Starting phenix.real_space_refine on Fri Aug 2 23:21:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/08_2024/8roz_19408.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/08_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/08_2024/8roz_19408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/08_2024/8roz_19408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/08_2024/8roz_19408.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/08_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 Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "C TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 482": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.25, per 1000 atoms: 1.03 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 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: 0.61 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: 1.57 Time building geometry restraints manager: 2.82 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: 99.76 - 106.62: 212 106.62 - 113.48: 3383 113.48 - 120.35: 2320 120.35 - 127.21: 2451 127.21 - 134.07: 79 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: 1.66 - 2.31: 4 2.31 - 2.95: 2631 2.95 - 3.60: 8798 3.60 - 4.25: 14688 4.25 - 4.90: 24966 Nonbonded interactions: 51087 Sorted by model distance: nonbonded pdb=" NH1 ARG C 437 " pdb=" CE MET C 489 " model vdw 1.656 3.540 nonbonded pdb=" CZ ARG C 437 " pdb=" CE MET C 489 " model vdw 2.052 3.690 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 ... (remaining 51082 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: 4.420 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.350 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:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- 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 : 1.656 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 fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 0.711 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: 1.2908 time to fit residues: 159.1033 Evaluate side-chains 95 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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: 0.8239 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6234 Z= 0.331 Angle : 0.551 7.654 8445 Z= 0.283 Chirality : 0.044 0.144 928 Planarity : 0.005 0.047 1069 Dihedral : 6.361 88.752 838 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.84 % Allowed : 18.76 % 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: 1.25 (0.32), residues: 739 helix: 1.72 (0.29), residues: 357 sheet: -0.24 (0.70), residues: 58 loop : 0.13 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 370 HIS 0.006 0.001 HIS C 430 PHE 0.018 0.002 PHE A 152 TYR 0.017 0.002 TYR B 411 ARG 0.008 0.001 ARG A 199 *********************** 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 126 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7163 (p) REVERT: A 200 ARG cc_start: 0.7316 (ptp90) cc_final: 0.6792 (ptt-90) REVERT: A 237 LYS cc_start: 0.7382 (mttt) cc_final: 0.6613 (mmtt) REVERT: A 261 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7817 (m) REVERT: B 194 LYS cc_start: 0.7628 (mttt) cc_final: 0.6680 (mptt) REVERT: B 291 ARG cc_start: 0.7270 (tpt170) cc_final: 0.6637 (mtt90) REVERT: B 372 GLU cc_start: 0.7763 (tp30) cc_final: 0.7557 (tm-30) REVERT: B 375 VAL cc_start: 0.8352 (p) cc_final: 0.8121 (t) REVERT: C 372 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7471 (mmtp) REVERT: C 406 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: C 472 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6228 (tt0) REVERT: C 475 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6405 (mpt) REVERT: C 502 ARG cc_start: 0.7282 (mmt90) cc_final: 0.6701 (mtp180) REVERT: C 506 ARG cc_start: 0.6516 (ttm110) cc_final: 0.6102 (ttp-110) REVERT: C 519 SER cc_start: 0.7399 (m) cc_final: 0.7171 (m) outliers start: 32 outliers final: 11 residues processed: 116 average time/residue: 1.2163 time to fit residues: 147.9087 Evaluate side-chains 100 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 384 THR 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: 1.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 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 268 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1854 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= 0.281 Angle : 0.507 6.167 8445 Z= 0.262 Chirality : 0.043 0.136 928 Planarity : 0.005 0.048 1069 Dihedral : 5.984 86.542 835 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.93 % Allowed : 20.88 % Favored : 75.19 % 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: 1.27 (0.32), residues: 739 helix: 1.76 (0.29), residues: 356 sheet: -0.38 (0.74), residues: 53 loop : 0.13 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 PHE 0.014 0.001 PHE B 276 TYR 0.013 0.001 TYR B 411 ARG 0.008 0.001 ARG A 199 *********************** 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 112 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7246 (p) REVERT: A 200 ARG cc_start: 0.7348 (ptp90) cc_final: 0.6760 (ptt-90) REVERT: A 233 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8329 (mtt) REVERT: A 237 LYS cc_start: 0.7380 (mttt) cc_final: 0.6627 (mmtt) REVERT: B 194 LYS cc_start: 0.7634 (mttt) cc_final: 0.6709 (mptt) REVERT: B 291 ARG cc_start: 0.7306 (tpt170) cc_final: 0.6640 (mtt90) REVERT: B 303 ASP cc_start: 0.8287 (m-30) cc_final: 0.7869 (m-30) REVERT: B 346 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7667 (mp) REVERT: B 372 GLU cc_start: 0.7773 (tp30) cc_final: 0.7422 (tm-30) REVERT: C 406 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6478 (mp0) REVERT: C 502 ARG cc_start: 0.7253 (mmt90) cc_final: 0.6607 (mtp180) REVERT: C 506 ARG cc_start: 0.6465 (ttm110) cc_final: 0.6009 (ttp-110) REVERT: C 519 SER cc_start: 0.7331 (m) cc_final: 0.7087 (m) outliers start: 26 outliers final: 10 residues processed: 104 average time/residue: 1.3166 time to fit residues: 143.2469 Evaluate side-chains 94 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 184 VAL 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 346 LEU Chi-restraints excluded: chain B residue 382 LEU 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 66 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 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: 0.8213 moved from start: 0.1976 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= 0.183 Angle : 0.457 6.090 8445 Z= 0.238 Chirality : 0.040 0.125 928 Planarity : 0.005 0.046 1069 Dihedral : 5.796 85.799 835 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 1.51 (0.32), residues: 739 helix: 1.99 (0.29), residues: 357 sheet: -0.28 (0.75), residues: 53 loop : 0.21 (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 0.007 0.000 ARG A 199 *********************** 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 106 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7149 (p) REVERT: A 233 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8284 (mtt) REVERT: A 237 LYS cc_start: 0.7390 (mttt) cc_final: 0.6635 (mmtt) REVERT: A 261 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7889 (m) REVERT: B 194 LYS cc_start: 0.7640 (mttt) cc_final: 0.6711 (mptt) REVERT: B 272 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6432 (mm-30) REVERT: B 291 ARG cc_start: 0.7286 (tpt170) cc_final: 0.6612 (mtt90) REVERT: B 303 ASP cc_start: 0.8258 (m-30) cc_final: 0.7843 (m-30) REVERT: B 346 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 372 GLU cc_start: 0.7742 (tp30) cc_final: 0.7429 (tm-30) REVERT: C 372 LYS cc_start: 0.7748 (mmtp) cc_final: 0.7429 (mmtp) REVERT: C 406 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: C 485 SER cc_start: 0.8066 (t) cc_final: 0.7670 (p) REVERT: C 502 ARG cc_start: 0.7232 (mmt90) cc_final: 0.6571 (mtp180) REVERT: C 506 ARG cc_start: 0.6415 (ttm110) cc_final: 0.6044 (ttp-110) REVERT: C 519 SER cc_start: 0.7244 (m) cc_final: 0.7003 (m) outliers start: 24 outliers final: 13 residues processed: 100 average time/residue: 1.2819 time to fit residues: 134.3445 Evaluate side-chains 98 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 223 ASP 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 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 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 462 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.2016 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= 0.227 Angle : 0.474 6.108 8445 Z= 0.245 Chirality : 0.041 0.128 928 Planarity : 0.005 0.048 1069 Dihedral : 5.732 85.529 835 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.78 % Allowed : 21.94 % 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: 1.48 (0.32), residues: 739 helix: 1.97 (0.28), residues: 357 sheet: -0.20 (0.75), residues: 53 loop : 0.17 (0.35), residues: 329 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 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR B 411 ARG 0.008 0.000 ARG A 199 *********************** 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 108 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7076 (p) REVERT: A 237 LYS cc_start: 0.7395 (mttt) cc_final: 0.6635 (mmtt) REVERT: A 261 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7916 (m) REVERT: A 265 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: B 194 LYS cc_start: 0.7666 (mttt) cc_final: 0.6726 (mptt) REVERT: B 272 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6470 (mm-30) REVERT: B 291 ARG cc_start: 0.7295 (tpt170) cc_final: 0.6619 (mtt90) REVERT: B 303 ASP cc_start: 0.8263 (m-30) cc_final: 0.7845 (m-30) REVERT: B 346 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7632 (mp) REVERT: B 372 GLU cc_start: 0.7791 (tp30) cc_final: 0.7474 (tm-30) REVERT: C 372 LYS cc_start: 0.7768 (mmtp) cc_final: 0.7469 (mmtp) REVERT: C 406 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: C 485 SER cc_start: 0.8056 (t) cc_final: 0.7652 (p) REVERT: C 502 ARG cc_start: 0.7240 (mmt90) cc_final: 0.6591 (mtp180) REVERT: C 506 ARG cc_start: 0.6422 (ttm110) cc_final: 0.6066 (ttp-110) REVERT: C 519 SER cc_start: 0.7243 (m) cc_final: 0.7004 (m) outliers start: 25 outliers final: 15 residues processed: 99 average time/residue: 1.2947 time to fit residues: 134.2853 Evaluate side-chains 99 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 B residue 346 LEU Chi-restraints excluded: chain B residue 382 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.2099 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= 0.191 Angle : 0.458 6.117 8445 Z= 0.237 Chirality : 0.041 0.126 928 Planarity : 0.005 0.047 1069 Dihedral : 5.605 85.181 835 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.78 % Allowed : 22.09 % 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: 1.56 (0.32), residues: 739 helix: 2.04 (0.29), residues: 357 sheet: -0.13 (0.75), residues: 53 loop : 0.19 (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 0.010 0.000 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 108 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7137 (p) REVERT: A 233 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: A 237 LYS cc_start: 0.7394 (mttt) cc_final: 0.6633 (mmtt) REVERT: A 261 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7892 (m) REVERT: B 194 LYS cc_start: 0.7669 (mttt) cc_final: 0.6705 (mptt) REVERT: B 272 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6394 (mm-30) REVERT: B 291 ARG cc_start: 0.7299 (tpt170) cc_final: 0.6618 (mtt90) REVERT: B 303 ASP cc_start: 0.8262 (m-30) cc_final: 0.7850 (m-30) REVERT: B 372 GLU cc_start: 0.7776 (tp30) cc_final: 0.7419 (tm-30) REVERT: C 372 LYS cc_start: 0.7766 (mmtp) cc_final: 0.7487 (mmtp) REVERT: C 406 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: C 485 SER cc_start: 0.8047 (t) cc_final: 0.7641 (p) REVERT: C 502 ARG cc_start: 0.7230 (mmt90) cc_final: 0.6573 (mtp180) REVERT: C 506 ARG cc_start: 0.6402 (ttm110) cc_final: 0.6029 (ttp-110) REVERT: C 519 SER cc_start: 0.7144 (m) cc_final: 0.6895 (m) outliers start: 25 outliers final: 16 residues processed: 99 average time/residue: 1.2975 time to fit residues: 134.3411 Evaluate side-chains 97 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 382 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 28 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2133 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= 0.201 Angle : 0.464 6.102 8445 Z= 0.240 Chirality : 0.041 0.127 928 Planarity : 0.005 0.048 1069 Dihedral : 5.545 85.062 835 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.78 % Allowed : 22.24 % 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: 1.56 (0.32), residues: 739 helix: 2.09 (0.29), residues: 356 sheet: -0.08 (0.75), residues: 53 loop : 0.12 (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 0.011 0.001 TYR B 411 ARG 0.009 0.000 ARG A 199 *********************** 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 107 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7061 (p) REVERT: A 237 LYS cc_start: 0.7402 (mttt) cc_final: 0.6640 (mmtt) REVERT: A 261 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7914 (m) REVERT: B 194 LYS cc_start: 0.7659 (mttt) cc_final: 0.6703 (mptt) REVERT: B 272 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6411 (mm-30) REVERT: B 291 ARG cc_start: 0.7297 (tpt170) cc_final: 0.6616 (mtt90) REVERT: B 303 ASP cc_start: 0.8276 (m-30) cc_final: 0.7887 (m-30) REVERT: B 372 GLU cc_start: 0.7774 (tp30) cc_final: 0.7408 (tm-30) REVERT: C 406 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: C 415 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.6775 (tmtm) REVERT: C 485 SER cc_start: 0.8049 (t) cc_final: 0.7649 (p) REVERT: C 502 ARG cc_start: 0.7248 (mmt90) cc_final: 0.6570 (mtp180) REVERT: C 506 ARG cc_start: 0.6410 (ttm110) cc_final: 0.6075 (ttp-110) REVERT: C 519 SER cc_start: 0.7127 (m) cc_final: 0.6884 (m) outliers start: 25 outliers final: 18 residues processed: 98 average time/residue: 1.3166 time to fit residues: 135.1231 Evaluate side-chains 99 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 A residue 289 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 382 LEU 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 415 LYS 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: 0.6980 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.2197 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= 0.242 Angle : 0.490 6.095 8445 Z= 0.252 Chirality : 0.042 0.137 928 Planarity : 0.005 0.048 1069 Dihedral : 5.570 85.040 834 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.33 % Allowed : 22.54 % 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: 1.47 (0.32), residues: 739 helix: 2.02 (0.29), residues: 355 sheet: -0.09 (0.74), residues: 53 loop : 0.07 (0.35), residues: 331 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 0.000 ARG A 199 *********************** 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 101 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7066 (p) REVERT: A 237 LYS cc_start: 0.7409 (mttt) cc_final: 0.6648 (mmtt) REVERT: A 261 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7896 (m) REVERT: B 194 LYS cc_start: 0.7663 (mttt) cc_final: 0.6700 (mptt) REVERT: B 272 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6412 (mm-30) REVERT: B 291 ARG cc_start: 0.7319 (tpt170) cc_final: 0.6609 (mtt90) REVERT: B 303 ASP cc_start: 0.8296 (m-30) cc_final: 0.7886 (m-30) REVERT: B 372 GLU cc_start: 0.7810 (tp30) cc_final: 0.7392 (tm-30) REVERT: C 406 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: C 485 SER cc_start: 0.8036 (t) cc_final: 0.7624 (p) REVERT: C 502 ARG cc_start: 0.7270 (mtt90) cc_final: 0.6576 (mtp180) REVERT: C 506 ARG cc_start: 0.6368 (ttm110) cc_final: 0.6096 (ttp-110) REVERT: C 519 SER cc_start: 0.7253 (m) cc_final: 0.7017 (m) outliers start: 22 outliers final: 16 residues processed: 93 average time/residue: 1.3952 time to fit residues: 136.0160 Evaluate side-chains 96 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 B residue 382 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 42 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 C 354 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2217 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= 0.151 Angle : 0.440 6.095 8445 Z= 0.229 Chirality : 0.040 0.130 928 Planarity : 0.005 0.047 1069 Dihedral : 5.474 84.959 834 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.18 % Allowed : 22.69 % 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: 1.68 (0.32), residues: 739 helix: 2.23 (0.29), residues: 356 sheet: -0.00 (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 0.010 0.001 PHE A 152 TYR 0.008 0.001 TYR A 180 ARG 0.009 0.000 ARG A 199 *********************** 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 107 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.741 Fit side-chains REVERT: A 177 CYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7082 (p) REVERT: A 233 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8253 (mtt) REVERT: A 237 LYS cc_start: 0.7399 (mttt) cc_final: 0.6624 (mmtt) REVERT: A 261 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7838 (m) REVERT: B 194 LYS cc_start: 0.7642 (mttt) cc_final: 0.6684 (mptt) REVERT: B 272 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6385 (mm-30) REVERT: B 291 ARG cc_start: 0.7289 (tpt170) cc_final: 0.6615 (mtt90) REVERT: B 303 ASP cc_start: 0.8277 (m-30) cc_final: 0.7863 (m-30) REVERT: B 372 GLU cc_start: 0.7757 (tp30) cc_final: 0.7395 (tm-30) REVERT: C 372 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7459 (mmtp) REVERT: C 406 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: C 485 SER cc_start: 0.8025 (t) cc_final: 0.7644 (p) REVERT: C 502 ARG cc_start: 0.7245 (mtt90) cc_final: 0.6542 (mtp180) REVERT: C 506 ARG cc_start: 0.6372 (ttm110) cc_final: 0.6089 (ttp-110) REVERT: C 519 SER cc_start: 0.7142 (m) cc_final: 0.6894 (m) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 1.2158 time to fit residues: 125.0043 Evaluate side-chains 99 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 67 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8231 moved from start: 0.2230 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= 0.246 Angle : 0.496 6.129 8445 Z= 0.254 Chirality : 0.042 0.141 928 Planarity : 0.005 0.048 1069 Dihedral : 5.534 84.603 834 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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 : 0.00 % 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: 1.50 (0.32), residues: 739 helix: 2.07 (0.29), residues: 355 sheet: -0.06 (0.74), residues: 53 loop : 0.06 (0.35), residues: 331 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 0.013 0.001 TYR B 411 ARG 0.009 0.000 ARG A 199 ********************** 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 99 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7070 (p) REVERT: A 237 LYS cc_start: 0.7449 (mttt) cc_final: 0.6692 (mmtt) REVERT: A 261 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7899 (m) REVERT: B 194 LYS cc_start: 0.7674 (mttt) cc_final: 0.6715 (mptt) REVERT: B 272 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6438 (mm-30) REVERT: B 291 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6609 (mtt90) REVERT: B 303 ASP cc_start: 0.8294 (m-30) cc_final: 0.7883 (m-30) REVERT: B 372 GLU cc_start: 0.7748 (tp30) cc_final: 0.7358 (tm-30) REVERT: C 372 LYS cc_start: 0.7767 (mmtp) cc_final: 0.7532 (mmtp) REVERT: C 406 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6517 (mp0) REVERT: C 485 SER cc_start: 0.8035 (t) cc_final: 0.7631 (p) REVERT: C 502 ARG cc_start: 0.7263 (mtt90) cc_final: 0.6551 (mtp180) REVERT: C 506 ARG cc_start: 0.6348 (ttm110) cc_final: 0.6069 (ttp-110) REVERT: C 519 SER cc_start: 0.7221 (m) cc_final: 0.6981 (m) outliers start: 18 outliers final: 16 residues processed: 92 average time/residue: 1.3666 time to fit residues: 131.4837 Evaluate side-chains 98 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.167478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127720 restraints weight = 6162.595| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.83 r_work: 0.3354 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2228 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= 0.180 Angle : 0.457 6.106 8445 Z= 0.237 Chirality : 0.041 0.133 928 Planarity : 0.005 0.047 1069 Dihedral : 5.478 84.714 834 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.18 % Allowed : 22.39 % 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: 1.62 (0.32), residues: 739 helix: 2.17 (0.29), residues: 356 sheet: 0.02 (0.74), residues: 53 loop : 0.10 (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 0.009 0.001 TYR B 411 ARG 0.009 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2822.80 seconds wall clock time: 58 minutes 28.11 seconds (3508.11 seconds total)