Starting phenix.real_space_refine on Mon Sep 23 18:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/09_2024/7uh3_26504.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/09_2024/7uh3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/09_2024/7uh3_26504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/09_2024/7uh3_26504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/09_2024/7uh3_26504.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uh3_26504/09_2024/7uh3_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-5461/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: 3.40, per 1000 atoms: 1.10 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: 0.88 Conformation dependent library (CDL) restraints added in 596.2 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: 0.28 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: 0.76 Time building geometry restraints manager: 0.99 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: 3.390 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.290 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.369 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: 1.0809 time to fit residues: 62.5041 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 11.307 4300 Z= 0.345 Chirality : 0.042 0.122 538 Planarity : 0.004 0.032 530 Dihedral : 6.561 94.163 446 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 fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.336 Fit side-chains REVERT: A 125 HIS cc_start: 0.6647 (t-90) cc_final: 0.6162 (t-170) REVERT: A 296 GLU cc_start: 0.7789 (tp30) cc_final: 0.7462 (tp30) outliers start: 11 outliers final: 4 residues processed: 57 average time/residue: 0.8170 time to fit residues: 48.5500 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.5980 chunk 11 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2909 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= 0.177 Angle : 0.620 11.048 4300 Z= 0.305 Chirality : 0.040 0.150 538 Planarity : 0.004 0.033 530 Dihedral : 4.351 33.944 443 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.72 % Allowed : 13.31 % Favored : 82.97 % 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: 2.05 (0.41), residues: 410 helix: 1.89 (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 0.020 0.002 PHE A 273 TYR 0.018 0.001 TYR A 299 ARG 0.003 0.001 ARG A 287 *********************** 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 fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.316 Fit side-chains REVERT: A 95 PHE cc_start: 0.8379 (t80) cc_final: 0.7843 (t80) REVERT: A 125 HIS cc_start: 0.6647 (t-90) cc_final: 0.6125 (t-170) REVERT: A 292 MET cc_start: 0.5294 (tpp) cc_final: 0.4907 (ttp) REVERT: A 323 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8774 (m-10) outliers start: 12 outliers final: 4 residues processed: 48 average time/residue: 0.9656 time to fit residues: 48.1252 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3154 Z= 0.246 Angle : 0.629 10.926 4300 Z= 0.310 Chirality : 0.041 0.141 538 Planarity : 0.004 0.034 530 Dihedral : 4.238 28.313 443 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.10 % Allowed : 15.17 % 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 (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: 1.96 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -1.27 (0.68), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.026 0.002 PHE A 324 TYR 0.017 0.001 TYR A 299 ARG 0.003 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 50 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.351 Fit side-chains REVERT: A 95 PHE cc_start: 0.8423 (t80) cc_final: 0.7877 (t80) REVERT: A 125 HIS cc_start: 0.6585 (t-90) cc_final: 0.6009 (t-170) REVERT: A 292 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.5070 (ttp) REVERT: A 323 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8785 (m-10) outliers start: 10 outliers final: 4 residues processed: 45 average time/residue: 1.0781 time to fit residues: 50.3180 Evaluate side-chains 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.0040 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3171 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= 0.233 Angle : 0.636 11.077 4300 Z= 0.314 Chirality : 0.041 0.132 538 Planarity : 0.004 0.035 530 Dihedral : 4.261 28.529 443 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.72 % Allowed : 15.79 % 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 (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: 2.01 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -1.35 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 32 PHE 0.017 0.002 PHE A 273 TYR 0.018 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 *********************** 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 53 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8392 (t80) cc_final: 0.7857 (t80) REVERT: A 125 HIS cc_start: 0.6647 (t-90) cc_final: 0.6042 (t-170) REVERT: A 292 MET cc_start: 0.5419 (OUTLIER) cc_final: 0.5171 (ttp) outliers start: 12 outliers final: 4 residues processed: 45 average time/residue: 1.0956 time to fit residues: 51.0722 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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 23 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3384 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= 0.174 Angle : 0.625 11.098 4300 Z= 0.305 Chirality : 0.040 0.134 538 Planarity : 0.004 0.035 530 Dihedral : 4.292 28.498 443 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.10 % Allowed : 17.65 % 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 (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: 2.08 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -1.44 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.026 0.002 PHE A 324 TYR 0.015 0.001 TYR A 299 ARG 0.002 0.000 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 49 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8379 (t80) cc_final: 0.7841 (t80) REVERT: A 125 HIS cc_start: 0.6624 (t-90) cc_final: 0.6052 (t-170) REVERT: A 292 MET cc_start: 0.5370 (tpp) cc_final: 0.4975 (ttp) outliers start: 10 outliers final: 4 residues processed: 44 average time/residue: 1.0035 time to fit residues: 45.7185 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3559 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= 0.171 Angle : 0.624 11.068 4300 Z= 0.305 Chirality : 0.040 0.137 538 Planarity : 0.004 0.035 530 Dihedral : 4.230 25.707 443 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.79 % Allowed : 19.81 % 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: 2.25 (0.41), residues: 410 helix: 2.13 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.53 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.017 0.001 PHE A 273 TYR 0.015 0.001 TYR A 299 ARG 0.002 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 49 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8321 (t80) cc_final: 0.7654 (t80) REVERT: A 125 HIS cc_start: 0.6614 (t-90) cc_final: 0.6099 (t-170) outliers start: 9 outliers final: 4 residues processed: 44 average time/residue: 1.0770 time to fit residues: 49.0928 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.0020 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6110 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3707 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= 0.172 Angle : 0.652 11.043 4300 Z= 0.319 Chirality : 0.042 0.225 538 Planarity : 0.004 0.035 530 Dihedral : 4.211 25.146 443 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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: 2.25 (0.41), residues: 410 helix: 2.07 (0.28), residues: 339 sheet: None (None), residues: 0 loop : -1.43 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.025 0.002 PHE A 324 TYR 0.016 0.001 TYR A 299 ARG 0.002 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 47 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8311 (t80) cc_final: 0.7699 (t80) REVERT: A 125 HIS cc_start: 0.6501 (t-90) cc_final: 0.6021 (t-170) REVERT: A 269 MET cc_start: 0.8531 (mpt) cc_final: 0.8217 (mpp) outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 0.9837 time to fit residues: 44.0343 Evaluate side-chains 40 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR 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 11 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3154 Z= 0.197 Angle : 0.670 11.053 4300 Z= 0.327 Chirality : 0.043 0.289 538 Planarity : 0.004 0.034 530 Dihedral : 4.233 24.220 443 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.93 % Allowed : 21.67 % 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: 2.22 (0.41), residues: 410 helix: 2.10 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.45 (0.64), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 215 PHE 0.018 0.001 PHE A 273 TYR 0.016 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 42 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8291 (t80) cc_final: 0.7712 (t80) REVERT: A 125 HIS cc_start: 0.6510 (t-90) cc_final: 0.5995 (t-170) REVERT: A 269 MET cc_start: 0.8529 (mpt) cc_final: 0.8176 (mpp) outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.9484 time to fit residues: 41.4149 Evaluate side-chains 41 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR 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 32 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3838 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= 0.173 Angle : 0.672 10.983 4300 Z= 0.327 Chirality : 0.042 0.269 538 Planarity : 0.004 0.035 530 Dihedral : 4.200 23.733 443 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.86 % Allowed : 21.36 % 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: 2.26 (0.41), residues: 410 helix: 2.12 (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 40 PHE 0.025 0.002 PHE A 324 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 ********************** 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 43 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8293 (t80) cc_final: 0.7742 (t80) REVERT: A 125 HIS cc_start: 0.6451 (t-90) cc_final: 0.5956 (t-170) REVERT: A 269 MET cc_start: 0.8564 (mpt) cc_final: 0.8230 (mpp) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.9911 time to fit residues: 43.2804 Evaluate side-chains 39 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0040 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.135816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086779 restraints weight = 6261.618| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.56 r_work: 0.3144 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3845 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= 0.182 Angle : 0.693 11.013 4300 Z= 0.332 Chirality : 0.043 0.340 538 Planarity : 0.004 0.034 530 Dihedral : 4.171 23.080 443 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.24 % Allowed : 21.98 % 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: 2.16 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.36 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.016 0.001 PHE A 273 TYR 0.014 0.001 TYR A 299 ARG 0.002 0.000 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.02 seconds wall clock time: 29 minutes 39.87 seconds (1779.87 seconds total)