Starting phenix.real_space_refine on Fri Aug 2 16:21:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qt7_18645/08_2024/8qt7_18645.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qt7_18645/08_2024/8qt7_18645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qt7_18645/08_2024/8qt7_18645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qt7_18645/08_2024/8qt7_18645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qt7_18645/08_2024/8qt7_18645.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qt7_18645/08_2024/8qt7_18645.cif" } resolution = 2.2 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= 0.082 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 Fe 2 7.16 5 P 5 5.49 5 S 11 5.16 5 C 2282 2.51 5 N 555 2.21 5 O 661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 323": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3264 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 252 Unusual residues: {'FAD': 1, 'HEM': 2, 'NDP': 1} Classifications: {'undetermined': 4, 'water': 65} Link IDs: {None: 68} Time building chain proxies: 3.37, per 1000 atoms: 0.96 Number of scatterers: 3516 At special positions: 0 Unit cell: (59.592, 67.8432, 92.5968, 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) Fe 2 26.01 S 11 16.00 P 5 15.00 O 661 8.00 N 555 7.00 C 2282 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 568.4 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 56.1% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.501A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 147 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.535A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.638A pdb=" N ALA A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 195 removed outlier: 8.084A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A 246 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR A 248 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N SER A 236 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N LYS A 250 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 220 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG A 273 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LYS A 222 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU A 271 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 224 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL A 269 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.726A pdb=" N GLN A 287 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR A 316 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP A 289 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER A 318 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 291 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 391 " --> pdb=" O ALA A 365 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 555 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: 1.05 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 1513 1.39 - 1.57: 2020 1.57 - 1.75: 8 1.75 - 1.93: 22 1.93 - 2.12: 7 Bond restraints: 3570 Sorted by residual: bond pdb=" O2B NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.833 1.599 0.234 3.80e-02 6.93e+02 3.78e+01 bond pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.757 1.590 0.167 3.50e-02 8.16e+02 2.29e+01 bond pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " ideal model delta sigma weight residual 1.544 1.458 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O2X NDP A 501 " pdb=" P2B NDP A 501 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.00e-02 1.00e+04 1.78e+01 bond pdb=" O2N NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 1.513 1.475 0.038 1.00e-02 1.00e+04 1.41e+01 ... (remaining 3565 not shown) Histogram of bond angle deviations from ideal: 87.20 - 105.41: 69 105.41 - 123.62: 4637 123.62 - 141.83: 171 141.83 - 160.04: 0 160.04 - 178.24: 4 Bond angle restraints: 4881 Sorted by residual: angle pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 107.74 135.37 -27.63 1.95e+00 2.62e-01 2.00e+02 angle pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " ideal model delta sigma weight residual 103.84 121.33 -17.49 1.91e+00 2.73e-01 8.34e+01 angle pdb=" C5D NDP A 501 " pdb=" O5D NDP A 501 " pdb=" PN NDP A 501 " ideal model delta sigma weight residual 104.93 120.33 -15.40 2.66e+00 1.41e-01 3.35e+01 angle pdb=" O1X NDP A 501 " pdb=" P2B NDP A 501 " pdb=" O3X NDP A 501 " ideal model delta sigma weight residual 117.46 111.64 5.82 1.17e+00 7.36e-01 2.50e+01 angle pdb=" O3 NDP A 501 " pdb=" PA NDP A 501 " pdb=" O5B NDP A 501 " ideal model delta sigma weight residual 108.94 98.09 10.85 2.49e+00 1.62e-01 1.90e+01 ... (remaining 4876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 1740 20.28 - 40.57: 199 40.57 - 60.85: 58 60.85 - 81.13: 8 81.13 - 101.42: 7 Dihedral angle restraints: 2012 sinusoidal: 850 harmonic: 1162 Sorted by residual: dihedral pdb=" C2B HEM A 503 " pdb=" C3B HEM A 503 " pdb=" CAB HEM A 503 " pdb=" CBB HEM A 503 " ideal model delta sinusoidal sigma weight residual -0.00 49.42 -49.42 2 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" C5B NDP A 501 " pdb=" O5B NDP A 501 " pdb=" PA NDP A 501 " pdb=" O3 NDP A 501 " ideal model delta sinusoidal sigma weight residual 175.04 -83.54 -101.42 1 3.00e+01 1.11e-03 1.28e+01 dihedral pdb=" C1A HEM A 504 " pdb=" C2A HEM A 504 " pdb=" CAA HEM A 504 " pdb=" CBA HEM A 504 " ideal model delta sinusoidal sigma weight residual 180.00 94.44 85.56 2 2.00e+01 2.50e-03 1.19e+01 ... (remaining 2009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 416 0.053 - 0.106: 74 0.106 - 0.158: 17 0.158 - 0.211: 1 0.211 - 0.264: 1 Chirality restraints: 509 Sorted by residual: chirality pdb=" C4D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" C5D NDP A 501 " pdb=" O4D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2D NDP A 501 " pdb=" C1D NDP A 501 " pdb=" C3D NDP A 501 " pdb=" O2D NDP A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.50 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3B NDP A 501 " pdb=" C2B NDP A 501 " pdb=" C4B NDP A 501 " pdb=" O3B NDP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 506 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4N NDP A 501 " -0.013 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C5N NDP A 501 " 0.027 2.00e-02 2.50e+03 pdb=" C6N NDP A 501 " -0.028 2.00e-02 2.50e+03 pdb=" N1N NDP A 501 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM A 503 " -0.010 2.00e-02 2.50e+03 1.33e-02 3.98e+00 pdb=" C2A HEM A 503 " -0.014 2.00e-02 2.50e+03 pdb=" C3A HEM A 503 " 0.001 2.00e-02 2.50e+03 pdb=" C4A HEM A 503 " -0.000 2.00e-02 2.50e+03 pdb=" CAA HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" CHA HEM A 503 " 0.024 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " 0.015 2.00e-02 2.50e+03 pdb=" CMA HEM A 503 " 0.003 2.00e-02 2.50e+03 pdb=" NA HEM A 503 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A 503 " 0.008 2.00e-02 2.50e+03 1.01e-02 2.28e+00 pdb=" C1B HEM A 503 " 0.012 2.00e-02 2.50e+03 pdb=" C2B HEM A 503 " 0.002 2.00e-02 2.50e+03 pdb=" C3B HEM A 503 " 0.013 2.00e-02 2.50e+03 pdb=" C4B HEM A 503 " 0.006 2.00e-02 2.50e+03 pdb=" CAB HEM A 503 " -0.005 2.00e-02 2.50e+03 pdb=" CHB HEM A 503 " -0.014 2.00e-02 2.50e+03 pdb=" CHC HEM A 503 " -0.015 2.00e-02 2.50e+03 pdb=" CMB HEM A 503 " -0.006 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 141 2.72 - 3.26: 3343 3.26 - 3.81: 6373 3.81 - 4.35: 8207 4.35 - 4.90: 13086 Nonbonded interactions: 31150 Sorted by model distance: nonbonded pdb=" NE2 HIS A 69 " pdb="FE HEM A 504 " model vdw 2.169 3.080 nonbonded pdb=" NE2 HIS A 142 " pdb="FE HEM A 503 " model vdw 2.174 3.080 nonbonded pdb=" O1P FAD A 502 " pdb=" O HOH A 601 " model vdw 2.214 3.040 nonbonded pdb=" CG2 THR A 28 " pdb=" O HOH A 662 " model vdw 2.230 3.460 nonbonded pdb=" OE1 GLU A 229 " pdb=" O HOH A 602 " model vdw 2.232 3.040 ... (remaining 31145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 16.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 : 0.009 0.234 3570 Z= 0.607 Angle : 0.959 27.630 4881 Z= 0.431 Chirality : 0.045 0.264 509 Planarity : 0.003 0.021 581 Dihedral : 19.299 101.415 1272 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.86 % Allowed : 19.31 % Favored : 79.83 % 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: 1.00 (0.42), residues: 397 helix: 1.33 (0.37), residues: 193 sheet: 0.26 (0.52), residues: 96 loop : 0.05 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 127 HIS 0.006 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.011 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.370 Fit side-chains REVERT: A 226 GLU cc_start: 0.7138 (tt0) cc_final: 0.6912 (mp0) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 1.0196 time to fit residues: 54.0626 Evaluate side-chains 48 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3570 Z= 0.219 Angle : 0.636 14.209 4881 Z= 0.282 Chirality : 0.042 0.139 509 Planarity : 0.003 0.022 581 Dihedral : 12.659 107.693 513 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.88 % Allowed : 17.00 % Favored : 80.12 % 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: 1.67 (0.43), residues: 397 helix: 2.18 (0.36), residues: 196 sheet: 0.29 (0.52), residues: 96 loop : -0.05 (0.64), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.012 0.001 PHE A 218 TYR 0.012 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.416 Fit side-chains REVERT: A 226 GLU cc_start: 0.7191 (tt0) cc_final: 0.6989 (mp0) REVERT: A 323 GLU cc_start: 0.6728 (pm20) cc_final: 0.6345 (pm20) REVERT: A 385 LYS cc_start: 0.7106 (tmmt) cc_final: 0.6355 (tttp) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.9364 time to fit residues: 56.5115 Evaluate side-chains 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 38 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3570 Z= 0.163 Angle : 0.569 12.974 4881 Z= 0.250 Chirality : 0.039 0.137 509 Planarity : 0.003 0.021 581 Dihedral : 12.076 105.370 512 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 17.58 % Favored : 80.12 % 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: 1.78 (0.43), residues: 397 helix: 2.34 (0.36), residues: 196 sheet: 0.30 (0.53), residues: 95 loop : -0.12 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 25 HIS 0.006 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 52 time to evaluate : 0.408 Fit side-chains REVERT: A 323 GLU cc_start: 0.6739 (pm20) cc_final: 0.6386 (pm20) REVERT: A 385 LYS cc_start: 0.6979 (tmmt) cc_final: 0.6449 (tmmt) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.9640 time to fit residues: 59.1701 Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3570 Z= 0.189 Angle : 0.609 13.801 4881 Z= 0.264 Chirality : 0.040 0.140 509 Planarity : 0.003 0.021 581 Dihedral : 12.225 107.422 511 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.31 % Allowed : 17.87 % Favored : 79.83 % 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: 1.70 (0.43), residues: 397 helix: 2.30 (0.36), residues: 196 sheet: 0.23 (0.53), residues: 95 loop : -0.17 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.394 Fit side-chains REVERT: A 323 GLU cc_start: 0.6607 (pm20) cc_final: 0.6179 (pm20) REVERT: A 385 LYS cc_start: 0.7148 (tmmt) cc_final: 0.6500 (tmmt) outliers start: 8 outliers final: 5 residues processed: 58 average time/residue: 0.9795 time to fit residues: 59.2065 Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 353 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3570 Z= 0.209 Angle : 0.624 13.839 4881 Z= 0.273 Chirality : 0.041 0.140 509 Planarity : 0.003 0.022 581 Dihedral : 12.331 108.805 511 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.02 % Allowed : 17.58 % Favored : 80.40 % 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: 1.65 (0.43), residues: 397 helix: 2.24 (0.36), residues: 196 sheet: 0.24 (0.53), residues: 95 loop : -0.20 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.012 0.001 PHE A 218 TYR 0.011 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.366 Fit side-chains REVERT: A 285 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6506 (tt0) REVERT: A 323 GLU cc_start: 0.6607 (pm20) cc_final: 0.6091 (pm20) REVERT: A 385 LYS cc_start: 0.7250 (tmmt) cc_final: 0.6516 (tmmt) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 0.9998 time to fit residues: 56.2197 Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3570 Z= 0.198 Angle : 0.611 13.627 4881 Z= 0.267 Chirality : 0.041 0.141 509 Planarity : 0.003 0.022 581 Dihedral : 12.299 109.905 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.12 % 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: 1.65 (0.43), residues: 397 helix: 2.25 (0.36), residues: 196 sheet: 0.23 (0.53), residues: 95 loop : -0.19 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.012 0.001 PHE A 218 TYR 0.011 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.405 Fit side-chains REVERT: A 285 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6521 (tt0) REVERT: A 323 GLU cc_start: 0.6619 (pm20) cc_final: 0.6083 (pm20) REVERT: A 385 LYS cc_start: 0.7223 (tmmt) cc_final: 0.6477 (tmmt) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.9396 time to fit residues: 52.9172 Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3570 Z= 0.161 Angle : 0.568 12.443 4881 Z= 0.251 Chirality : 0.040 0.141 509 Planarity : 0.003 0.021 581 Dihedral : 12.020 109.026 511 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.44 % Allowed : 18.44 % Favored : 80.12 % 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: 1.78 (0.43), residues: 397 helix: 2.38 (0.36), residues: 197 sheet: 0.21 (0.53), residues: 95 loop : -0.13 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.005 0.001 HIS A 142 PHE 0.010 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.408 Fit side-chains REVERT: A 285 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6503 (tt0) REVERT: A 323 GLU cc_start: 0.6752 (pm20) cc_final: 0.6283 (pm20) REVERT: A 385 LYS cc_start: 0.7164 (tmmt) cc_final: 0.6433 (tmmt) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.9929 time to fit residues: 57.8829 Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.0000 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3570 Z= 0.233 Angle : 0.643 14.088 4881 Z= 0.285 Chirality : 0.042 0.140 509 Planarity : 0.003 0.022 581 Dihedral : 12.496 114.195 511 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.15 % Allowed : 18.73 % Favored : 80.12 % 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: 1.63 (0.43), residues: 397 helix: 2.18 (0.36), residues: 197 sheet: 0.22 (0.53), residues: 95 loop : -0.12 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.008 0.001 HIS A 142 PHE 0.013 0.001 PHE A 218 TYR 0.011 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.407 Fit side-chains REVERT: A 285 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6526 (tt0) REVERT: A 323 GLU cc_start: 0.6604 (pm20) cc_final: 0.6239 (pm20) REVERT: A 385 LYS cc_start: 0.7283 (tmmt) cc_final: 0.6523 (tmmt) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.9317 time to fit residues: 50.5385 Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3570 Z= 0.186 Angle : 0.600 13.374 4881 Z= 0.264 Chirality : 0.041 0.142 509 Planarity : 0.003 0.021 581 Dihedral : 12.334 114.668 511 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.44 % Allowed : 18.44 % Favored : 80.12 % 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: 1.68 (0.43), residues: 397 helix: 2.26 (0.36), residues: 197 sheet: 0.21 (0.54), residues: 95 loop : -0.15 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.422 Fit side-chains REVERT: A 285 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6546 (tt0) REVERT: A 323 GLU cc_start: 0.6627 (pm20) cc_final: 0.6075 (pm20) REVERT: A 385 LYS cc_start: 0.7200 (tmmt) cc_final: 0.6458 (tmmt) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.0058 time to fit residues: 56.5171 Evaluate side-chains 54 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 285 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3570 Z= 0.206 Angle : 0.623 13.653 4881 Z= 0.275 Chirality : 0.042 0.141 509 Planarity : 0.003 0.022 581 Dihedral : 12.404 115.339 511 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.15 % Allowed : 18.73 % Favored : 80.12 % 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: 1.64 (0.43), residues: 397 helix: 2.20 (0.36), residues: 197 sheet: 0.22 (0.54), residues: 95 loop : -0.13 (0.63), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.012 0.001 PHE A 218 TYR 0.011 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.393 Fit side-chains REVERT: A 323 GLU cc_start: 0.6620 (pm20) cc_final: 0.6252 (pm20) REVERT: A 385 LYS cc_start: 0.7216 (tmmt) cc_final: 0.6466 (tmmt) outliers start: 4 outliers final: 3 residues processed: 52 average time/residue: 0.9587 time to fit residues: 51.9833 Evaluate side-chains 52 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 160 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110902 restraints weight = 3310.910| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.37 r_work: 0.3189 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3570 Z= 0.182 Angle : 0.596 13.115 4881 Z= 0.264 Chirality : 0.041 0.142 509 Planarity : 0.003 0.022 581 Dihedral : 12.264 115.065 511 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.86 % Allowed : 19.02 % Favored : 80.12 % 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: 1.70 (0.43), residues: 397 helix: 2.29 (0.36), residues: 197 sheet: 0.21 (0.54), residues: 95 loop : -0.15 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.007 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.48 seconds wall clock time: 30 minutes 42.79 seconds (1842.79 seconds total)