Starting phenix.real_space_refine on Tue Feb 11 01:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt7_18645/02_2025/8qt7_18645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt7_18645/02_2025/8qt7_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/cci-nas-00/data/ceres_data/8qt7_18645/02_2025/8qt7_18645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt7_18645/02_2025/8qt7_18645.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt7_18645/02_2025/8qt7_18645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt7_18645/02_2025/8qt7_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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.93, per 1000 atoms: 0.83 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 - 3.00 Amino acid : True - 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: 1.16 Conformation dependent library (CDL) restraints added in 413.4 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: 0.44 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: 1.14 Time building geometry restraints manager: 1.21 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: 0.00 - 5.53: 4857 5.53 - 11.05: 21 11.05 - 16.58: 1 16.58 - 22.10: 1 22.10 - 27.63: 1 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: 0.920 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.640 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.422 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: 1.0300 time to fit residues: 54.6749 Evaluate side-chains 48 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109096 restraints weight = 3276.114| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.25 r_work: 0.3147 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.380 Fit side-chains REVERT: A 226 GLU cc_start: 0.7769 (tt0) cc_final: 0.7077 (mp0) REVERT: A 323 GLU cc_start: 0.6799 (pm20) cc_final: 0.6323 (pm20) REVERT: A 385 LYS cc_start: 0.7150 (tmmt) cc_final: 0.6391 (tttp) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 1.0028 time to fit residues: 60.5714 Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.128554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109189 restraints weight = 3326.778| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.26 r_work: 0.3146 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0893 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= 0.206 Angle : 0.624 14.269 4881 Z= 0.272 Chirality : 0.041 0.139 509 Planarity : 0.003 0.021 581 Dihedral : 12.485 108.055 512 Min Nonbonded Distance : 2.553 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: 1.64 (0.43), residues: 397 helix: 2.18 (0.36), residues: 196 sheet: 0.26 (0.53), residues: 95 loop : -0.12 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.400 Fit side-chains REVERT: A 226 GLU cc_start: 0.7809 (tt0) cc_final: 0.7092 (mp0) REVERT: A 385 LYS cc_start: 0.7125 (tmmt) cc_final: 0.6644 (tmmt) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 1.0156 time to fit residues: 59.2446 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3493 r_free = 0.3493 target = 0.129060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110209 restraints weight = 3309.050| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.23 r_work: 0.3163 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3570 Z= 0.182 Angle : 0.594 13.686 4881 Z= 0.260 Chirality : 0.040 0.140 509 Planarity : 0.003 0.022 581 Dihedral : 12.287 107.781 511 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.59 % Allowed : 17.58 % 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: 1.69 (0.43), residues: 397 helix: 2.27 (0.36), residues: 196 sheet: 0.25 (0.53), residues: 95 loop : -0.15 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.006 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 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.305 Fit side-chains REVERT: A 226 GLU cc_start: 0.7764 (tt0) cc_final: 0.7091 (mp0) REVERT: A 385 LYS cc_start: 0.7203 (tmmt) cc_final: 0.6564 (tmmt) outliers start: 9 outliers final: 4 residues processed: 57 average time/residue: 0.9636 time to fit residues: 57.1410 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.128291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109007 restraints weight = 3339.855| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.26 r_work: 0.3143 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3570 Z= 0.222 Angle : 0.639 14.225 4881 Z= 0.278 Chirality : 0.042 0.142 509 Planarity : 0.003 0.022 581 Dihedral : 12.456 109.290 511 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.02 % Allowed : 18.16 % 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: 1.57 (0.43), residues: 397 helix: 2.17 (0.36), residues: 196 sheet: 0.20 (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 0.008 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 320 *********************** 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 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.389 Fit side-chains REVERT: A 226 GLU cc_start: 0.7812 (tt0) cc_final: 0.7106 (mp0) REVERT: A 285 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: A 323 GLU cc_start: 0.6720 (pm20) cc_final: 0.6361 (pm20) REVERT: A 385 LYS cc_start: 0.7315 (tmmt) cc_final: 0.6588 (tmmt) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 1.0036 time to fit residues: 55.4577 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.126700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107294 restraints weight = 3382.622| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.27 r_work: 0.3119 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3570 Z= 0.292 Angle : 0.686 14.319 4881 Z= 0.305 Chirality : 0.044 0.143 509 Planarity : 0.003 0.022 581 Dihedral : 12.967 117.522 511 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.38 (0.42), residues: 397 helix: 1.96 (0.36), residues: 196 sheet: 0.15 (0.52), residues: 95 loop : -0.22 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.009 0.002 HIS A 142 PHE 0.016 0.002 PHE A 218 TYR 0.011 0.002 TYR A 66 ARG 0.001 0.000 ARG A 320 *********************** 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 to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.354 Fit side-chains REVERT: A 226 GLU cc_start: 0.7826 (tt0) cc_final: 0.7106 (mp0) REVERT: A 323 GLU cc_start: 0.6821 (pm20) cc_final: 0.6470 (pm20) REVERT: A 385 LYS cc_start: 0.7296 (tmmt) cc_final: 0.6571 (tmmt) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.9896 time to fit residues: 55.6911 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.126925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108092 restraints weight = 3328.583| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.23 r_work: 0.3133 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1013 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= 0.249 Angle : 0.662 14.368 4881 Z= 0.292 Chirality : 0.043 0.144 509 Planarity : 0.003 0.023 581 Dihedral : 12.823 120.911 509 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.37 (0.42), residues: 397 helix: 1.97 (0.36), residues: 196 sheet: 0.14 (0.52), residues: 95 loop : -0.24 (0.62), residues: 106 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 0.014 0.001 PHE A 218 TYR 0.010 0.002 TYR A 275 ARG 0.001 0.000 ARG A 273 *********************** 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 to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.378 Fit side-chains REVERT: A 226 GLU cc_start: 0.7811 (tt0) cc_final: 0.7110 (mp0) REVERT: A 323 GLU cc_start: 0.6815 (pm20) cc_final: 0.6423 (pm20) REVERT: A 385 LYS cc_start: 0.7310 (tmmt) cc_final: 0.6570 (tmmt) outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.9509 time to fit residues: 56.4442 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.128334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109500 restraints weight = 3354.737| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.24 r_work: 0.3152 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3570 Z= 0.199 Angle : 0.621 13.998 4881 Z= 0.272 Chirality : 0.041 0.144 509 Planarity : 0.003 0.023 581 Dihedral : 12.604 120.271 509 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.86 % Allowed : 18.73 % 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: 1.49 (0.43), residues: 397 helix: 2.10 (0.36), residues: 196 sheet: 0.19 (0.53), residues: 95 loop : -0.26 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 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 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.412 Fit side-chains REVERT: A 226 GLU cc_start: 0.7822 (tt0) cc_final: 0.7101 (mp0) REVERT: A 323 GLU cc_start: 0.6812 (pm20) cc_final: 0.6389 (pm20) REVERT: A 385 LYS cc_start: 0.7322 (tmmt) cc_final: 0.6579 (tmmt) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.9533 time to fit residues: 51.6559 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.129924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110761 restraints weight = 3250.665| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.25 r_work: 0.3168 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1016 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= 0.179 Angle : 0.599 13.555 4881 Z= 0.262 Chirality : 0.041 0.144 509 Planarity : 0.003 0.023 581 Dihedral : 12.315 118.712 509 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.44 % Allowed : 18.16 % 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: 1.59 (0.43), residues: 397 helix: 2.22 (0.36), residues: 196 sheet: 0.19 (0.53), residues: 95 loop : -0.25 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.006 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.364 Fit side-chains REVERT: A 226 GLU cc_start: 0.7799 (tt0) cc_final: 0.7082 (mp0) REVERT: A 385 LYS cc_start: 0.7219 (tmmt) cc_final: 0.6488 (tmmt) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.9785 time to fit residues: 57.0443 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0970 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.130331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111051 restraints weight = 3291.522| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.26 r_work: 0.3170 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1056 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= 0.176 Angle : 0.602 13.495 4881 Z= 0.265 Chirality : 0.041 0.144 509 Planarity : 0.003 0.022 581 Dihedral : 12.194 117.798 509 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.15 % Allowed : 18.44 % 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: 1.62 (0.43), residues: 397 helix: 2.25 (0.36), residues: 196 sheet: 0.20 (0.53), residues: 95 loop : -0.25 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 25 HIS 0.006 0.001 HIS A 142 PHE 0.011 0.001 PHE A 154 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 201 ********************** 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.367 Fit side-chains REVERT: A 226 GLU cc_start: 0.7803 (tt0) cc_final: 0.7096 (mp0) REVERT: A 385 LYS cc_start: 0.7216 (tmmt) cc_final: 0.6493 (tmmt) outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.9707 time to fit residues: 54.5232 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108739 restraints weight = 3329.116| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.23 r_work: 0.3142 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3570 Z= 0.245 Angle : 0.664 14.390 4881 Z= 0.294 Chirality : 0.043 0.143 509 Planarity : 0.003 0.023 581 Dihedral : 12.558 119.522 509 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.15 % Allowed : 18.16 % Favored : 80.69 % 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: 1.48 (0.42), residues: 397 helix: 2.06 (0.36), residues: 196 sheet: 0.21 (0.53), residues: 95 loop : -0.23 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.008 0.001 HIS A 142 PHE 0.013 0.001 PHE A 218 TYR 0.010 0.002 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: 3103.31 seconds wall clock time: 55 minutes 19.59 seconds (3319.59 seconds total)