Starting phenix.real_space_refine on Wed Mar 5 20:45:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt7_18645/03_2025/8qt7_18645.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt7_18645/03_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_18645/03_2025/8qt7_18645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt7_18645/03_2025/8qt7_18645.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt7_18645/03_2025/8qt7_18645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt7_18645/03_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-5624/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: 3.51, per 1000 atoms: 1.00 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: 1.03 Conformation dependent library (CDL) restraints added in 368.4 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: 0.40 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: 0.97 Time building geometry restraints manager: 1.20 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: 2.420 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.280 Find NCS groups from input model: 0.030 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- 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 : 0.376 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: 0.9646 time to fit residues: 51.2398 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 : 0.355 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.127855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109028 restraints weight = 3295.448| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.23 r_work: 0.3148 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.346 Fit side-chains REVERT: A 226 GLU cc_start: 0.7783 (tt0) cc_final: 0.7089 (mp0) REVERT: A 323 GLU cc_start: 0.6808 (pm20) cc_final: 0.6332 (pm20) REVERT: A 385 LYS cc_start: 0.7165 (tmmt) cc_final: 0.6408 (tttp) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 1.0460 time to fit residues: 62.9864 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 : 0.390 ------------------------------------------------------------------------------- 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: 0.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 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 = 0.3480 r_free = 0.3480 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109135 restraints weight = 3350.755| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.24 r_work: 0.3152 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3570 Z= 0.198 Angle : 0.614 14.036 4881 Z= 0.268 Chirality : 0.041 0.138 509 Planarity : 0.003 0.021 581 Dihedral : 12.412 107.941 512 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 : 2.02 % Allowed : 17.29 % 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: 1.65 (0.43), residues: 397 helix: 2.20 (0.36), residues: 196 sheet: 0.27 (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 0.006 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 : 0.351 Fit side-chains REVERT: A 226 GLU cc_start: 0.7801 (tt0) cc_final: 0.7092 (mp0) REVERT: A 385 LYS cc_start: 0.7117 (tmmt) cc_final: 0.6636 (tmmt) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.9503 time to fit residues: 55.4599 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 : 0.407 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.129361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110052 restraints weight = 3295.367| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.26 r_work: 0.3156 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3570 Z= 0.192 Angle : 0.604 13.849 4881 Z= 0.264 Chirality : 0.041 0.140 509 Planarity : 0.003 0.022 581 Dihedral : 12.317 108.059 511 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 1.68 (0.43), residues: 397 helix: 2.26 (0.36), residues: 196 sheet: 0.24 (0.53), residues: 95 loop : -0.14 (0.63), 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 0.012 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.386 Fit side-chains REVERT: A 226 GLU cc_start: 0.7786 (tt0) cc_final: 0.7094 (mp0) REVERT: A 385 LYS cc_start: 0.7300 (tmmt) cc_final: 0.6608 (tmmt) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.9472 time to fit residues: 54.3488 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 : 0.381 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.128445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109013 restraints weight = 3336.970| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.27 r_work: 0.3141 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0969 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= 0.227 Angle : 0.636 14.274 4881 Z= 0.279 Chirality : 0.042 0.142 509 Planarity : 0.003 0.022 581 Dihedral : 12.499 109.916 511 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.58 (0.43), residues: 397 helix: 2.16 (0.36), residues: 196 sheet: 0.21 (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 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 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.419 Fit side-chains REVERT: A 226 GLU cc_start: 0.7822 (tt0) cc_final: 0.7099 (mp0) REVERT: A 323 GLU cc_start: 0.6754 (pm20) cc_final: 0.6390 (pm20) REVERT: A 385 LYS cc_start: 0.7321 (tmmt) cc_final: 0.6588 (tmmt) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.9742 time to fit residues: 54.8501 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 : 0.434 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 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: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.127611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108169 restraints weight = 3375.790| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.27 r_work: 0.3129 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3570 Z= 0.257 Angle : 0.657 14.302 4881 Z= 0.291 Chirality : 0.043 0.143 509 Planarity : 0.003 0.022 581 Dihedral : 12.822 115.122 511 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 1.45 (0.42), residues: 397 helix: 2.04 (0.36), residues: 196 sheet: 0.16 (0.52), residues: 95 loop : -0.20 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.009 0.001 HIS A 142 PHE 0.015 0.001 PHE A 218 TYR 0.010 0.002 TYR A 275 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.353 Fit side-chains REVERT: A 226 GLU cc_start: 0.7815 (tt0) cc_final: 0.7096 (mp0) REVERT: A 385 LYS cc_start: 0.7325 (tmmt) cc_final: 0.6590 (tmmt) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.9373 time to fit residues: 52.7461 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.126304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106939 restraints weight = 3312.519| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.25 r_work: 0.3114 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3570 Z= 0.321 Angle : 0.706 14.400 4881 Z= 0.318 Chirality : 0.045 0.142 509 Planarity : 0.004 0.023 581 Dihedral : 12.986 121.504 509 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.44 % Allowed : 17.87 % 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: 1.29 (0.42), residues: 397 helix: 1.84 (0.36), residues: 196 sheet: 0.11 (0.52), residues: 95 loop : -0.18 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 125 HIS 0.010 0.002 HIS A 142 PHE 0.017 0.002 PHE A 218 TYR 0.011 0.002 TYR A 66 ARG 0.002 0.000 ARG A 320 *********************** 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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.359 Fit side-chains REVERT: A 226 GLU cc_start: 0.7842 (tt0) cc_final: 0.7111 (mp0) REVERT: A 385 LYS cc_start: 0.7315 (tmmt) cc_final: 0.6511 (tttp) outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 0.9565 time to fit residues: 53.7531 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.128324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109499 restraints weight = 3356.946| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.24 r_work: 0.3150 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1017 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= 0.197 Angle : 0.615 14.016 4881 Z= 0.271 Chirality : 0.041 0.145 509 Planarity : 0.003 0.023 581 Dihedral : 12.638 120.623 509 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.44 % Allowed : 17.87 % 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 (0.43), residues: 397 helix: 2.09 (0.36), residues: 196 sheet: 0.14 (0.52), residues: 95 loop : -0.22 (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 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.414 Fit side-chains REVERT: A 226 GLU cc_start: 0.7810 (tt0) cc_final: 0.7102 (mp0) REVERT: A 385 LYS cc_start: 0.7269 (tmmt) cc_final: 0.6537 (tmmt) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.9143 time to fit residues: 51.5389 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 : 0.396 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.0010 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 3.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.131466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112254 restraints weight = 3232.003| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.24 r_work: 0.3186 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3570 Z= 0.162 Angle : 0.574 12.800 4881 Z= 0.255 Chirality : 0.040 0.143 509 Planarity : 0.003 0.023 581 Dihedral : 12.128 116.856 509 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 1.67 (0.43), residues: 397 helix: 2.30 (0.36), residues: 196 sheet: 0.17 (0.53), residues: 95 loop : -0.19 (0.62), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 142 PHE 0.009 0.001 PHE A 218 TYR 0.012 0.001 TYR A 275 ARG 0.001 0.000 ARG A 201 *********************** 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.355 Fit side-chains REVERT: A 226 GLU cc_start: 0.7770 (tt0) cc_final: 0.7090 (mp0) REVERT: A 323 GLU cc_start: 0.6635 (pm20) cc_final: 0.6349 (pm20) REVERT: A 385 LYS cc_start: 0.7172 (tmmt) cc_final: 0.6454 (tmmt) outliers start: 4 outliers final: 0 residues processed: 57 average time/residue: 1.0252 time to fit residues: 60.5739 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112102 restraints weight = 3294.464| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.26 r_work: 0.3183 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1080 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= 0.165 Angle : 0.589 13.346 4881 Z= 0.260 Chirality : 0.040 0.144 509 Planarity : 0.003 0.022 581 Dihedral : 12.038 115.269 509 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 19.31 % 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: 1.72 (0.43), residues: 397 helix: 2.33 (0.36), residues: 196 sheet: 0.20 (0.54), residues: 95 loop : -0.14 (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 154 TYR 0.012 0.001 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 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.326 Fit side-chains REVERT: A 226 GLU cc_start: 0.7809 (tt0) cc_final: 0.7085 (mp0) REVERT: A 385 LYS cc_start: 0.7157 (tmmt) cc_final: 0.6442 (tmmt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.0624 time to fit residues: 56.3222 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 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: 2.9990 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.129877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111128 restraints weight = 3316.209| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.23 r_work: 0.3173 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1023 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= 0.181 Angle : 0.608 13.729 4881 Z= 0.269 Chirality : 0.041 0.144 509 Planarity : 0.003 0.022 581 Dihedral : 12.095 115.916 509 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.67 (0.43), residues: 397 helix: 2.28 (0.36), residues: 196 sheet: 0.19 (0.54), residues: 95 loop : -0.16 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 25 HIS 0.006 0.001 HIS A 142 PHE 0.011 0.001 PHE A 218 TYR 0.011 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: 3134.24 seconds wall clock time: 54 minutes 8.24 seconds (3248.24 seconds total)