Starting phenix.real_space_refine on Tue Jan 14 07:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8roz_19408/01_2025/8roz_19408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8roz_19408/01_2025/8roz_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_19408/01_2025/8roz_19408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8roz_19408/01_2025/8roz_19408.map" model { file = "/net/cci-nas-00/data/ceres_data/8roz_19408/01_2025/8roz_19408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8roz_19408/01_2025/8roz_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 4.17, per 1000 atoms: 0.69 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: 1.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.63 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: 1.59 Time building geometry restraints manager: 1.60 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: 2.060 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.100 ------------------------------------------------------------------------------- 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 : 0.686 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: 1.3778 time to fit residues: 169.6420 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 : 0.703 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.122672 restraints weight = 6131.257| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.94 r_work: 0.3263 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7359 (p) REVERT: A 200 ARG cc_start: 0.7682 (ptp90) cc_final: 0.7168 (ptt-90) REVERT: A 237 LYS cc_start: 0.7696 (mttt) cc_final: 0.6994 (mmtt) REVERT: A 261 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8001 (m) REVERT: B 194 LYS cc_start: 0.7821 (mttt) cc_final: 0.6958 (mptt) REVERT: B 291 ARG cc_start: 0.7864 (tpt170) cc_final: 0.7078 (mtt90) REVERT: B 346 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7719 (mp) REVERT: B 375 VAL cc_start: 0.8474 (p) cc_final: 0.8181 (t) REVERT: C 372 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7586 (mmtp) REVERT: C 406 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: C 472 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6643 (tt0) REVERT: C 475 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6807 (mpt) REVERT: C 485 SER cc_start: 0.8111 (t) cc_final: 0.7521 (p) REVERT: C 502 ARG cc_start: 0.7810 (mmt90) cc_final: 0.7251 (mtp180) REVERT: C 506 ARG cc_start: 0.7000 (ttm110) cc_final: 0.6608 (ttp-110) REVERT: C 519 SER cc_start: 0.7797 (m) cc_final: 0.7579 (m) outliers start: 32 outliers final: 12 residues processed: 117 average time/residue: 1.4175 time to fit residues: 173.5621 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 : 0.668 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125465 restraints weight = 6191.843| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.95 r_work: 0.3313 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1729 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= 0.158 Angle : 0.453 6.117 8445 Z= 0.235 Chirality : 0.040 0.122 928 Planarity : 0.006 0.130 1069 Dihedral : 6.097 86.722 835 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.57 % Allowed : 22.54 % Favored : 74.89 % 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: 1.63 (0.32), residues: 739 helix: 2.07 (0.29), residues: 357 sheet: -0.26 (0.76), residues: 48 loop : 0.30 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.002 0.001 HIS C 430 PHE 0.011 0.001 PHE A 152 TYR 0.009 0.001 TYR B 411 ARG 0.025 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 107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 233 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8354 (mtt) REVERT: A 237 LYS cc_start: 0.7680 (mttt) cc_final: 0.6968 (mmtt) REVERT: B 175 ASP cc_start: 0.8286 (m-30) cc_final: 0.8033 (m-30) REVERT: B 194 LYS cc_start: 0.7810 (mttt) cc_final: 0.6942 (mptt) REVERT: B 291 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7040 (mtt90) REVERT: B 303 ASP cc_start: 0.8450 (m-30) cc_final: 0.8095 (m-30) REVERT: C 372 LYS cc_start: 0.7974 (mmtp) cc_final: 0.7469 (mmtp) REVERT: C 406 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: C 472 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6570 (tt0) REVERT: C 502 ARG cc_start: 0.7743 (mmt90) cc_final: 0.7144 (mtp180) REVERT: C 506 ARG cc_start: 0.6962 (ttm110) cc_final: 0.6544 (ttp-110) REVERT: C 519 SER cc_start: 0.7655 (m) cc_final: 0.7424 (m) outliers start: 17 outliers final: 5 residues processed: 99 average time/residue: 1.3025 time to fit residues: 135.1475 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL 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 B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.164181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121952 restraints weight = 6339.730| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.99 r_work: 0.3252 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1929 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= 0.285 Angle : 0.536 8.408 8445 Z= 0.271 Chirality : 0.043 0.135 928 Planarity : 0.006 0.123 1069 Dihedral : 6.040 85.333 835 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.93 % Allowed : 21.63 % 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: 1.41 (0.32), residues: 739 helix: 1.89 (0.28), residues: 356 sheet: -0.30 (0.74), residues: 53 loop : 0.19 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 PHE 0.014 0.001 PHE A 152 TYR 0.014 0.001 TYR B 411 ARG 0.015 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 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7349 (p) REVERT: A 237 LYS cc_start: 0.7701 (mttt) cc_final: 0.7009 (mmtt) REVERT: A 261 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8085 (m) REVERT: B 175 ASP cc_start: 0.8282 (m-30) cc_final: 0.8078 (m-30) REVERT: B 194 LYS cc_start: 0.7837 (mttt) cc_final: 0.6978 (mptt) REVERT: B 291 ARG cc_start: 0.7936 (tpt170) cc_final: 0.7120 (mtt90) REVERT: B 303 ASP cc_start: 0.8497 (m-30) cc_final: 0.8211 (m-30) REVERT: B 346 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7794 (mp) REVERT: C 372 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7485 (mmtp) REVERT: C 383 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8576 (mt) REVERT: C 406 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: C 502 ARG cc_start: 0.7773 (mmt90) cc_final: 0.7126 (mtp180) REVERT: C 506 ARG cc_start: 0.7004 (ttm110) cc_final: 0.6567 (ttp-110) REVERT: C 519 SER cc_start: 0.7732 (m) cc_final: 0.7515 (m) outliers start: 26 outliers final: 11 residues processed: 99 average time/residue: 1.3171 time to fit residues: 136.6127 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 383 ILE 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 10 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.165761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124016 restraints weight = 6179.497| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.97 r_work: 0.3300 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2006 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= 0.195 Angle : 0.475 7.933 8445 Z= 0.246 Chirality : 0.041 0.125 928 Planarity : 0.006 0.101 1069 Dihedral : 5.791 85.078 835 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.48 % Allowed : 22.24 % 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: 1.57 (0.32), residues: 739 helix: 2.04 (0.28), residues: 357 sheet: -0.23 (0.75), residues: 53 loop : 0.22 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.018 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: 23 poor density : 80 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7347 (p) REVERT: A 233 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: A 237 LYS cc_start: 0.7683 (mttt) cc_final: 0.6969 (mmtt) REVERT: B 175 ASP cc_start: 0.8240 (m-30) cc_final: 0.7993 (m-30) REVERT: B 194 LYS cc_start: 0.7822 (mttt) cc_final: 0.6953 (mptt) REVERT: B 291 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7023 (mtt90) REVERT: B 303 ASP cc_start: 0.8484 (m-30) cc_final: 0.8139 (m-30) REVERT: C 372 LYS cc_start: 0.7863 (mmtp) cc_final: 0.7519 (mmtp) REVERT: C 383 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8547 (mt) REVERT: C 406 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: C 485 SER cc_start: 0.8101 (t) cc_final: 0.7683 (p) REVERT: C 502 ARG cc_start: 0.7737 (mmt90) cc_final: 0.7090 (mtp180) REVERT: C 506 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6470 (ttp-110) REVERT: C 519 SER cc_start: 0.7630 (m) cc_final: 0.7398 (m) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 1.3396 time to fit residues: 133.2538 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 268 HIS Chi-restraints excluded: chain A residue 289 VAL 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 383 ILE Chi-restraints excluded: chain C residue 397 LYS 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 34 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 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 B 376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122206 restraints weight = 6142.112| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.96 r_work: 0.3267 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6234 Z= 0.274 Angle : 0.521 8.154 8445 Z= 0.266 Chirality : 0.042 0.134 928 Planarity : 0.006 0.124 1069 Dihedral : 5.780 85.221 835 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.08 % Allowed : 22.24 % Favored : 73.68 % 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: 1.43 (0.32), residues: 739 helix: 1.92 (0.28), residues: 357 sheet: -0.18 (0.75), residues: 53 loop : 0.14 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 PHE 0.014 0.001 PHE A 152 TYR 0.013 0.001 TYR B 411 ARG 0.022 0.001 ARG C 437 *********************** 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 106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7327 (p) REVERT: A 237 LYS cc_start: 0.7741 (mttt) cc_final: 0.7043 (mmtt) REVERT: A 261 SER cc_start: 0.8464 (OUTLIER) cc_final: 0.8085 (m) REVERT: A 265 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8655 (mt0) REVERT: B 175 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: B 194 LYS cc_start: 0.7854 (mttt) cc_final: 0.6987 (mptt) REVERT: B 272 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6967 (mm-30) REVERT: B 291 ARG cc_start: 0.7931 (tpt170) cc_final: 0.7094 (mtt90) REVERT: B 303 ASP cc_start: 0.8517 (m-30) cc_final: 0.8198 (m-30) REVERT: C 372 LYS cc_start: 0.7921 (mmtp) cc_final: 0.7592 (mmtp) REVERT: C 383 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (mt) REVERT: C 406 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: C 502 ARG cc_start: 0.7798 (mmt90) cc_final: 0.7171 (mtp180) REVERT: C 506 ARG cc_start: 0.6999 (ttm110) cc_final: 0.6632 (ttp-110) REVERT: C 519 SER cc_start: 0.7709 (m) cc_final: 0.7492 (m) outliers start: 27 outliers final: 13 residues processed: 98 average time/residue: 1.3714 time to fit residues: 140.8962 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 383 ILE Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123899 restraints weight = 6162.427| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.97 r_work: 0.3293 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2132 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= 0.200 Angle : 0.491 11.000 8445 Z= 0.252 Chirality : 0.041 0.126 928 Planarity : 0.006 0.123 1069 Dihedral : 5.637 85.432 835 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.08 % Allowed : 21.94 % Favored : 73.98 % 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: 1.57 (0.32), residues: 739 helix: 2.11 (0.29), residues: 356 sheet: -0.11 (0.75), residues: 53 loop : 0.13 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.028 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 110 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7301 (p) REVERT: A 237 LYS cc_start: 0.7725 (mttt) cc_final: 0.7023 (mmtt) REVERT: A 261 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8137 (m) REVERT: B 175 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: B 194 LYS cc_start: 0.7835 (mttt) cc_final: 0.6979 (mptt) REVERT: B 272 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6874 (mm-30) REVERT: B 291 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7084 (mtt90) REVERT: B 303 ASP cc_start: 0.8507 (m-30) cc_final: 0.8197 (m-30) REVERT: C 372 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7632 (mmtp) REVERT: C 383 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8541 (mt) REVERT: C 406 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: C 485 SER cc_start: 0.8127 (t) cc_final: 0.7760 (p) REVERT: C 502 ARG cc_start: 0.7797 (mmt90) cc_final: 0.7150 (mtp180) REVERT: C 506 ARG cc_start: 0.7005 (ttm110) cc_final: 0.6633 (ttp-110) REVERT: C 519 SER cc_start: 0.7653 (m) cc_final: 0.7438 (m) REVERT: C 521 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6349 (mp) outliers start: 27 outliers final: 13 residues processed: 98 average time/residue: 1.3726 time to fit residues: 140.6617 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 383 ILE 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 Chi-restraints excluded: chain C residue 521 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 55 optimal weight: 0.0020 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 4 optimal weight: 0.0170 chunk 1 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 HIS B 376 GLN C 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126453 restraints weight = 6130.763| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.94 r_work: 0.3362 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6234 Z= 0.145 Angle : 0.505 15.542 8445 Z= 0.257 Chirality : 0.040 0.154 928 Planarity : 0.007 0.149 1069 Dihedral : 5.639 85.074 835 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.48 % Allowed : 22.84 % Favored : 73.68 % 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: 1.69 (0.32), residues: 739 helix: 2.25 (0.29), residues: 358 sheet: -0.06 (0.75), residues: 53 loop : 0.11 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.002 0.000 HIS C 430 PHE 0.009 0.001 PHE A 152 TYR 0.007 0.001 TYR C 389 ARG 0.030 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 109 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7252 (p) REVERT: A 233 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8371 (mtt) REVERT: A 237 LYS cc_start: 0.7708 (mttt) cc_final: 0.7001 (mmtt) REVERT: A 261 SER cc_start: 0.8403 (OUTLIER) cc_final: 0.8010 (m) REVERT: B 175 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 194 LYS cc_start: 0.7832 (mttt) cc_final: 0.6977 (mptt) REVERT: B 272 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6813 (mm-30) REVERT: B 291 ARG cc_start: 0.7845 (tpt170) cc_final: 0.7079 (mtt90) REVERT: B 303 ASP cc_start: 0.8473 (m-30) cc_final: 0.8147 (m-30) REVERT: C 383 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8515 (mt) REVERT: C 406 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: C 485 SER cc_start: 0.8116 (t) cc_final: 0.7755 (p) REVERT: C 502 ARG cc_start: 0.7682 (mmt90) cc_final: 0.7052 (mtp180) REVERT: C 506 ARG cc_start: 0.6808 (ttm110) cc_final: 0.6570 (ttp-110) REVERT: C 519 SER cc_start: 0.7574 (m) cc_final: 0.7353 (m) REVERT: C 521 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6345 (mp) REVERT: C 522 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6177 (tppt) outliers start: 23 outliers final: 11 residues processed: 98 average time/residue: 1.2544 time to fit residues: 128.8538 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 : 0.747 ------------------------------------------------------------------------------- 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 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 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 383 ILE 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 Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 522 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119259 restraints weight = 6189.673| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.98 r_work: 0.3198 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 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 : 0.004 0.035 6234 Z= 0.267 Angle : 0.613 19.622 8445 Z= 0.304 Chirality : 0.043 0.140 928 Planarity : 0.007 0.179 1069 Dihedral : 7.867 157.137 834 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.18 % Allowed : 23.30 % Favored : 73.52 % 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: 1.49 (0.32), residues: 739 helix: 2.06 (0.28), residues: 356 sheet: -0.13 (0.74), residues: 53 loop : 0.04 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 PHE 0.013 0.001 PHE A 152 TYR 0.014 0.001 TYR B 411 ARG 0.011 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 : 0.643 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7277 (p) REVERT: A 237 LYS cc_start: 0.7731 (mttt) cc_final: 0.7023 (mmtt) REVERT: A 261 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8067 (m) REVERT: B 175 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: B 194 LYS cc_start: 0.7817 (mttt) cc_final: 0.6945 (mptt) REVERT: B 272 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6910 (mm-30) REVERT: B 291 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7069 (mtt90) REVERT: B 303 ASP cc_start: 0.8512 (m-30) cc_final: 0.8188 (m-30) REVERT: C 383 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8506 (mt) REVERT: C 406 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: C 485 SER cc_start: 0.8154 (t) cc_final: 0.7765 (p) REVERT: C 502 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7088 (mtp180) REVERT: C 506 ARG cc_start: 0.6834 (ttm110) cc_final: 0.6570 (ttp-110) REVERT: C 519 SER cc_start: 0.7657 (m) cc_final: 0.7446 (m) REVERT: C 521 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6304 (mp) outliers start: 21 outliers final: 12 residues processed: 94 average time/residue: 1.3669 time to fit residues: 134.2281 Evaluate side-chains 99 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 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 383 ILE 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 Chi-restraints excluded: chain C residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.167179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125819 restraints weight = 6203.023| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6234 Z= 0.169 Angle : 0.589 19.525 8445 Z= 0.290 Chirality : 0.041 0.185 928 Planarity : 0.014 0.427 1069 Dihedral : 6.771 110.673 834 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.03 % Allowed : 23.75 % Favored : 73.22 % 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: 1.62 (0.32), residues: 739 helix: 2.23 (0.29), residues: 358 sheet: -0.11 (0.74), residues: 53 loop : 0.04 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.003 0.001 HIS C 490 PHE 0.010 0.001 PHE A 152 TYR 0.013 0.001 TYR C 389 ARG 0.014 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 102 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7278 (p) REVERT: A 233 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8392 (mtt) REVERT: A 237 LYS cc_start: 0.7756 (mttt) cc_final: 0.7065 (mmtt) REVERT: A 261 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8064 (m) REVERT: B 175 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: B 194 LYS cc_start: 0.7822 (mttt) cc_final: 0.6965 (mptt) REVERT: B 272 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 291 ARG cc_start: 0.7831 (tpt170) cc_final: 0.7056 (mtt90) REVERT: B 303 ASP cc_start: 0.8491 (m-30) cc_final: 0.8157 (m-30) REVERT: C 383 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8530 (mt) REVERT: C 406 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: C 485 SER cc_start: 0.8127 (t) cc_final: 0.7760 (p) REVERT: C 502 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7017 (mtp180) REVERT: C 506 ARG cc_start: 0.6886 (ttm110) cc_final: 0.6634 (ttp-110) REVERT: C 519 SER cc_start: 0.7572 (m) cc_final: 0.7347 (m) REVERT: C 521 LEU cc_start: 0.6693 (OUTLIER) cc_final: 0.6263 (mp) outliers start: 20 outliers final: 13 residues processed: 93 average time/residue: 1.3363 time to fit residues: 130.0005 Evaluate side-chains 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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 A residue 289 VAL 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 383 ILE 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 Chi-restraints excluded: chain C residue 521 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 1.1300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126245 restraints weight = 6354.194| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.90 r_work: 0.3329 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6234 Z= 0.263 Angle : 0.599 22.461 8445 Z= 0.292 Chirality : 0.043 0.149 928 Planarity : 0.005 0.064 1069 Dihedral : 8.219 171.794 834 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.03 % Allowed : 23.75 % Favored : 73.22 % 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: 1.49 (0.32), residues: 739 helix: 2.08 (0.28), residues: 356 sheet: -0.16 (0.75), residues: 53 loop : 0.03 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.009 0.001 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4998.37 seconds wall clock time: 90 minutes 8.74 seconds (5408.74 seconds total)