Starting phenix.real_space_refine on Thu Mar 6 02:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uh3_26504/03_2025/7uh3_26504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uh3_26504/03_2025/7uh3_26504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2025/7uh3_26504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2025/7uh3_26504.map" model { file = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2025/7uh3_26504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2025/7uh3_26504.cif" } resolution = 2.99 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= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1615 atoms to isotropic. 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 S 16 5.16 5 Na 3 4.78 5 C 2032 2.51 5 N 504 2.21 5 O 540 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 3096 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3093 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.84, per 1000 atoms: 1.56 Number of scatterers: 3096 At special positions: 0 Unit cell: (68.16, 74.124, 75.828, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 Na 3 11.00 F 1 9.00 O 540 8.00 N 504 7.00 C 2032 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=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 397.3 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 88.2% alpha, 0.0% 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 2 through 10 removed outlier: 3.541A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 10 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 Processing helix chain 'A' and resid 35 through 72 removed outlier: 3.994A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.662A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.719A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 3.758A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.523A pdb=" N ILE A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 220 removed outlier: 3.565A pdb=" N TYR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.506A pdb=" N VAL A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 removed outlier: 4.260A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 3.504A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.555A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.740A pdb=" N MET A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.807A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.699A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.214A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.600A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 4.109A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.711A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 removed outlier: 3.559A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 416 removed outlier: 3.888A pdb=" N ARG A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 687 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: 1.71 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 981 1.37 - 1.55: 2142 1.55 - 1.74: 0 1.74 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3154 Sorted by residual: bond pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.31e-02 5.83e+03 6.42e+00 bond pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.09e+00 bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.102 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" N LEU A 316 " pdb=" CA LEU A 316 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+00 bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.186 0.045 2.00e-02 2.50e+03 5.05e+00 ... (remaining 3149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 4218 1.97 - 3.93: 65 3.93 - 5.90: 13 5.90 - 7.86: 1 7.86 - 9.83: 3 Bond angle restraints: 4300 Sorted by residual: angle pdb=" N THR A 308 " pdb=" CA THR A 308 " pdb=" C THR A 308 " ideal model delta sigma weight residual 114.31 109.51 4.80 1.29e+00 6.01e-01 1.39e+01 angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 110.15 -8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" CA LEU A 244 " pdb=" CB LEU A 244 " pdb=" CG LEU A 244 " ideal model delta sigma weight residual 116.30 126.13 -9.83 3.50e+00 8.16e-02 7.89e+00 angle pdb=" CA LEU A 372 " pdb=" CB LEU A 372 " pdb=" CG LEU A 372 " ideal model delta sigma weight residual 116.30 125.98 -9.68 3.50e+00 8.16e-02 7.65e+00 angle pdb=" CA ASN A 310 " pdb=" C ASN A 310 " pdb=" O ASN A 310 " ideal model delta sigma weight residual 120.98 118.11 2.87 1.08e+00 8.57e-01 7.05e+00 ... (remaining 4295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 1717 14.14 - 28.28: 101 28.28 - 42.42: 27 42.42 - 56.55: 1 56.55 - 70.69: 2 Dihedral angle restraints: 1848 sinusoidal: 669 harmonic: 1179 Sorted by residual: dihedral pdb=" CA THR A 240 " pdb=" C THR A 240 " pdb=" N LEU A 241 " pdb=" CA LEU A 241 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB LYS A 175 " pdb=" CG LYS A 175 " pdb=" CD LYS A 175 " pdb=" CE LYS A 175 " ideal model delta sinusoidal sigma weight residual -180.00 -139.25 -40.75 3 1.50e+01 4.44e-03 7.27e+00 dihedral pdb=" CA GLU A 9 " pdb=" CB GLU A 9 " pdb=" CG GLU A 9 " pdb=" CD GLU A 9 " ideal model delta sinusoidal sigma weight residual 60.00 100.17 -40.17 3 1.50e+01 4.44e-03 7.15e+00 ... (remaining 1845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 359 0.032 - 0.064: 131 0.064 - 0.096: 30 0.096 - 0.128: 15 0.128 - 0.160: 3 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA ILE A 309 " pdb=" N ILE A 309 " pdb=" C ILE A 309 " pdb=" CB ILE A 309 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA LEU A 316 " pdb=" N LEU A 316 " pdb=" C LEU A 316 " pdb=" CB LEU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA MET A 311 " pdb=" N MET A 311 " pdb=" C MET A 311 " pdb=" CB MET A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 535 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 45 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 172 " -0.005 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" CD GLU A 172 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLU A 172 " -0.007 2.00e-02 2.50e+03 pdb=" OE2 GLU A 172 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 152 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.40e-01 pdb=" N PRO A 153 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.013 5.00e-02 4.00e+02 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 16 2.51 - 3.11: 2469 3.11 - 3.70: 4758 3.70 - 4.30: 6560 4.30 - 4.90: 10616 Nonbonded interactions: 24419 Sorted by model distance: nonbonded pdb=" OD1 ASP A 312 " pdb="NA NA A 504 " model vdw 1.909 2.470 nonbonded pdb=" O ASN A 310 " pdb="NA NA A 503 " model vdw 2.302 2.470 nonbonded pdb=" O SER A 171 " pdb=" NH1 ARG A 177 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLU A 296 " pdb=" OH TYR A 299 " model vdw 2.315 3.040 nonbonded pdb=" O SER A 349 " pdb="NA NA A 502 " model vdw 2.347 2.470 ... (remaining 24414 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: 68.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:30.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.003 0.048 3154 Z= 0.192 Angle : 0.614 9.828 4300 Z= 0.314 Chirality : 0.040 0.160 538 Planarity : 0.003 0.032 530 Dihedral : 10.051 70.692 1100 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.91 (0.39), residues: 410 helix: 1.01 (0.27), residues: 333 sheet: None (None), residues: 0 loop : -0.91 (0.58), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.007 0.001 PHE A 156 TYR 0.009 0.001 TYR A 247 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.372 Fit side-chains REVERT: A 125 HIS cc_start: 0.6593 (t-90) cc_final: 0.6131 (OUTLIER) outliers start: 0 outliers final: 2 residues processed: 56 average time/residue: 1.5368 time to fit residues: 89.2038 Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.133092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083868 restraints weight = 6326.326| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.74 r_work: 0.3073 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3154 Z= 0.210 Angle : 0.683 11.306 4300 Z= 0.345 Chirality : 0.042 0.122 538 Planarity : 0.004 0.032 530 Dihedral : 6.561 94.167 446 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.41 % Allowed : 9.29 % Favored : 87.31 % 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: 1.75 (0.40), residues: 410 helix: 1.67 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -1.27 (0.63), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 32 PHE 0.024 0.002 PHE A 273 TYR 0.018 0.002 TYR A 299 ARG 0.005 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.309 Fit side-chains REVERT: A 125 HIS cc_start: 0.6582 (t-90) cc_final: 0.6032 (t-170) REVERT: A 296 GLU cc_start: 0.7807 (tp30) cc_final: 0.7408 (tp30) REVERT: A 311 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.5268 (mtp) outliers start: 11 outliers final: 4 residues processed: 57 average time/residue: 0.8675 time to fit residues: 51.3793 Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.133685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084795 restraints weight = 6384.366| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.59 r_work: 0.3104 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3154 Z= 0.204 Angle : 0.627 10.845 4300 Z= 0.310 Chirality : 0.041 0.156 538 Planarity : 0.004 0.034 530 Dihedral : 4.290 31.275 443 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.02 % Allowed : 12.69 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.41), residues: 410 helix: 1.88 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -1.40 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.023 0.002 PHE A 273 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.349 Fit side-chains REVERT: A 95 PHE cc_start: 0.8252 (t80) cc_final: 0.7814 (t80) REVERT: A 125 HIS cc_start: 0.6697 (t-90) cc_final: 0.6125 (t-170) REVERT: A 292 MET cc_start: 0.5128 (OUTLIER) cc_final: 0.4846 (ttp) REVERT: A 311 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5960 (mtp) REVERT: A 323 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8803 (m-10) outliers start: 13 outliers final: 4 residues processed: 47 average time/residue: 1.2581 time to fit residues: 61.1882 Evaluate side-chains 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.134806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.086046 restraints weight = 6434.220| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.65 r_work: 0.3123 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3154 Z= 0.176 Angle : 0.606 10.842 4300 Z= 0.298 Chirality : 0.040 0.124 538 Planarity : 0.004 0.035 530 Dihedral : 4.234 27.528 443 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.10 % Allowed : 15.79 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.41), residues: 410 helix: 2.01 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.35 (0.64), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.025 0.002 PHE A 324 TYR 0.017 0.001 TYR A 299 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8352 (t80) cc_final: 0.7890 (t80) REVERT: A 125 HIS cc_start: 0.6637 (t-90) cc_final: 0.6036 (t-170) REVERT: A 292 MET cc_start: 0.5118 (tpp) cc_final: 0.4808 (ttp) REVERT: A 311 MET cc_start: 0.5964 (mtp) cc_final: 0.5686 (mtp) REVERT: A 323 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8759 (m-10) outliers start: 10 outliers final: 4 residues processed: 47 average time/residue: 0.9587 time to fit residues: 46.7155 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.134704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085502 restraints weight = 6351.450| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.61 r_work: 0.3128 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3154 Z= 0.193 Angle : 0.622 11.100 4300 Z= 0.305 Chirality : 0.040 0.145 538 Planarity : 0.004 0.035 530 Dihedral : 4.207 26.020 443 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.72 % Allowed : 16.10 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.42), residues: 410 helix: 2.03 (0.28), residues: 338 sheet: None (None), residues: 0 loop : -1.41 (0.67), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.015 0.001 PHE A 273 TYR 0.017 0.001 TYR A 299 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8326 (t80) cc_final: 0.7845 (t80) REVERT: A 125 HIS cc_start: 0.6643 (t-90) cc_final: 0.6058 (t-170) REVERT: A 292 MET cc_start: 0.5205 (OUTLIER) cc_final: 0.4891 (ttp) REVERT: A 296 GLU cc_start: 0.8287 (tp30) cc_final: 0.8043 (tp30) REVERT: A 311 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5822 (mtp) outliers start: 12 outliers final: 3 residues processed: 49 average time/residue: 1.0477 time to fit residues: 53.0919 Evaluate side-chains 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.136600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087760 restraints weight = 6458.833| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.61 r_work: 0.3167 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3154 Z= 0.157 Angle : 0.618 11.042 4300 Z= 0.301 Chirality : 0.040 0.132 538 Planarity : 0.004 0.035 530 Dihedral : 4.192 24.773 443 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.10 % Allowed : 18.89 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.41), residues: 410 helix: 2.16 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.40 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.028 0.002 PHE A 324 TYR 0.015 0.001 TYR A 299 ARG 0.004 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8297 (t80) cc_final: 0.7657 (t80) REVERT: A 125 HIS cc_start: 0.6667 (t-90) cc_final: 0.6143 (t-170) REVERT: A 292 MET cc_start: 0.5269 (tpp) cc_final: 0.4939 (ttp) REVERT: A 296 GLU cc_start: 0.8206 (tp30) cc_final: 0.7974 (tp30) REVERT: A 311 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5525 (mtp) outliers start: 10 outliers final: 3 residues processed: 43 average time/residue: 0.9382 time to fit residues: 41.9287 Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.136360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087507 restraints weight = 6327.281| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.60 r_work: 0.3163 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3154 Z= 0.174 Angle : 0.628 10.974 4300 Z= 0.306 Chirality : 0.040 0.143 538 Planarity : 0.004 0.034 530 Dihedral : 4.127 23.105 443 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.41 % Allowed : 19.81 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.41), residues: 410 helix: 2.17 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.43 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.016 0.001 PHE A 273 TYR 0.015 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8296 (t80) cc_final: 0.7667 (t80) REVERT: A 125 HIS cc_start: 0.6588 (t-90) cc_final: 0.6100 (t-170) REVERT: A 269 MET cc_start: 0.8661 (mpt) cc_final: 0.8364 (mpp) REVERT: A 296 GLU cc_start: 0.8143 (tp30) cc_final: 0.7922 (tp30) REVERT: A 311 MET cc_start: 0.5982 (OUTLIER) cc_final: 0.5582 (mtp) outliers start: 11 outliers final: 3 residues processed: 45 average time/residue: 0.9973 time to fit residues: 46.5066 Evaluate side-chains 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.133567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.084020 restraints weight = 6343.016| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.54 r_work: 0.3087 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3154 Z= 0.270 Angle : 0.675 11.012 4300 Z= 0.333 Chirality : 0.043 0.249 538 Planarity : 0.004 0.034 530 Dihedral : 4.208 22.464 443 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.17 % Allowed : 20.43 % Favored : 77.40 % 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: 2.17 (0.41), residues: 410 helix: 2.00 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.28 (0.67), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.026 0.002 PHE A 324 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8276 (t80) cc_final: 0.7739 (t80) REVERT: A 125 HIS cc_start: 0.6526 (t-90) cc_final: 0.6002 (t-170) REVERT: A 296 GLU cc_start: 0.8189 (tp30) cc_final: 0.7970 (tp30) REVERT: A 311 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6019 (mtp) outliers start: 7 outliers final: 3 residues processed: 42 average time/residue: 0.9960 time to fit residues: 43.5723 Evaluate side-chains 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.133463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084189 restraints weight = 6339.189| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.55 r_work: 0.3093 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3154 Z= 0.239 Angle : 0.681 10.968 4300 Z= 0.334 Chirality : 0.043 0.258 538 Planarity : 0.004 0.035 530 Dihedral : 4.276 23.016 443 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.55 % Allowed : 21.36 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.41), residues: 410 helix: 2.05 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.20 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 215 PHE 0.019 0.002 PHE A 273 TYR 0.018 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8272 (t80) cc_final: 0.7705 (t80) REVERT: A 125 HIS cc_start: 0.6477 (t-90) cc_final: 0.5940 (t-170) REVERT: A 269 MET cc_start: 0.8607 (mpt) cc_final: 0.8292 (mpp) REVERT: A 311 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.6051 (mtp) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 1.0152 time to fit residues: 43.0941 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 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 = 0.4100 r_free = 0.4100 target = 0.135357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086375 restraints weight = 6210.755| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.55 r_work: 0.3133 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3154 Z= 0.178 Angle : 0.665 11.211 4300 Z= 0.323 Chirality : 0.042 0.260 538 Planarity : 0.004 0.035 530 Dihedral : 4.314 23.103 443 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.48 % Allowed : 20.43 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.41), residues: 410 helix: 2.12 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.28 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.024 0.002 PHE A 324 TYR 0.013 0.001 TYR A 299 ARG 0.002 0.000 ARG A 397 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8248 (t80) cc_final: 0.7734 (t80) REVERT: A 125 HIS cc_start: 0.6481 (t-90) cc_final: 0.5972 (t-170) REVERT: A 269 MET cc_start: 0.8632 (mpt) cc_final: 0.8317 (mpp) REVERT: A 311 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5883 (mtp) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.9900 time to fit residues: 45.1011 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 355 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.135386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086358 restraints weight = 6391.969| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.54 r_work: 0.3137 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3154 Z= 0.191 Angle : 0.692 10.977 4300 Z= 0.333 Chirality : 0.045 0.343 538 Planarity : 0.004 0.034 530 Dihedral : 4.280 22.547 443 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.55 % Allowed : 21.67 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.41), residues: 410 helix: 2.10 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.27 (0.65), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.016 0.001 PHE A 273 TYR 0.016 0.001 TYR A 299 ARG 0.001 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.30 seconds wall clock time: 62 minutes 53.31 seconds (3773.31 seconds total)