Starting phenix.real_space_refine on Tue Jun 25 00:20:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/06_2024/8roz_19408_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/06_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_19408/06_2024/8roz_19408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/06_2024/8roz_19408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/06_2024/8roz_19408_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8roz_19408/06_2024/8roz_19408_updated.pdb" } 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-5370/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: 4.30, per 1000 atoms: 0.71 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: 2.62 Conformation dependent library (CDL) restraints added in 1.3 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 3 sheets defined 46.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 87 through 93 Processing helix chain 'A' and resid 101 through 121 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.674A pdb=" N ILE A 186 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 190 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 206 through 222 Processing helix chain 'B' and resid 227 through 243 removed outlier: 3.601A pdb=" N SER B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 266 removed outlier: 4.429A pdb=" N GLN B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 286 through 300 Processing helix chain 'B' and resid 309 through 319 removed outlier: 3.652A pdb=" N GLN B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N HIS B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 340 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) Processing helix chain 'B' and resid 342 through 345 No H-bonds generated for 'chain 'B' and resid 342 through 345' Processing helix chain 'B' and resid 350 through 365 Processing helix chain 'B' and resid 372 through 378 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 386 through 397 removed outlier: 3.717A pdb=" N ASP B 391 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 388 through 393 removed outlier: 3.669A pdb=" N GLY C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 Processing helix chain 'C' and resid 437 through 451 Processing helix chain 'C' and resid 469 through 476 removed outlier: 3.605A pdb=" N PHE C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 495 through 523 removed outlier: 3.760A pdb=" N LYS C 523 " --> pdb=" O SER C 519 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 66 through 71 removed outlier: 6.915A pdb=" N VAL A 79 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 69 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 77 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N HIS A 71 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS A 75 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG A 22 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS A 6 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 133 through 135 Processing sheet with id= C, first strand: chain 'C' and resid 462 through 465 removed outlier: 4.275A pdb=" N GLU C 462 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE C 426 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE C 380 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 428 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE C 382 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N HIS C 430 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP C 384 " --> pdb=" O HIS C 430 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 615 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: 1.54 Time building geometry restraints manager: 2.89 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: 2657 2.95 - 3.60: 8848 3.60 - 4.25: 14828 4.25 - 4.90: 24998 Nonbonded interactions: 51335 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 2.440 nonbonded pdb=" OD1 ASP C 340 " pdb=" OG SER C 342 " model vdw 2.269 2.440 nonbonded pdb=" OD1 ASP A 210 " pdb=" OH TYR C 455 " model vdw 2.312 2.440 ... (remaining 51330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.070 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: 5.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.410 Find NCS groups from input model: 0.180 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:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- 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= 0.276 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 : 0.701 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: 1.2944 time to fit residues: 159.5731 Evaluate side-chains 95 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.0170 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- 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 B 429 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1273 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= 0.265 Angle : 0.490 6.348 8445 Z= 0.248 Chirality : 0.042 0.147 928 Planarity : 0.005 0.047 1069 Dihedral : 6.216 89.609 838 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.99 % Allowed : 19.82 % 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: 1.22 (0.32), residues: 739 helix: 1.62 (0.29), residues: 354 sheet: -0.01 (0.68), residues: 58 loop : 0.18 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 PHE 0.012 0.001 PHE A 152 TYR 0.014 0.001 TYR B 411 ARG 0.008 0.000 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 131 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7865 (OUTLIER) cc_final: 0.6992 (p) REVERT: A 200 ARG cc_start: 0.7342 (ptp90) cc_final: 0.6775 (ptt-90) REVERT: A 237 LYS cc_start: 0.7365 (mttt) cc_final: 0.6578 (mmtt) REVERT: A 261 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.7761 (m) REVERT: B 172 GLU cc_start: 0.5550 (pt0) cc_final: 0.5293 (mp0) REVERT: B 194 LYS cc_start: 0.7618 (mttt) cc_final: 0.6699 (mptt) REVERT: B 272 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6921 (mm-30) REVERT: B 291 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6627 (mtt90) REVERT: B 346 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7602 (mp) REVERT: B 372 GLU cc_start: 0.7826 (tp30) cc_final: 0.7446 (tm-30) REVERT: C 372 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7215 (mmtp) REVERT: C 406 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: C 485 SER cc_start: 0.7970 (t) cc_final: 0.7295 (p) REVERT: C 502 ARG cc_start: 0.7221 (mmt90) cc_final: 0.6663 (mtp180) REVERT: C 506 ARG cc_start: 0.6492 (ttm110) cc_final: 0.6092 (ttp-110) REVERT: C 519 SER cc_start: 0.7330 (m) cc_final: 0.7086 (m) outliers start: 33 outliers final: 14 residues processed: 120 average time/residue: 1.1303 time to fit residues: 142.5768 Evaluate side-chains 106 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.0070 chunk 66 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS B 177 HIS B 429 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6234 Z= 0.136 Angle : 0.415 6.074 8445 Z= 0.213 Chirality : 0.039 0.122 928 Planarity : 0.005 0.045 1069 Dihedral : 5.774 87.835 836 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.18 % Allowed : 21.79 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.32), residues: 739 helix: 1.87 (0.29), residues: 351 sheet: 0.35 (0.75), residues: 48 loop : 0.21 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.002 0.000 HIS B 359 PHE 0.008 0.001 PHE A 152 TYR 0.009 0.001 TYR C 389 ARG 0.008 0.000 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 111 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.739 Fit side-chains REVERT: A 177 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6801 (p) REVERT: A 200 ARG cc_start: 0.7335 (ptp90) cc_final: 0.6782 (ptt-90) REVERT: A 237 LYS cc_start: 0.7367 (mttt) cc_final: 0.6606 (mmtt) REVERT: A 261 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.7773 (m) REVERT: B 194 LYS cc_start: 0.7626 (mttt) cc_final: 0.6698 (mptt) REVERT: B 272 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6790 (mm-30) REVERT: B 291 ARG cc_start: 0.7221 (tpt170) cc_final: 0.6591 (mtt90) REVERT: B 303 ASP cc_start: 0.8256 (m-30) cc_final: 0.7854 (m-30) REVERT: B 372 GLU cc_start: 0.7829 (tp30) cc_final: 0.7458 (tm-30) REVERT: C 372 LYS cc_start: 0.7722 (mmtp) cc_final: 0.7365 (mmtp) REVERT: C 406 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: C 485 SER cc_start: 0.7969 (t) cc_final: 0.7294 (p) REVERT: C 502 ARG cc_start: 0.7213 (mmt90) cc_final: 0.6588 (mtp180) REVERT: C 506 ARG cc_start: 0.6537 (ttm110) cc_final: 0.6057 (ttp-110) REVERT: C 519 SER cc_start: 0.7118 (m) cc_final: 0.6860 (m) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 1.2298 time to fit residues: 132.9270 Evaluate side-chains 99 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 207 SER Chi-restraints excluded: chain A residue 223 ASP 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 C residue 367 SER 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: 2.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.1598 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= 0.206 Angle : 0.451 6.083 8445 Z= 0.229 Chirality : 0.041 0.126 928 Planarity : 0.005 0.047 1069 Dihedral : 5.579 86.450 835 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.39 % Allowed : 21.33 % 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: 1.32 (0.32), residues: 739 helix: 1.60 (0.29), residues: 361 sheet: 0.19 (0.69), residues: 58 loop : 0.30 (0.36), residues: 320 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 0.011 0.001 PHE A 152 TYR 0.011 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 115 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 86 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6924 (p) REVERT: A 200 ARG cc_start: 0.7361 (ptp90) cc_final: 0.6757 (ptt-90) REVERT: A 237 LYS cc_start: 0.7404 (mttt) cc_final: 0.6637 (mmtt) REVERT: A 261 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.7823 (m) REVERT: B 172 GLU cc_start: 0.5568 (pt0) cc_final: 0.5288 (mp0) REVERT: B 194 LYS cc_start: 0.7672 (mttt) cc_final: 0.6751 (mptt) REVERT: B 272 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6890 (mm-30) REVERT: B 291 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6581 (mtt90) REVERT: B 303 ASP cc_start: 0.8306 (m-30) cc_final: 0.7919 (m-30) REVERT: B 346 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7592 (mp) REVERT: B 372 GLU cc_start: 0.7836 (tp30) cc_final: 0.7436 (tm-30) REVERT: C 372 LYS cc_start: 0.7707 (mmtp) cc_final: 0.7423 (mmtp) REVERT: C 406 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: C 485 SER cc_start: 0.8059 (t) cc_final: 0.7424 (p) REVERT: C 502 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6608 (mtp180) REVERT: C 506 ARG cc_start: 0.6507 (ttm110) cc_final: 0.6073 (ttp-110) REVERT: C 519 SER cc_start: 0.7221 (m) cc_final: 0.6968 (m) outliers start: 29 outliers final: 13 residues processed: 106 average time/residue: 1.2589 time to fit residues: 139.8291 Evaluate side-chains 103 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 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 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 346 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 0.0060 chunk 61 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.3212 ------------------------------------------------------------------------------- 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: 0.8183 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6234 Z= 0.118 Angle : 0.397 6.124 8445 Z= 0.203 Chirality : 0.039 0.119 928 Planarity : 0.005 0.045 1069 Dihedral : 5.314 85.747 835 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.18 % Allowed : 22.24 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.32), residues: 739 helix: 1.86 (0.29), residues: 360 sheet: 0.31 (0.69), residues: 58 loop : 0.39 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 370 HIS 0.001 0.000 HIS B 359 PHE 0.006 0.001 PHE A 152 TYR 0.009 0.001 TYR C 486 ARG 0.007 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 113 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.747 Fit side-chains REVERT: A 177 CYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6911 (p) REVERT: A 200 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6729 (ptt-90) REVERT: A 233 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8221 (mtt) REVERT: A 237 LYS cc_start: 0.7384 (mttt) cc_final: 0.6622 (mmtt) REVERT: B 194 LYS cc_start: 0.7665 (mttt) cc_final: 0.6724 (mptt) REVERT: B 272 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6743 (mm-30) REVERT: B 291 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6562 (mtt90) REVERT: B 303 ASP cc_start: 0.8264 (m-30) cc_final: 0.7906 (m-30) REVERT: B 372 GLU cc_start: 0.7858 (tp30) cc_final: 0.7475 (tm-30) REVERT: C 406 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: C 485 SER cc_start: 0.8156 (t) cc_final: 0.7541 (p) REVERT: C 502 ARG cc_start: 0.7172 (mmt90) cc_final: 0.6538 (mtp180) REVERT: C 506 ARG cc_start: 0.6490 (ttm110) cc_final: 0.6057 (ttp-110) outliers start: 21 outliers final: 11 residues processed: 104 average time/residue: 1.2020 time to fit residues: 131.2499 Evaluate side-chains 103 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 268 HIS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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: 0.8235 moved from start: 0.1829 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= 0.247 Angle : 0.473 6.097 8445 Z= 0.238 Chirality : 0.041 0.130 928 Planarity : 0.005 0.048 1069 Dihedral : 5.443 85.039 834 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.93 % Allowed : 21.03 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.32), residues: 739 helix: 1.73 (0.29), residues: 355 sheet: 0.24 (0.70), residues: 58 loop : 0.22 (0.36), residues: 326 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 0.012 0.001 PHE A 152 TYR 0.013 0.001 TYR B 411 ARG 0.008 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 110 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.715 Fit side-chains REVERT: A 148 LEU cc_start: 0.8465 (tp) cc_final: 0.8206 (tp) REVERT: A 177 CYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7067 (p) REVERT: A 200 ARG cc_start: 0.7368 (ptp90) cc_final: 0.6695 (ptt-90) REVERT: A 237 LYS cc_start: 0.7390 (mttt) cc_final: 0.6618 (mmtt) REVERT: A 261 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7839 (m) REVERT: B 172 GLU cc_start: 0.5589 (pt0) cc_final: 0.5313 (mp0) REVERT: B 194 LYS cc_start: 0.7678 (mttt) cc_final: 0.6742 (mptt) REVERT: B 272 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6847 (mm-30) REVERT: B 291 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6618 (mtt90) REVERT: B 303 ASP cc_start: 0.8315 (m-30) cc_final: 0.7973 (m-30) REVERT: B 372 GLU cc_start: 0.7862 (tp30) cc_final: 0.7441 (tm-30) REVERT: C 406 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6457 (mp0) REVERT: C 436 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: C 502 ARG cc_start: 0.7266 (mmt90) cc_final: 0.6576 (mtp180) REVERT: C 506 ARG cc_start: 0.6452 (ttm110) cc_final: 0.6013 (ttp-110) outliers start: 26 outliers final: 16 residues processed: 101 average time/residue: 1.2145 time to fit residues: 128.6346 Evaluate side-chains 103 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 184 VAL 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 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 436 GLU Chi-restraints excluded: chain C residue 451 LEU 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: 8.9990 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8232 moved from start: 0.1895 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= 0.221 Angle : 0.457 6.085 8445 Z= 0.232 Chirality : 0.041 0.127 928 Planarity : 0.005 0.048 1069 Dihedral : 5.436 85.013 834 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.78 % Allowed : 21.33 % 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: 1.30 (0.32), residues: 739 helix: 1.71 (0.29), residues: 352 sheet: 0.21 (0.70), residues: 58 loop : 0.15 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 PHE 0.011 0.001 PHE A 152 TYR 0.010 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 108 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7046 (p) REVERT: A 200 ARG cc_start: 0.7396 (ptp90) cc_final: 0.6722 (ptt-90) REVERT: A 237 LYS cc_start: 0.7400 (mttt) cc_final: 0.6639 (mmtt) REVERT: A 261 SER cc_start: 0.8319 (OUTLIER) cc_final: 0.7858 (m) REVERT: B 172 GLU cc_start: 0.5624 (pt0) cc_final: 0.5340 (mp0) REVERT: B 194 LYS cc_start: 0.7686 (mttt) cc_final: 0.6744 (mptt) REVERT: B 272 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6853 (mm-30) REVERT: B 291 ARG cc_start: 0.7275 (tpt170) cc_final: 0.6607 (mtt90) REVERT: B 303 ASP cc_start: 0.8311 (m-30) cc_final: 0.7994 (m-30) REVERT: B 372 GLU cc_start: 0.7841 (tp30) cc_final: 0.7436 (tm-30) REVERT: C 406 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: C 436 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: C 502 ARG cc_start: 0.7267 (mmt90) cc_final: 0.6584 (mtp180) REVERT: C 506 ARG cc_start: 0.6403 (ttm110) cc_final: 0.5975 (ttp-110) outliers start: 25 outliers final: 15 residues processed: 100 average time/residue: 1.3279 time to fit residues: 139.3573 Evaluate side-chains 101 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 184 VAL 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 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 436 GLU Chi-restraints excluded: chain C residue 451 LEU 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: 0.5980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1943 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= 0.189 Angle : 0.448 6.300 8445 Z= 0.225 Chirality : 0.040 0.125 928 Planarity : 0.005 0.048 1069 Dihedral : 5.372 84.743 834 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 4.24 % Allowed : 20.73 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.32), residues: 739 helix: 1.76 (0.29), residues: 354 sheet: 0.26 (0.70), residues: 58 loop : 0.18 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.010 0.001 PHE A 152 TYR 0.010 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 113 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8424 (tp) cc_final: 0.8183 (tp) REVERT: A 177 CYS cc_start: 0.7840 (OUTLIER) cc_final: 0.6940 (p) REVERT: A 200 ARG cc_start: 0.7409 (ptp90) cc_final: 0.6736 (ptt-90) REVERT: A 237 LYS cc_start: 0.7399 (mttt) cc_final: 0.6620 (mmtt) REVERT: A 261 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7857 (m) REVERT: B 172 GLU cc_start: 0.5616 (pt0) cc_final: 0.5366 (mp0) REVERT: B 194 LYS cc_start: 0.7689 (mttt) cc_final: 0.6746 (mptt) REVERT: B 272 GLU cc_start: 0.7490 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 291 ARG cc_start: 0.7266 (tpt170) cc_final: 0.6607 (mtt90) REVERT: B 303 ASP cc_start: 0.8307 (m-30) cc_final: 0.8032 (m-30) REVERT: B 372 GLU cc_start: 0.7805 (tp30) cc_final: 0.7405 (tm-30) REVERT: C 406 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: C 436 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: C 502 ARG cc_start: 0.7211 (mtt90) cc_final: 0.6535 (mtp180) REVERT: C 506 ARG cc_start: 0.6348 (ttm110) cc_final: 0.5968 (ttp-110) outliers start: 28 outliers final: 17 residues processed: 105 average time/residue: 1.2933 time to fit residues: 142.6420 Evaluate side-chains 103 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 39 THR 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 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 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 436 GLU Chi-restraints excluded: chain C residue 451 LEU 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: 0.7980 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.1973 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= 0.166 Angle : 0.436 6.116 8445 Z= 0.220 Chirality : 0.040 0.133 928 Planarity : 0.005 0.048 1069 Dihedral : 5.325 84.413 834 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.78 % Allowed : 21.48 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.32), residues: 739 helix: 1.85 (0.29), residues: 352 sheet: 0.24 (0.70), residues: 58 loop : 0.22 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 PHE 0.009 0.001 PHE A 152 TYR 0.009 0.001 TYR C 389 ARG 0.010 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 112 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7801 (OUTLIER) cc_final: 0.6904 (p) REVERT: A 200 ARG cc_start: 0.7398 (ptp90) cc_final: 0.6733 (ptt-90) REVERT: A 237 LYS cc_start: 0.7418 (mttt) cc_final: 0.6655 (mmtt) REVERT: A 261 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7868 (m) REVERT: B 194 LYS cc_start: 0.7691 (mttt) cc_final: 0.6747 (mptt) REVERT: B 272 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6782 (mm-30) REVERT: B 291 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6611 (mtt90) REVERT: B 303 ASP cc_start: 0.8294 (m-30) cc_final: 0.7992 (m-30) REVERT: B 372 GLU cc_start: 0.7816 (tp30) cc_final: 0.7419 (tm-30) REVERT: C 406 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6475 (mp0) REVERT: C 424 ARG cc_start: 0.7747 (ptm160) cc_final: 0.7513 (ptm160) REVERT: C 436 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: C 485 SER cc_start: 0.8114 (t) cc_final: 0.7696 (p) REVERT: C 502 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6543 (mtp180) REVERT: C 506 ARG cc_start: 0.6287 (ttm110) cc_final: 0.5969 (ttp-110) outliers start: 25 outliers final: 16 residues processed: 104 average time/residue: 1.2874 time to fit residues: 140.0216 Evaluate side-chains 107 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 184 VAL 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 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 436 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 462 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.0040 chunk 62 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.2037 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= 0.167 Angle : 0.437 6.096 8445 Z= 0.220 Chirality : 0.040 0.129 928 Planarity : 0.005 0.047 1069 Dihedral : 5.316 84.321 834 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.48 % Allowed : 21.63 % 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: 1.43 (0.32), residues: 739 helix: 1.83 (0.29), residues: 353 sheet: 0.30 (0.70), residues: 58 loop : 0.19 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.002 0.001 HIS C 430 PHE 0.010 0.001 PHE C 429 TYR 0.009 0.001 TYR B 411 ARG 0.010 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 108 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7797 (OUTLIER) cc_final: 0.6897 (p) REVERT: A 237 LYS cc_start: 0.7437 (mttt) cc_final: 0.6671 (mmtt) REVERT: A 261 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7866 (m) REVERT: B 194 LYS cc_start: 0.7694 (mttt) cc_final: 0.6752 (mptt) REVERT: B 272 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6773 (mm-30) REVERT: B 291 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6644 (mtt90) REVERT: B 303 ASP cc_start: 0.8293 (m-30) cc_final: 0.7993 (m-30) REVERT: B 372 GLU cc_start: 0.7817 (tp30) cc_final: 0.7420 (tm-30) REVERT: C 406 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: C 424 ARG cc_start: 0.7746 (ptm160) cc_final: 0.7513 (ptm160) REVERT: C 436 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6544 (tm-30) REVERT: C 485 SER cc_start: 0.8124 (t) cc_final: 0.7711 (p) REVERT: C 502 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6539 (mtp180) REVERT: C 506 ARG cc_start: 0.6312 (ttm110) cc_final: 0.5990 (ttp-110) outliers start: 23 outliers final: 16 residues processed: 101 average time/residue: 1.2139 time to fit residues: 128.6223 Evaluate side-chains 103 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 184 VAL 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 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 436 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 462 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.0050 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.0070 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.4212 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.168579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129166 restraints weight = 6149.390| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.84 r_work: 0.3387 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2049 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= 0.134 Angle : 0.417 6.105 8445 Z= 0.211 Chirality : 0.039 0.126 928 Planarity : 0.005 0.047 1069 Dihedral : 5.196 84.150 834 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.72 % Allowed : 22.54 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.32), residues: 739 helix: 1.94 (0.29), residues: 352 sheet: 0.39 (0.69), residues: 58 loop : 0.27 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.002 0.000 HIS C 430 PHE 0.007 0.001 PHE A 152 TYR 0.009 0.001 TYR A 180 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: 2888.94 seconds wall clock time: 51 minutes 21.47 seconds (3081.47 seconds total)