Starting phenix.real_space_refine on Fri Dec 27 17:00:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8roz_19408/12_2024/8roz_19408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8roz_19408/12_2024/8roz_19408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8roz_19408/12_2024/8roz_19408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8roz_19408/12_2024/8roz_19408.map" model { file = "/net/cci-nas-00/data/ceres_data/8roz_19408/12_2024/8roz_19408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8roz_19408/12_2024/8roz_19408.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 3930 2.51 5 N 1021 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6079 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2385 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 278} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'PTR:plan-2': 1, 'ARG:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2118 Classifications: {'peptide': 263} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 248} Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1576 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 179} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.37, per 1000 atoms: 0.72 Number of scatterers: 6079 At special positions: 0 Unit cell: (73.425, 80.85, 107.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 1096 8.00 N 1021 7.00 C 3930 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 862.0 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1426 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 145 through 149 removed outlier: 4.356A pdb=" N LEU A 148 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 182 through 199 removed outlier: 3.596A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.695A pdb=" N VAL A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'B' and resid 168 through 173 removed outlier: 3.956A pdb=" N ASN B 171 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 191 removed outlier: 4.128A pdb=" N VAL B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.734A pdb=" N LYS B 199 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 223 Processing helix chain 'B' and resid 226 through 244 removed outlier: 3.509A pdb=" N LEU B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 285 through 301 Processing helix chain 'B' and resid 308 through 317 removed outlier: 3.652A pdb=" N GLN B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.577A pdb=" N LEU B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 346 removed outlier: 4.084A pdb=" N TYR B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 366 Processing helix chain 'B' and resid 371 through 379 removed outlier: 3.777A pdb=" N GLN B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 398 removed outlier: 3.717A pdb=" N ASP B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 412 through 417 removed outlier: 6.259A pdb=" N LYS B 415 " --> pdb=" O LYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.741A pdb=" N MET C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 404 through 413 Processing helix chain 'C' and resid 436 through 452 Processing helix chain 'C' and resid 468 through 477 removed outlier: 3.906A pdb=" N GLU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 522 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 5.375A pdb=" N LYS A 6 " --> pdb=" O ARG A 22 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG A 22 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 68 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU A 81 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 66 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.668A pdb=" N GLN A 85 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'C' and resid 359 through 360 removed outlier: 4.275A pdb=" N GLU C 462 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE C 377 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE C 426 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C 379 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL C 428 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 381 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N HIS C 430 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 383 " --> pdb=" O HIS C 430 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1928 1.34 - 1.46: 1423 1.46 - 1.58: 2829 1.58 - 1.70: 4 1.70 - 1.82: 50 Bond restraints: 6234 Sorted by residual: bond pdb=" OH PTR A 15 " pdb=" P PTR A 15 " ideal model delta sigma weight residual 1.769 1.608 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O1P TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.525 1.605 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" O3P TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O2P TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.528 1.475 0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 6229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 8344 2.12 - 4.24: 81 4.24 - 6.36: 14 6.36 - 8.48: 2 8.48 - 10.60: 4 Bond angle restraints: 8445 Sorted by residual: angle pdb=" CB TPO A 160 " pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 119.31 108.71 10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " pdb=" O1P TPO A 160 " ideal model delta sigma weight residual 100.43 110.24 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA TYR C 455 " pdb=" C TYR C 455 " pdb=" O TYR C 455 " ideal model delta sigma weight residual 120.17 116.82 3.35 1.04e+00 9.25e-01 1.04e+01 angle pdb=" CB MET C 336 " pdb=" CG MET C 336 " pdb=" SD MET C 336 " ideal model delta sigma weight residual 112.70 122.25 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CA TYR B 284 " pdb=" C TYR B 284 " pdb=" O TYR B 284 " ideal model delta sigma weight residual 121.06 117.66 3.40 1.16e+00 7.43e-01 8.57e+00 ... (remaining 8440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3234 17.69 - 35.39: 376 35.39 - 53.08: 119 53.08 - 70.78: 31 70.78 - 88.47: 8 Dihedral angle restraints: 3768 sinusoidal: 1556 harmonic: 2212 Sorted by residual: dihedral pdb=" CA LEU A 83 " pdb=" C LEU A 83 " pdb=" N HIS A 84 " pdb=" CA HIS A 84 " ideal model delta harmonic sigma weight residual -180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.93e+00 dihedral pdb=" CB GLU C 436 " pdb=" CG GLU C 436 " pdb=" CD GLU C 436 " pdb=" OE1 GLU C 436 " ideal model delta sinusoidal sigma weight residual 0.00 -84.67 84.67 1 3.00e+01 1.11e-03 9.68e+00 dihedral pdb=" N ARG C 520 " pdb=" CA ARG C 520 " pdb=" CB ARG C 520 " pdb=" CG ARG C 520 " ideal model delta sinusoidal sigma weight residual -60.00 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 594 0.032 - 0.064: 226 0.064 - 0.096: 64 0.096 - 0.128: 42 0.128 - 0.160: 2 Chirality restraints: 928 Sorted by residual: chirality pdb=" CA TYR B 284 " pdb=" N TYR B 284 " pdb=" C TYR B 284 " pdb=" CB TYR B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA PTR A 15 " pdb=" N PTR A 15 " pdb=" C PTR A 15 " pdb=" CB PTR A 15 " both_signs ideal model delta sigma weight residual False 2.35 2.51 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB VAL B 254 " pdb=" CA VAL B 254 " pdb=" CG1 VAL B 254 " pdb=" CG2 VAL B 254 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 925 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 343 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 344 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 438 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO C 439 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 439 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 439 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 260 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU B 260 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU B 260 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 261 " -0.010 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 898 2.75 - 3.29: 5597 3.29 - 3.83: 10350 3.83 - 4.36: 12608 4.36 - 4.90: 21631 Nonbonded interactions: 51084 Sorted by model distance: nonbonded pdb=" OH TYR B 236 " pdb=" O LEU B 304 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP C 340 " pdb=" OG SER C 342 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 210 " pdb=" OH TYR C 455 " model vdw 2.312 3.040 nonbonded pdb=" NH2 ARG B 209 " pdb=" O LEU B 339 " model vdw 2.320 3.120 nonbonded pdb=" O LEU C 412 " pdb=" OH TYR C 460 " model vdw 2.328 3.040 ... (remaining 51079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.930 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.005 0.161 6234 Z= 0.272 Angle : 0.556 10.596 8445 Z= 0.273 Chirality : 0.041 0.160 928 Planarity : 0.005 0.043 1069 Dihedral : 17.455 88.471 2342 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 22.54 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.04 (0.31), residues: 739 helix: 1.43 (0.29), residues: 351 sheet: 0.12 (0.72), residues: 48 loop : 0.10 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.010 0.001 PHE A 152 TYR 0.013 0.001 TYR B 284 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7277 (m) cc_final: 0.6613 (p) REVERT: A 233 MET cc_start: 0.8614 (mtt) cc_final: 0.8152 (mtt) REVERT: A 237 LYS cc_start: 0.7340 (mttt) cc_final: 0.6533 (mmtt) REVERT: B 194 LYS cc_start: 0.7618 (mttt) cc_final: 0.6771 (mptt) REVERT: B 272 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6989 (mm-30) REVERT: B 291 ARG cc_start: 0.7222 (tpt170) cc_final: 0.6589 (mtt90) REVERT: B 372 GLU cc_start: 0.7839 (tp30) cc_final: 0.7547 (tm-30) REVERT: B 375 VAL cc_start: 0.8353 (p) cc_final: 0.8139 (t) REVERT: C 472 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6041 (tt0) REVERT: C 502 ARG cc_start: 0.7290 (mmt90) cc_final: 0.6673 (mtp180) REVERT: C 506 ARG cc_start: 0.6430 (ttm110) cc_final: 0.6075 (ttp-110) REVERT: C 519 SER cc_start: 0.7165 (m) cc_final: 0.6923 (m) REVERT: C 522 LYS cc_start: 0.5917 (pttt) cc_final: 0.5666 (tppt) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 1.3898 time to fit residues: 171.2313 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 254 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 84 HIS A 85 GLN B 177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6234 Z= 0.335 Angle : 0.560 7.651 8445 Z= 0.287 Chirality : 0.044 0.150 928 Planarity : 0.006 0.075 1069 Dihedral : 6.412 89.144 838 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.84 % Allowed : 19.06 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.26 (0.32), residues: 739 helix: 1.72 (0.29), residues: 357 sheet: -0.23 (0.70), residues: 58 loop : 0.14 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 370 HIS 0.006 0.001 HIS C 430 PHE 0.018 0.002 PHE A 152 TYR 0.016 0.002 TYR B 411 ARG 0.012 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7169 (p) REVERT: A 200 ARG cc_start: 0.7319 (ptp90) cc_final: 0.6814 (ptt-90) REVERT: A 237 LYS cc_start: 0.7381 (mttt) cc_final: 0.6611 (mmtt) REVERT: A 261 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.7812 (m) REVERT: B 194 LYS cc_start: 0.7622 (mttt) cc_final: 0.6695 (mptt) REVERT: B 291 ARG cc_start: 0.7268 (tpt170) cc_final: 0.6637 (mtt90) REVERT: B 346 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 372 GLU cc_start: 0.7763 (tp30) cc_final: 0.7554 (tm-30) REVERT: B 375 VAL cc_start: 0.8351 (p) cc_final: 0.8135 (t) REVERT: C 372 LYS cc_start: 0.7853 (mmtp) cc_final: 0.7467 (mmtp) REVERT: C 406 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: C 472 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6230 (tt0) REVERT: C 475 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6391 (mpt) REVERT: C 485 SER cc_start: 0.8027 (t) cc_final: 0.7380 (p) REVERT: C 502 ARG cc_start: 0.7285 (mmt90) cc_final: 0.6704 (mtp180) REVERT: C 506 ARG cc_start: 0.6515 (ttm110) cc_final: 0.6102 (ttp-110) REVERT: C 519 SER cc_start: 0.7399 (m) cc_final: 0.7169 (m) outliers start: 32 outliers final: 12 residues processed: 117 average time/residue: 1.5113 time to fit residues: 184.7837 Evaluate side-chains 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6234 Z= 0.190 Angle : 0.471 6.125 8445 Z= 0.244 Chirality : 0.041 0.125 928 Planarity : 0.006 0.133 1069 Dihedral : 6.136 86.990 835 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.18 % Allowed : 21.79 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.32), residues: 739 helix: 1.97 (0.29), residues: 357 sheet: -0.33 (0.70), residues: 58 loop : 0.22 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.012 0.001 PHE A 152 TYR 0.010 0.001 TYR B 411 ARG 0.020 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7119 (p) REVERT: A 233 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: A 237 LYS cc_start: 0.7397 (mttt) cc_final: 0.6639 (mmtt) REVERT: B 194 LYS cc_start: 0.7632 (mttt) cc_final: 0.6690 (mptt) REVERT: B 291 ARG cc_start: 0.7295 (tpt170) cc_final: 0.6628 (mtt90) REVERT: B 303 ASP cc_start: 0.8203 (m-30) cc_final: 0.7791 (m-30) REVERT: B 372 GLU cc_start: 0.7724 (tp30) cc_final: 0.7407 (tm-30) REVERT: C 372 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7330 (mmtp) REVERT: C 406 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: C 472 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6200 (tt0) REVERT: C 485 SER cc_start: 0.8030 (t) cc_final: 0.7826 (t) REVERT: C 502 ARG cc_start: 0.7278 (mmt90) cc_final: 0.6622 (mtp180) REVERT: C 506 ARG cc_start: 0.6501 (ttm110) cc_final: 0.6060 (ttp-110) REVERT: C 519 SER cc_start: 0.7289 (m) cc_final: 0.7044 (m) outliers start: 21 outliers final: 9 residues processed: 98 average time/residue: 1.4357 time to fit residues: 147.4054 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6234 Z= 0.202 Angle : 0.475 6.120 8445 Z= 0.244 Chirality : 0.041 0.127 928 Planarity : 0.005 0.082 1069 Dihedral : 5.921 85.669 835 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.78 % Allowed : 21.48 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.55 (0.32), residues: 739 helix: 2.01 (0.28), residues: 357 sheet: -0.31 (0.74), residues: 53 loop : 0.26 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.012 0.001 PHE A 152 TYR 0.011 0.001 TYR B 411 ARG 0.009 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7013 (p) REVERT: A 237 LYS cc_start: 0.7389 (mttt) cc_final: 0.6642 (mmtt) REVERT: A 261 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7854 (m) REVERT: B 194 LYS cc_start: 0.7649 (mttt) cc_final: 0.6707 (mptt) REVERT: B 291 ARG cc_start: 0.7305 (tpt170) cc_final: 0.6622 (mtt90) REVERT: B 303 ASP cc_start: 0.8207 (m-30) cc_final: 0.7793 (m-30) REVERT: B 346 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7603 (mp) REVERT: B 372 GLU cc_start: 0.7780 (tp30) cc_final: 0.7468 (tm-30) REVERT: C 372 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7374 (mmtp) REVERT: C 406 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: C 472 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6217 (tt0) REVERT: C 502 ARG cc_start: 0.7291 (mmt90) cc_final: 0.6643 (mtp180) REVERT: C 506 ARG cc_start: 0.6514 (ttm110) cc_final: 0.6058 (ttp-110) REVERT: C 519 SER cc_start: 0.7256 (m) cc_final: 0.7016 (m) outliers start: 25 outliers final: 13 residues processed: 105 average time/residue: 1.2218 time to fit residues: 134.7086 Evaluate side-chains 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 0.0770 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6234 Z= 0.177 Angle : 0.463 6.145 8445 Z= 0.239 Chirality : 0.040 0.124 928 Planarity : 0.006 0.126 1069 Dihedral : 5.800 85.613 835 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 22.24 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.66 (0.32), residues: 739 helix: 2.12 (0.29), residues: 357 sheet: -0.18 (0.75), residues: 53 loop : 0.27 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.011 0.001 PHE A 152 TYR 0.010 0.001 TYR B 411 ARG 0.015 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7123 (p) REVERT: A 233 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8266 (mtt) REVERT: A 237 LYS cc_start: 0.7401 (mttt) cc_final: 0.6645 (mmtt) REVERT: A 261 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7864 (m) REVERT: B 194 LYS cc_start: 0.7644 (mttt) cc_final: 0.6686 (mptt) REVERT: B 291 ARG cc_start: 0.7284 (tpt170) cc_final: 0.6606 (mtt90) REVERT: B 303 ASP cc_start: 0.8207 (m-30) cc_final: 0.7804 (m-30) REVERT: B 372 GLU cc_start: 0.7742 (tp30) cc_final: 0.7406 (tm-30) REVERT: C 372 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7435 (mmtp) REVERT: C 406 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: C 502 ARG cc_start: 0.7251 (mmt90) cc_final: 0.6573 (mtp180) REVERT: C 506 ARG cc_start: 0.6459 (ttm110) cc_final: 0.6013 (ttp-110) REVERT: C 519 SER cc_start: 0.7160 (m) cc_final: 0.6917 (m) outliers start: 22 outliers final: 10 residues processed: 96 average time/residue: 1.3560 time to fit residues: 136.2250 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6234 Z= 0.240 Angle : 0.510 8.878 8445 Z= 0.261 Chirality : 0.042 0.129 928 Planarity : 0.006 0.093 1069 Dihedral : 5.698 85.642 835 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.08 % Allowed : 21.79 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.54 (0.32), residues: 739 helix: 2.02 (0.28), residues: 357 sheet: -0.13 (0.75), residues: 53 loop : 0.18 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 PHE 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR B 411 ARG 0.009 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.704 Fit side-chains REVERT: A 177 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7091 (p) REVERT: A 237 LYS cc_start: 0.7404 (mttt) cc_final: 0.6643 (mmtt) REVERT: A 261 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.7895 (m) REVERT: A 265 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: B 194 LYS cc_start: 0.7658 (mttt) cc_final: 0.6698 (mptt) REVERT: B 272 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6405 (mm-30) REVERT: B 291 ARG cc_start: 0.7321 (tpt170) cc_final: 0.6638 (mtt90) REVERT: B 372 GLU cc_start: 0.7776 (tp30) cc_final: 0.7429 (tm-30) REVERT: C 372 LYS cc_start: 0.7790 (mmtp) cc_final: 0.7519 (mmtp) REVERT: C 406 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: C 485 SER cc_start: 0.8058 (t) cc_final: 0.7616 (p) REVERT: C 502 ARG cc_start: 0.7245 (mmt90) cc_final: 0.6577 (mtp180) REVERT: C 506 ARG cc_start: 0.6449 (ttm110) cc_final: 0.6066 (ttp-110) REVERT: C 519 SER cc_start: 0.7228 (m) cc_final: 0.6989 (m) outliers start: 27 outliers final: 14 residues processed: 98 average time/residue: 1.3923 time to fit residues: 142.6594 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6234 Z= 0.179 Angle : 0.499 10.796 8445 Z= 0.254 Chirality : 0.040 0.125 928 Planarity : 0.006 0.132 1069 Dihedral : 5.569 85.289 835 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.63 % Allowed : 22.09 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.32), residues: 739 helix: 2.16 (0.29), residues: 357 sheet: -0.03 (0.75), residues: 53 loop : 0.21 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.011 0.001 PHE A 152 TYR 0.009 0.001 TYR A 180 ARG 0.020 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7114 (p) REVERT: A 233 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8269 (mtt) REVERT: A 237 LYS cc_start: 0.7394 (mttt) cc_final: 0.6633 (mmtt) REVERT: A 261 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.7893 (m) REVERT: B 187 MET cc_start: 0.8176 (mmp) cc_final: 0.7914 (mmp) REVERT: B 194 LYS cc_start: 0.7656 (mttt) cc_final: 0.6696 (mptt) REVERT: B 272 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6382 (mm-30) REVERT: B 291 ARG cc_start: 0.7297 (tpt170) cc_final: 0.6623 (mtt90) REVERT: B 372 GLU cc_start: 0.7751 (tp30) cc_final: 0.7407 (tm-30) REVERT: C 406 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: C 485 SER cc_start: 0.8087 (t) cc_final: 0.7672 (p) REVERT: C 502 ARG cc_start: 0.7241 (mmt90) cc_final: 0.6557 (mtp180) REVERT: C 506 ARG cc_start: 0.6417 (ttm110) cc_final: 0.6045 (ttp-110) REVERT: C 519 SER cc_start: 0.7155 (m) cc_final: 0.6912 (m) outliers start: 24 outliers final: 14 residues processed: 97 average time/residue: 1.3869 time to fit residues: 140.5952 Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6234 Z= 0.262 Angle : 0.556 12.101 8445 Z= 0.280 Chirality : 0.042 0.147 928 Planarity : 0.006 0.132 1069 Dihedral : 5.668 85.502 835 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.63 % Allowed : 21.79 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.51 (0.32), residues: 739 helix: 2.03 (0.28), residues: 356 sheet: -0.03 (0.75), residues: 53 loop : 0.10 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 PHE 0.013 0.001 PHE A 152 TYR 0.013 0.001 TYR B 411 ARG 0.025 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7080 (p) REVERT: A 237 LYS cc_start: 0.7409 (mttt) cc_final: 0.6648 (mmtt) REVERT: A 261 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7896 (m) REVERT: B 194 LYS cc_start: 0.7659 (mttt) cc_final: 0.6703 (mptt) REVERT: B 272 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6422 (mm-30) REVERT: B 291 ARG cc_start: 0.7286 (tpt170) cc_final: 0.6611 (mtt90) REVERT: B 372 GLU cc_start: 0.7810 (tp30) cc_final: 0.7394 (tm-30) REVERT: C 406 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: C 485 SER cc_start: 0.8077 (t) cc_final: 0.7666 (p) REVERT: C 502 ARG cc_start: 0.7271 (mmt90) cc_final: 0.6593 (mtp180) REVERT: C 506 ARG cc_start: 0.6422 (ttm110) cc_final: 0.6040 (ttp-110) REVERT: C 519 SER cc_start: 0.7257 (m) cc_final: 0.7018 (m) outliers start: 24 outliers final: 15 residues processed: 95 average time/residue: 1.4420 time to fit residues: 143.2907 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS C 354 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6234 Z= 0.212 Angle : 0.605 23.696 8445 Z= 0.290 Chirality : 0.041 0.183 928 Planarity : 0.009 0.248 1069 Dihedral : 5.781 84.870 835 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.18 % Allowed : 22.09 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.60 (0.32), residues: 739 helix: 2.13 (0.29), residues: 356 sheet: -0.10 (0.75), residues: 53 loop : 0.14 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 PHE 0.012 0.001 PHE A 152 TYR 0.010 0.001 TYR B 411 ARG 0.040 0.001 ARG C 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7073 (p) REVERT: A 237 LYS cc_start: 0.7402 (mttt) cc_final: 0.6646 (mmtt) REVERT: A 261 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7900 (m) REVERT: B 194 LYS cc_start: 0.7654 (mttt) cc_final: 0.6698 (mptt) REVERT: B 272 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6387 (mm-30) REVERT: B 291 ARG cc_start: 0.7292 (tpt170) cc_final: 0.6606 (mtt90) REVERT: B 372 GLU cc_start: 0.7775 (tp30) cc_final: 0.7397 (tm-30) REVERT: C 406 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: C 485 SER cc_start: 0.8086 (t) cc_final: 0.7679 (p) REVERT: C 502 ARG cc_start: 0.7279 (mmt90) cc_final: 0.6585 (mtp180) REVERT: C 506 ARG cc_start: 0.6349 (ttm110) cc_final: 0.6029 (ttp-110) REVERT: C 519 SER cc_start: 0.7235 (m) cc_final: 0.6992 (m) outliers start: 21 outliers final: 16 residues processed: 94 average time/residue: 1.5152 time to fit residues: 148.7487 Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6234 Z= 0.276 Angle : 0.607 18.173 8445 Z= 0.306 Chirality : 0.043 0.202 928 Planarity : 0.011 0.339 1069 Dihedral : 7.239 130.799 834 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.72 % Allowed : 22.84 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % 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: 1.44 (0.32), residues: 739 helix: 1.99 (0.28), residues: 356 sheet: -0.15 (0.74), residues: 53 loop : 0.08 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.006 0.001 HIS C 430 PHE 0.013 0.001 PHE A 152 TYR 0.013 0.001 TYR B 411 ARG 0.018 0.001 ARG C 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 237 LYS cc_start: 0.7460 (mttt) cc_final: 0.6630 (mmtt) REVERT: A 261 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7900 (m) REVERT: B 194 LYS cc_start: 0.7665 (mttt) cc_final: 0.6719 (mptt) REVERT: B 272 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6431 (mm-30) REVERT: B 291 ARG cc_start: 0.7312 (tpt170) cc_final: 0.6607 (mtt90) REVERT: B 372 GLU cc_start: 0.7801 (tp30) cc_final: 0.7397 (tm-30) REVERT: C 406 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: C 485 SER cc_start: 0.8115 (t) cc_final: 0.7686 (p) REVERT: C 502 ARG cc_start: 0.7276 (mtt90) cc_final: 0.6571 (mtp180) REVERT: C 506 ARG cc_start: 0.6308 (ttm110) cc_final: 0.6038 (ttp-110) REVERT: C 519 SER cc_start: 0.7260 (m) cc_final: 0.7025 (m) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 1.4366 time to fit residues: 141.2150 Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 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 85 GLN B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127096 restraints weight = 6168.102| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.85 r_work: 0.3339 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6234 Z= 0.221 Angle : 0.610 20.491 8445 Z= 0.301 Chirality : 0.042 0.184 928 Planarity : 0.014 0.427 1069 Dihedral : 6.919 110.130 834 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.72 % Allowed : 23.00 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.55 (0.32), residues: 739 helix: 2.11 (0.29), residues: 356 sheet: -0.14 (0.75), residues: 53 loop : 0.09 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 PHE 0.012 0.001 PHE A 152 TYR 0.012 0.001 TYR C 389 ARG 0.013 0.001 ARG C 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2804.95 seconds wall clock time: 51 minutes 59.16 seconds (3119.16 seconds total)