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhp_18415/12_2023/8qhp_18415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhp_18415/12_2023/8qhp_18415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhp_18415/12_2023/8qhp_18415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhp_18415/12_2023/8qhp_18415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhp_18415/12_2023/8qhp_18415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qhp_18415/12_2023/8qhp_18415.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 22 5.16 5 C 4392 2.51 5 N 1128 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3393 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3393 Classifications: {'peptide': 410} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 393} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 236 SG CYS A 28 36.433 38.017 33.062 1.00137.77 S ATOM 1644 SG CYS A 208 33.883 39.740 30.430 1.00155.64 S ATOM 3629 SG CYS B 28 36.336 40.874 90.477 1.00138.97 S ATOM 5037 SG CYS B 208 37.721 38.524 92.922 1.00158.95 S Time building chain proxies: 4.23, per 1000 atoms: 0.62 Number of scatterers: 6788 At special positions: 0 Unit cell: (67.518, 71.148, 124.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 22 16.00 O 1244 8.00 N 1128 7.00 C 4392 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 208 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 233 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 28 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 28 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 208 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 233 " 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1520 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 55.7% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 103 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 158 through 163 removed outlier: 3.540A pdb=" N LEU A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.974A pdb=" N SER A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.679A pdb=" N PHE A 231 " --> pdb=" O ASP A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 304 through 329 Processing helix chain 'A' and resid 339 through 362 Processing helix chain 'A' and resid 365 through 387 Processing helix chain 'A' and resid 391 through 410 removed outlier: 3.502A pdb=" N LEU A 395 " --> pdb=" O LYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 418 removed outlier: 3.715A pdb=" N GLU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 57 Processing helix chain 'B' and resid 71 through 82 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 158 through 163 removed outlier: 3.572A pdb=" N LEU B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.927A pdb=" N SER B 209 " --> pdb=" O HIS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 304 through 332 removed outlier: 3.710A pdb=" N ARG B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 362 Processing helix chain 'B' and resid 365 through 387 Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 412 through 418 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65 removed outlier: 9.433A pdb=" N PHE A 220 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LYS A 24 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP A 221 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A 254 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS A 223 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR A 256 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY A 225 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 136 removed outlier: 6.453A pdb=" N ILE A 141 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 180 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65 removed outlier: 11.532A pdb=" N GLU B 22 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE B 222 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 24 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLY B 224 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR B 26 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N GLY B 226 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 221 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU B 254 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N HIS B 223 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR B 256 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B 225 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.385A pdb=" N ILE B 141 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 180 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265 363 hydrogen bonds defined for protein. 1071 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: 1.87 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2164 1.34 - 1.46: 1623 1.46 - 1.58: 3137 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 6962 Sorted by residual: bond pdb=" N VAL B 32 " pdb=" CA VAL B 32 " ideal model delta sigma weight residual 1.474 1.458 0.017 1.57e-02 4.06e+03 1.15e+00 bond pdb=" CA VAL A 32 " pdb=" C VAL A 32 " ideal model delta sigma weight residual 1.526 1.535 -0.008 9.00e-03 1.23e+04 8.57e-01 bond pdb=" CG ARG A 51 " pdb=" CD ARG A 51 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.18e-01 bond pdb=" CG1 ILE B 93 " pdb=" CD1 ILE B 93 " ideal model delta sigma weight residual 1.513 1.487 0.026 3.90e-02 6.57e+02 4.51e-01 bond pdb=" C ASP A 84 " pdb=" N PRO A 85 " ideal model delta sigma weight residual 1.336 1.342 -0.007 1.08e-02 8.57e+03 3.82e-01 ... (remaining 6957 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.90: 184 106.90 - 113.67: 3705 113.67 - 120.44: 2802 120.44 - 127.21: 2597 127.21 - 133.98: 82 Bond angle restraints: 9370 Sorted by residual: angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 106.21 110.47 -4.26 1.07e+00 8.73e-01 1.58e+01 angle pdb=" C VAL B 32 " pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta sigma weight residual 113.22 110.73 2.49 1.12e+00 7.97e-01 4.93e+00 angle pdb=" CA VAL B 32 " pdb=" C VAL B 32 " pdb=" O VAL B 32 " ideal model delta sigma weight residual 122.63 120.99 1.64 8.70e-01 1.32e+00 3.56e+00 angle pdb=" CA TYR A 44 " pdb=" CB TYR A 44 " pdb=" CG TYR A 44 " ideal model delta sigma weight residual 113.90 111.19 2.71 1.80e+00 3.09e-01 2.27e+00 angle pdb=" CA TYR B 44 " pdb=" CB TYR B 44 " pdb=" CG TYR B 44 " ideal model delta sigma weight residual 113.90 111.31 2.59 1.80e+00 3.09e-01 2.07e+00 ... (remaining 9365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 3658 12.35 - 24.70: 347 24.70 - 37.05: 86 37.05 - 49.40: 34 49.40 - 61.75: 19 Dihedral angle restraints: 4144 sinusoidal: 1762 harmonic: 2382 Sorted by residual: dihedral pdb=" CA LYS B 57 " pdb=" CB LYS B 57 " pdb=" CG LYS B 57 " pdb=" CD LYS B 57 " ideal model delta sinusoidal sigma weight residual -60.00 -119.56 59.56 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 295 " pdb=" CB LYS A 295 " pdb=" CG LYS A 295 " pdb=" CD LYS A 295 " ideal model delta sinusoidal sigma weight residual -60.00 -118.96 58.96 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG A 51 " pdb=" CB ARG A 51 " pdb=" CG ARG A 51 " pdb=" CD ARG A 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.05 -56.95 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 4141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 570 0.027 - 0.054: 237 0.054 - 0.082: 109 0.082 - 0.109: 33 0.109 - 0.136: 7 Chirality restraints: 956 Sorted by residual: chirality pdb=" CA ILE B 141 " pdb=" N ILE B 141 " pdb=" C ILE B 141 " pdb=" CB ILE B 141 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA PHE A 92 " pdb=" N PHE A 92 " pdb=" C PHE A 92 " pdb=" CB PHE A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 953 not shown) Planarity restraints: 1202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 195 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.46e+00 pdb=" N PRO A 196 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 201 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 202 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 148 " 0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO B 149 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.015 5.00e-02 4.00e+02 ... (remaining 1199 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 235 2.72 - 3.27: 6703 3.27 - 3.81: 11579 3.81 - 4.36: 14304 4.36 - 4.90: 24475 Nonbonded interactions: 57296 Sorted by model distance: nonbonded pdb=" OE2 GLU B 237 " pdb="ZN ZN B 501 " model vdw 2.176 2.230 nonbonded pdb=" OG SER B 195 " pdb=" O GLY B 198 " model vdw 2.192 2.440 nonbonded pdb=" OE1 GLU B 286 " pdb=" OH TYR B 319 " model vdw 2.194 2.440 nonbonded pdb=" OG SER A 335 " pdb=" O ASP B 109 " model vdw 2.198 2.440 nonbonded pdb=" OD1 ASP A 139 " pdb=" OH TYR A 142 " model vdw 2.219 2.440 ... (remaining 57291 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 5.850 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.002 0.026 6962 Z= 0.141 Angle : 0.384 4.260 9370 Z= 0.218 Chirality : 0.038 0.136 956 Planarity : 0.003 0.030 1202 Dihedral : 11.643 61.754 2624 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 812 helix: 1.87 (0.25), residues: 424 sheet: 0.25 (0.53), residues: 84 loop : 0.61 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 249 HIS 0.001 0.000 HIS A 40 PHE 0.007 0.001 PHE B 356 TYR 0.010 0.001 TYR A 44 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.847 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 1.3921 time to fit residues: 158.7518 Evaluate side-chains 72 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 11 GLN B 66 ASN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6962 Z= 0.381 Angle : 0.512 10.808 9370 Z= 0.268 Chirality : 0.042 0.159 956 Planarity : 0.004 0.035 1202 Dihedral : 3.989 16.295 902 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.37 % Allowed : 9.22 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.29), residues: 812 helix: 1.81 (0.24), residues: 442 sheet: 0.07 (0.50), residues: 92 loop : 0.94 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 249 HIS 0.003 0.001 HIS A 255 PHE 0.013 0.002 PHE A 67 TYR 0.019 0.001 TYR B 44 ARG 0.008 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 91 average time/residue: 1.4370 time to fit residues: 136.9721 Evaluate side-chains 70 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6962 Z= 0.185 Angle : 0.439 11.451 9370 Z= 0.228 Chirality : 0.039 0.144 956 Planarity : 0.003 0.035 1202 Dihedral : 3.752 14.553 902 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.54 % Allowed : 11.73 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.30), residues: 812 helix: 2.15 (0.25), residues: 442 sheet: -0.07 (0.50), residues: 92 loop : 1.08 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.002 0.000 HIS A 255 PHE 0.029 0.001 PHE A 273 TYR 0.012 0.001 TYR A 44 ARG 0.008 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 1.3604 time to fit residues: 117.4082 Evaluate side-chains 72 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1102 time to fit residues: 1.2462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN A 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6962 Z= 0.237 Angle : 0.459 11.620 9370 Z= 0.236 Chirality : 0.039 0.138 956 Planarity : 0.003 0.027 1202 Dihedral : 3.731 14.297 902 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.54 % Allowed : 12.57 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.30), residues: 812 helix: 2.30 (0.25), residues: 438 sheet: -0.04 (0.51), residues: 92 loop : 1.21 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.002 0.000 HIS A 255 PHE 0.010 0.001 PHE B 67 TYR 0.012 0.001 TYR B 44 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.838 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 1.3869 time to fit residues: 119.5456 Evaluate side-chains 74 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1129 time to fit residues: 1.2635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN A 294 GLN B 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6962 Z= 0.276 Angle : 0.459 10.589 9370 Z= 0.238 Chirality : 0.040 0.134 956 Planarity : 0.003 0.039 1202 Dihedral : 3.765 14.579 902 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.96 % Allowed : 12.85 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.30), residues: 812 helix: 2.32 (0.25), residues: 438 sheet: -0.02 (0.51), residues: 92 loop : 1.17 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 37 PHE 0.029 0.002 PHE A 273 TYR 0.013 0.001 TYR B 44 ARG 0.010 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.807 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 79 average time/residue: 1.2709 time to fit residues: 105.7705 Evaluate side-chains 72 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.5882 time to fit residues: 3.1042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6962 Z= 0.320 Angle : 0.490 10.646 9370 Z= 0.252 Chirality : 0.041 0.166 956 Planarity : 0.003 0.035 1202 Dihedral : 3.804 14.414 902 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.37 % Allowed : 13.27 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.30), residues: 812 helix: 2.31 (0.25), residues: 438 sheet: -0.11 (0.51), residues: 92 loop : 1.06 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.002 0.000 HIS A 37 PHE 0.021 0.002 PHE B 273 TYR 0.014 0.001 TYR B 44 ARG 0.006 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.887 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 79 average time/residue: 1.4506 time to fit residues: 120.2732 Evaluate side-chains 72 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1111 time to fit residues: 1.2679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6962 Z= 0.212 Angle : 0.465 11.328 9370 Z= 0.238 Chirality : 0.039 0.157 956 Planarity : 0.003 0.027 1202 Dihedral : 3.708 13.806 902 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.68 % Allowed : 14.80 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.30), residues: 812 helix: 2.44 (0.25), residues: 438 sheet: -0.19 (0.50), residues: 92 loop : 1.07 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 197 HIS 0.002 0.000 HIS A 255 PHE 0.029 0.001 PHE A 273 TYR 0.012 0.001 TYR A 44 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.741 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 78 average time/residue: 1.5651 time to fit residues: 127.6566 Evaluate side-chains 72 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1055 time to fit residues: 1.2732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6962 Z= 0.394 Angle : 0.542 13.869 9370 Z= 0.277 Chirality : 0.042 0.171 956 Planarity : 0.004 0.055 1202 Dihedral : 3.879 14.736 902 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.82 % Allowed : 14.80 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.30), residues: 812 helix: 2.22 (0.25), residues: 442 sheet: -0.21 (0.51), residues: 92 loop : 0.94 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 197 HIS 0.002 0.001 HIS A 37 PHE 0.013 0.002 PHE B 67 TYR 0.016 0.001 TYR A 44 ARG 0.012 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.865 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 1.4418 time to fit residues: 110.7993 Evaluate side-chains 73 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 1.0770 time to fit residues: 4.5243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.0770 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6962 Z= 0.174 Angle : 0.483 12.234 9370 Z= 0.245 Chirality : 0.039 0.132 956 Planarity : 0.003 0.046 1202 Dihedral : 3.669 13.337 902 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.98 % Allowed : 15.78 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.30), residues: 812 helix: 2.56 (0.25), residues: 434 sheet: -0.35 (0.50), residues: 92 loop : 1.01 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 204 HIS 0.002 0.000 HIS A 205 PHE 0.031 0.001 PHE A 273 TYR 0.010 0.001 TYR A 44 ARG 0.011 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.806 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 1.4046 time to fit residues: 118.2758 Evaluate side-chains 71 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.1279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 294 GLN B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6962 Z= 0.211 Angle : 0.499 13.981 9370 Z= 0.252 Chirality : 0.039 0.131 956 Planarity : 0.003 0.047 1202 Dihedral : 3.650 13.286 902 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.26 % Allowed : 15.92 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.30), residues: 812 helix: 2.53 (0.25), residues: 438 sheet: -0.36 (0.50), residues: 92 loop : 0.98 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 37 PHE 0.013 0.001 PHE B 67 TYR 0.011 0.001 TYR A 44 ARG 0.010 0.000 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.833 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 1.4989 time to fit residues: 117.9029 Evaluate side-chains 75 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6399 time to fit residues: 2.2314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 236 ASN B 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.076056 restraints weight = 9272.478| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.79 r_work: 0.2701 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6962 Z= 0.212 Angle : 0.488 13.979 9370 Z= 0.249 Chirality : 0.039 0.130 956 Planarity : 0.003 0.045 1202 Dihedral : 3.630 13.255 902 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.12 % Allowed : 16.06 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.30), residues: 812 helix: 2.55 (0.25), residues: 438 sheet: -0.31 (0.51), residues: 92 loop : 0.99 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 197 HIS 0.002 0.000 HIS A 255 PHE 0.030 0.002 PHE A 273 TYR 0.011 0.001 TYR A 44 ARG 0.010 0.000 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.94 seconds wall clock time: 47 minutes 59.63 seconds (2879.63 seconds total)