Starting phenix.real_space_refine on Tue Mar 3 12:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uh3_26504/03_2026/7uh3_26504.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uh3_26504/03_2026/7uh3_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 { model { file = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2026/7uh3_26504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2026/7uh3_26504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2026/7uh3_26504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uh3_26504/03_2026/7uh3_26504.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.79, per 1000 atoms: 0.26 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: 0.27 Conformation dependent library (CDL) restraints added in 127.6 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: 0.29 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: 0.50 Time building geometry restraints manager: 0.37 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- 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= 0.176 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 105 TYR 0.009 0.001 TYR A 247 PHE 0.007 0.001 PHE A 156 HIS 0.001 0.000 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3154) covalent geometry : angle 0.61351 ( 4300) hydrogen bonds : bond 0.31028 ( 229) hydrogen bonds : angle 6.87119 ( 687) *********************** 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 : 0.114 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: 0.5365 time to fit residues: 30.8703 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 : 0.109 ------------------------------------------------------------------------------- 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 24 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.130565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080851 restraints weight = 6464.947| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.73 r_work: 0.3021 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3154 Z= 0.197 Angle : 0.701 11.095 4300 Z= 0.357 Chirality : 0.043 0.125 538 Planarity : 0.004 0.032 530 Dihedral : 6.475 93.429 446 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.40 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.40), residues: 410 helix: 1.68 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -1.23 (0.64), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 287 TYR 0.019 0.002 TYR A 299 PHE 0.026 0.003 PHE A 273 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3154) covalent geometry : angle 0.70115 ( 4300) hydrogen bonds : bond 0.07789 ( 229) hydrogen bonds : angle 4.64736 ( 687) *********************** 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 53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.113 Fit side-chains REVERT: A 125 HIS cc_start: 0.6603 (t-90) cc_final: 0.6026 (t-170) REVERT: A 296 GLU cc_start: 0.7852 (tp30) cc_final: 0.7494 (tp30) REVERT: A 311 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.5764 (mtp) outliers start: 11 outliers final: 3 residues processed: 47 average time/residue: 0.4307 time to fit residues: 20.9886 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 : 0.084 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.133246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084614 restraints weight = 6384.557| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.57 r_work: 0.3102 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2740 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= 0.155 Angle : 0.627 11.213 4300 Z= 0.310 Chirality : 0.041 0.153 538 Planarity : 0.004 0.034 530 Dihedral : 4.349 31.903 443 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.41 % Allowed : 11.76 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.41), residues: 410 helix: 1.90 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.46 (0.64), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 177 TYR 0.018 0.001 TYR A 299 PHE 0.023 0.002 PHE A 273 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3154) covalent geometry : angle 0.62654 ( 4300) hydrogen bonds : bond 0.06260 ( 229) hydrogen bonds : angle 4.30785 ( 687) *********************** 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 53 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.119 Fit side-chains REVERT: A 125 HIS cc_start: 0.6653 (t-90) cc_final: 0.6049 (t-170) REVERT: A 296 GLU cc_start: 0.7742 (tp30) cc_final: 0.7509 (tp30) REVERT: A 311 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5994 (mtp) REVERT: A 323 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8772 (m-10) outliers start: 11 outliers final: 3 residues processed: 45 average time/residue: 0.5107 time to fit residues: 23.7072 Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 35 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.132004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082497 restraints weight = 6322.374| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.56 r_work: 0.3068 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3154 Z= 0.178 Angle : 0.638 11.055 4300 Z= 0.316 Chirality : 0.041 0.134 538 Planarity : 0.004 0.034 530 Dihedral : 4.296 28.612 443 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.48 % Allowed : 15.79 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.41), residues: 410 helix: 2.03 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.48 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.019 0.001 TYR A 299 PHE 0.026 0.002 PHE A 324 HIS 0.002 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3154) covalent geometry : angle 0.63803 ( 4300) hydrogen bonds : bond 0.06153 ( 229) hydrogen bonds : angle 4.20293 ( 687) *********************** 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 44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.120 Fit side-chains REVERT: A 95 PHE cc_start: 0.8256 (t80) cc_final: 0.7848 (t80) REVERT: A 125 HIS cc_start: 0.6686 (t-90) cc_final: 0.6069 (t-170) REVERT: A 273 PHE cc_start: 0.7907 (t80) cc_final: 0.7683 (t80) REVERT: A 311 MET cc_start: 0.6489 (OUTLIER) cc_final: 0.6215 (mtp) outliers start: 8 outliers final: 4 residues processed: 39 average time/residue: 0.4493 time to fit residues: 18.2179 Evaluate side-chains 39 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.0060 overall best weight: 0.3194 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.136003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.087181 restraints weight = 6375.136| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.61 r_work: 0.3151 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3311 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= 0.130 Angle : 0.610 11.121 4300 Z= 0.297 Chirality : 0.040 0.129 538 Planarity : 0.004 0.035 530 Dihedral : 4.275 26.965 443 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.48 % Allowed : 17.03 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.41), residues: 410 helix: 2.15 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.37 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.017 0.001 TYR A 299 PHE 0.010 0.001 PHE A 323 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3154) covalent geometry : angle 0.60977 ( 4300) hydrogen bonds : bond 0.04789 ( 229) hydrogen bonds : angle 4.01702 ( 687) *********************** 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 52 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8279 (t80) cc_final: 0.7834 (t80) REVERT: A 125 HIS cc_start: 0.6638 (t-90) cc_final: 0.5995 (t-170) REVERT: A 287 ARG cc_start: 0.8094 (tmm-80) cc_final: 0.7890 (tmm-80) REVERT: A 311 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5726 (mtp) outliers start: 8 outliers final: 3 residues processed: 47 average time/residue: 0.5017 time to fit residues: 24.3031 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 : 0.111 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.0000 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.135284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.086080 restraints weight = 6363.997| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.65 r_work: 0.3131 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3417 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= 0.132 Angle : 0.605 11.053 4300 Z= 0.295 Chirality : 0.040 0.130 538 Planarity : 0.004 0.034 530 Dihedral : 4.221 25.483 443 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.17 % Allowed : 18.58 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.41), residues: 410 helix: 2.14 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.45 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.016 0.001 TYR A 299 PHE 0.026 0.002 PHE A 324 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3154) covalent geometry : angle 0.60479 ( 4300) hydrogen bonds : bond 0.04902 ( 229) hydrogen bonds : angle 3.97673 ( 687) *********************** 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 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8273 (t80) cc_final: 0.7802 (t80) REVERT: A 125 HIS cc_start: 0.6655 (t-90) cc_final: 0.6050 (t-170) REVERT: A 296 GLU cc_start: 0.8203 (tp30) cc_final: 0.7923 (tp30) REVERT: A 311 MET cc_start: 0.6011 (mtp) cc_final: 0.5742 (mtp) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.5358 time to fit residues: 23.1479 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 : 0.110 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.134758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.085255 restraints weight = 6440.745| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.57 r_work: 0.3121 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3154 Z= 0.143 Angle : 0.633 11.106 4300 Z= 0.311 Chirality : 0.040 0.130 538 Planarity : 0.004 0.034 530 Dihedral : 4.186 23.997 443 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.79 % Allowed : 19.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.41), residues: 410 helix: 2.15 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -1.48 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.009 0.001 PHE A 323 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3154) covalent geometry : angle 0.63344 ( 4300) hydrogen bonds : bond 0.05004 ( 229) hydrogen bonds : angle 3.98037 ( 687) *********************** 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 49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8290 (t80) cc_final: 0.7846 (t80) REVERT: A 125 HIS cc_start: 0.6681 (t-90) cc_final: 0.6080 (t-170) REVERT: A 217 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8476 (mtp) REVERT: A 296 GLU cc_start: 0.8171 (tp30) cc_final: 0.7925 (tp30) REVERT: A 311 MET cc_start: 0.6167 (mtp) cc_final: 0.5858 (mtp) outliers start: 9 outliers final: 4 residues processed: 43 average time/residue: 0.5121 time to fit residues: 22.6830 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.135350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086064 restraints weight = 6449.638| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.58 r_work: 0.3120 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3571 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= 0.141 Angle : 0.645 11.076 4300 Z= 0.316 Chirality : 0.041 0.206 538 Planarity : 0.004 0.035 530 Dihedral : 4.197 22.985 443 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.41), residues: 410 helix: 2.14 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.41 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.028 0.002 PHE A 324 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3154) covalent geometry : angle 0.64504 ( 4300) hydrogen bonds : bond 0.04896 ( 229) hydrogen bonds : angle 3.96418 ( 687) *********************** 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 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8288 (t80) cc_final: 0.7827 (t80) REVERT: A 125 HIS cc_start: 0.6476 (t-90) cc_final: 0.5939 (t-170) REVERT: A 217 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: A 269 MET cc_start: 0.8618 (mpt) cc_final: 0.8279 (mpp) REVERT: A 296 GLU cc_start: 0.8158 (tp30) cc_final: 0.7923 (tp30) REVERT: A 311 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5792 (mtp) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.4617 time to fit residues: 20.0741 Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 236 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.135495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086190 restraints weight = 6394.860| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.58 r_work: 0.3119 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3621 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= 0.138 Angle : 0.657 11.169 4300 Z= 0.320 Chirality : 0.042 0.290 538 Planarity : 0.004 0.034 530 Dihedral : 4.184 22.463 443 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.10 % Allowed : 19.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.41), residues: 410 helix: 2.15 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.35 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.017 0.001 TYR A 299 PHE 0.009 0.001 PHE A 323 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 3154) covalent geometry : angle 0.65737 ( 4300) hydrogen bonds : bond 0.04828 ( 229) hydrogen bonds : angle 3.94231 ( 687) *********************** 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 47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8290 (t80) cc_final: 0.7829 (t80) REVERT: A 125 HIS cc_start: 0.6504 (t-90) cc_final: 0.5955 (t-170) REVERT: A 217 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8459 (mpp) REVERT: A 311 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5793 (mtp) outliers start: 10 outliers final: 5 residues processed: 42 average time/residue: 0.4806 time to fit residues: 20.8973 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 : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 MET 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 323 PHE 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 3 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.0040 chunk 7 optimal weight: 0.1980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087633 restraints weight = 6317.507| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.58 r_work: 0.3162 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3816 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= 0.131 Angle : 0.653 11.154 4300 Z= 0.318 Chirality : 0.042 0.266 538 Planarity : 0.004 0.035 530 Dihedral : 4.202 22.069 443 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.41), residues: 410 helix: 2.24 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.30 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 105 TYR 0.012 0.001 TYR A 299 PHE 0.027 0.002 PHE A 324 HIS 0.001 0.000 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3154) covalent geometry : angle 0.65264 ( 4300) hydrogen bonds : bond 0.04465 ( 229) hydrogen bonds : angle 3.90537 ( 687) ********************** 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 50 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8314 (t80) cc_final: 0.7779 (t80) REVERT: A 125 HIS cc_start: 0.6459 (t-90) cc_final: 0.5926 (t-170) REVERT: A 269 MET cc_start: 0.8569 (mpt) cc_final: 0.8170 (mpp) REVERT: A 311 MET cc_start: 0.6054 (OUTLIER) cc_final: 0.5673 (mtp) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.4319 time to fit residues: 20.5941 Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 323 PHE 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 36 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.134619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.085096 restraints weight = 6450.438| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.58 r_work: 0.3094 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3154 Z= 0.168 Angle : 0.690 10.986 4300 Z= 0.336 Chirality : 0.044 0.378 538 Planarity : 0.004 0.034 530 Dihedral : 4.273 21.869 443 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.17 % Allowed : 21.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.41), residues: 410 helix: 2.13 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.16 (0.65), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.018 0.001 TYR A 299 PHE 0.010 0.001 PHE A 210 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3154) covalent geometry : angle 0.69028 ( 4300) hydrogen bonds : bond 0.05202 ( 229) hydrogen bonds : angle 4.02307 ( 687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1386.54 seconds wall clock time: 24 minutes 14.47 seconds (1454.47 seconds total)