Starting phenix.real_space_refine on Tue Aug 4 18:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8roz_19408/08_2026/8roz_19408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8roz_19408/08_2026/8roz_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 { model { file = "/net/cci-nas-00/data/ceres_data/8roz_19408/08_2026/8roz_19408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8roz_19408/08_2026/8roz_19408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8roz_19408/08_2026/8roz_19408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8roz_19408/08_2026/8roz_19408.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 30 5.16 5 C 3930 2.51 5 N 1021 2.21 5 O 1096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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, 'TPO:plan-1': 1, 'ARG:plan': 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: 1.38, per 1000 atoms: 0.23 Number of scatterers: 6079 At special positions: 0 Unit cell: (73.425, 80.85, 107.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 2 15.00 O 1096 8.00 N 1021 7.00 C 3930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 152.6 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1426 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.2% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 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: 1.04 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1928 1.34 - 1.46: 1423 1.46 - 1.58: 2829 1.58 - 1.70: 4 1.70 - 1.82: 50 Bond restraints: 6234 Sorted by residual: bond pdb=" OH PTR A 15 " pdb=" P PTR A 15 " ideal model delta sigma weight residual 1.769 1.608 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O1P TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.525 1.605 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" O3P TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.528 1.606 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O2P TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 1.528 1.475 0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 6229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 8344 2.12 - 4.24: 81 4.24 - 6.36: 14 6.36 - 8.48: 2 8.48 - 10.60: 4 Bond angle restraints: 8445 Sorted by residual: angle pdb=" CB TPO A 160 " pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " ideal model delta sigma weight residual 119.31 108.71 10.60 3.00e+00 1.11e-01 1.25e+01 angle pdb=" OG1 TPO A 160 " pdb=" P TPO A 160 " pdb=" O1P TPO A 160 " ideal model delta sigma weight residual 100.43 110.24 -9.81 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA TYR C 455 " pdb=" C TYR C 455 " pdb=" O TYR C 455 " ideal model delta sigma weight residual 120.17 116.82 3.35 1.04e+00 9.25e-01 1.04e+01 angle pdb=" CB MET C 336 " pdb=" CG MET C 336 " pdb=" SD MET C 336 " ideal model delta sigma weight residual 112.70 122.25 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CA TYR B 284 " pdb=" C TYR B 284 " pdb=" O TYR B 284 " ideal model delta sigma weight residual 121.06 117.66 3.40 1.16e+00 7.43e-01 8.57e+00 ... (remaining 8440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3234 17.69 - 35.39: 376 35.39 - 53.08: 119 53.08 - 70.78: 31 70.78 - 88.47: 8 Dihedral angle restraints: 3768 sinusoidal: 1556 harmonic: 2212 Sorted by residual: dihedral pdb=" CA LEU A 83 " pdb=" C LEU A 83 " pdb=" N HIS A 84 " pdb=" CA HIS A 84 " ideal model delta harmonic sigma weight residual -180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.93e+00 dihedral pdb=" CB GLU C 436 " pdb=" CG GLU C 436 " pdb=" CD GLU C 436 " pdb=" OE1 GLU C 436 " ideal model delta sinusoidal sigma weight residual 0.00 -84.67 84.67 1 3.00e+01 1.11e-03 9.68e+00 dihedral pdb=" N ARG C 520 " pdb=" CA ARG C 520 " pdb=" CB ARG C 520 " pdb=" CG ARG C 520 " ideal model delta sinusoidal sigma weight residual -60.00 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 594 0.032 - 0.064: 226 0.064 - 0.096: 64 0.096 - 0.128: 42 0.128 - 0.160: 2 Chirality restraints: 928 Sorted by residual: chirality pdb=" CA TYR B 284 " pdb=" N TYR B 284 " pdb=" C TYR B 284 " pdb=" CB TYR B 284 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA PTR A 15 " pdb=" N PTR A 15 " pdb=" C PTR A 15 " pdb=" CB PTR A 15 " both_signs ideal model delta sigma weight residual False 2.35 2.51 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB VAL B 254 " pdb=" CA VAL B 254 " pdb=" CG1 VAL B 254 " pdb=" CG2 VAL B 254 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 925 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 343 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 344 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 344 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 344 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 438 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO C 439 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 439 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 439 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 260 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU B 260 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU B 260 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 261 " -0.010 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 898 2.75 - 3.29: 5597 3.29 - 3.83: 10350 3.83 - 4.36: 12608 4.36 - 4.90: 21631 Nonbonded interactions: 51084 Sorted by model distance: nonbonded pdb=" OH TYR B 236 " pdb=" O LEU B 304 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP C 340 " pdb=" OG SER C 342 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 210 " pdb=" OH TYR C 455 " model vdw 2.312 3.040 nonbonded pdb=" NH2 ARG B 209 " pdb=" O LEU B 339 " model vdw 2.320 3.120 nonbonded pdb=" O LEU C 412 " pdb=" OH TYR C 460 " model vdw 2.328 3.040 ... (remaining 51079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.610 Find NCS groups from input model: 0.030 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:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 0.226 6235 Z= 0.355 Angle : 0.556 10.596 8445 Z= 0.273 Chirality : 0.041 0.160 928 Planarity : 0.005 0.043 1069 Dihedral : 17.455 88.471 2342 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 22.54 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 199 TYR 0.013 0.001 TYR B 284 PHE 0.010 0.001 PHE A 152 TRP 0.008 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 ( 6234) covalent geometry : angle 0.55641 / 0.27 ( 8445) hydrogen bonds : bond 0.14260 / 9.37 ( 279) hydrogen bonds : angle 6.13994 / 4.17 ( 792) Misc. bond : bond 0.22636 / 11.91 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.177 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: 0.5412 time to fit residues: 66.5609 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 84 HIS A 85 GLN B 177 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122762 restraints weight = 6225.114| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.96 r_work: 0.3271 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6235 Z= 0.194 Angle : 0.540 7.070 8445 Z= 0.277 Chirality : 0.044 0.146 928 Planarity : 0.006 0.082 1069 Dihedral : 6.384 89.162 838 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.54 % Allowed : 19.36 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.32), residues: 739 helix: 1.78 (0.29), residues: 356 sheet: -0.12 (0.75), residues: 48 loop : 0.18 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 437 TYR 0.016 0.002 TYR B 411 PHE 0.017 0.002 PHE A 152 TRP 0.011 0.002 TRP B 370 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.19 ( 6234) covalent geometry : angle 0.53999 / 0.28 ( 8445) hydrogen bonds : bond 0.04512 / 2.89 ( 279) hydrogen bonds : angle 4.53899 / 3.17 ( 792) Misc. bond : bond 0.00213 / 0.11 ( 1) *********************** 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 122 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.8595 (mp-120) cc_final: 0.8384 (mp10) REVERT: A 177 CYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7239 (p) REVERT: A 200 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7146 (ptt-90) REVERT: A 237 LYS cc_start: 0.7670 (mttt) cc_final: 0.6947 (mmtt) REVERT: A 261 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.7954 (m) REVERT: B 194 LYS cc_start: 0.7819 (mttt) cc_final: 0.6953 (mptt) REVERT: B 291 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7046 (mtt90) REVERT: B 303 ASP cc_start: 0.8455 (m-30) cc_final: 0.8145 (m-30) REVERT: B 346 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7687 (mp) REVERT: B 372 GLU cc_start: 0.7895 (tp30) cc_final: 0.7669 (tm-30) REVERT: B 375 VAL cc_start: 0.8467 (p) cc_final: 0.8177 (t) REVERT: C 372 LYS cc_start: 0.7963 (mmtp) cc_final: 0.7556 (mmtp) REVERT: C 406 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: C 472 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6586 (tt0) REVERT: C 485 SER cc_start: 0.8105 (t) cc_final: 0.7510 (p) REVERT: C 502 ARG cc_start: 0.7764 (mmt90) cc_final: 0.7212 (mtp180) REVERT: C 506 ARG cc_start: 0.6967 (ttm110) cc_final: 0.6583 (ttp-110) REVERT: C 519 SER cc_start: 0.7740 (m) cc_final: 0.7523 (m) outliers start: 30 outliers final: 11 residues processed: 112 average time/residue: 0.4941 time to fit residues: 57.9611 Evaluate side-chains 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 346 LEU Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 69 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.166760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125110 restraints weight = 6135.716| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.95 r_work: 0.3308 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6235 Z= 0.111 Angle : 0.462 6.169 8445 Z= 0.239 Chirality : 0.040 0.124 928 Planarity : 0.006 0.114 1069 Dihedral : 6.095 87.024 835 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.18 % Allowed : 22.09 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.32), residues: 739 helix: 2.03 (0.29), residues: 358 sheet: -0.29 (0.76), residues: 48 loop : 0.21 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 199 TYR 0.009 0.001 TYR B 411 PHE 0.012 0.001 PHE A 152 TRP 0.010 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 6234) covalent geometry : angle 0.46213 / 0.24 ( 8445) hydrogen bonds : bond 0.03455 / 2.18 ( 279) hydrogen bonds : angle 4.29312 / 3.02 ( 792) Misc. bond : bond 0.00439 / 0.23 ( 1) *********************** 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 113 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7238 (p) REVERT: A 233 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8423 (mtt) REVERT: A 237 LYS cc_start: 0.7671 (mttt) cc_final: 0.6960 (mmtt) REVERT: B 175 ASP cc_start: 0.8281 (m-30) cc_final: 0.8055 (m-30) REVERT: B 194 LYS cc_start: 0.7807 (mttt) cc_final: 0.6936 (mptt) REVERT: B 291 ARG cc_start: 0.7832 (tpt170) cc_final: 0.7032 (mtt90) REVERT: B 303 ASP cc_start: 0.8445 (m-30) cc_final: 0.8142 (m-30) REVERT: B 372 GLU cc_start: 0.7836 (tp30) cc_final: 0.7572 (tm-30) REVERT: C 372 LYS cc_start: 0.7981 (mmtp) cc_final: 0.7465 (mmtp) REVERT: C 406 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: C 472 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6568 (tt0) REVERT: C 502 ARG cc_start: 0.7752 (mmt90) cc_final: 0.7141 (mtp180) REVERT: C 506 ARG cc_start: 0.7015 (ttm110) cc_final: 0.6542 (ttp-110) REVERT: C 519 SER cc_start: 0.7671 (m) cc_final: 0.7438 (m) outliers start: 21 outliers final: 7 residues processed: 104 average time/residue: 0.5171 time to fit residues: 56.2501 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3912 r_free = 0.3912 target = 0.167115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125823 restraints weight = 6169.231| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.96 r_work: 0.3316 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6235 Z= 0.097 Angle : 0.445 6.135 8445 Z= 0.230 Chirality : 0.040 0.121 928 Planarity : 0.005 0.071 1069 Dihedral : 5.880 85.808 835 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.72 % Allowed : 23.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.32), residues: 739 helix: 2.17 (0.29), residues: 358 sheet: -0.31 (0.75), residues: 48 loop : 0.30 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 437 TYR 0.009 0.001 TYR B 411 PHE 0.010 0.001 PHE A 152 TRP 0.008 0.001 TRP B 370 HIS 0.002 0.000 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 6234) covalent geometry : angle 0.44522 / 0.23 ( 8445) hydrogen bonds : bond 0.03187 / 2.01 ( 279) hydrogen bonds : angle 4.14292 / 2.92 ( 792) Misc. bond : bond 0.00343 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7146 (p) REVERT: A 233 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8390 (mtt) REVERT: A 237 LYS cc_start: 0.7643 (mttt) cc_final: 0.6946 (mmtt) REVERT: B 175 ASP cc_start: 0.8216 (m-30) cc_final: 0.7914 (m-30) REVERT: B 194 LYS cc_start: 0.7811 (mttt) cc_final: 0.6955 (mptt) REVERT: B 291 ARG cc_start: 0.7834 (tpt170) cc_final: 0.7040 (mtt90) REVERT: B 303 ASP cc_start: 0.8439 (m-30) cc_final: 0.8118 (m-30) REVERT: B 346 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7673 (mp) REVERT: B 372 GLU cc_start: 0.7853 (tp30) cc_final: 0.7503 (tm-30) REVERT: C 372 LYS cc_start: 0.7832 (mmtp) cc_final: 0.7455 (mmtp) REVERT: C 406 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: C 415 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.6845 (tmtm) REVERT: C 472 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6562 (tt0) REVERT: C 502 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7156 (mtp180) REVERT: C 506 ARG cc_start: 0.6959 (ttm110) cc_final: 0.6540 (ttp-110) REVERT: C 519 SER cc_start: 0.7556 (m) cc_final: 0.7330 (m) outliers start: 18 outliers final: 6 residues processed: 100 average time/residue: 0.4875 time to fit residues: 50.9585 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 415 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3895 r_free = 0.3895 target = 0.165428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124770 restraints weight = 6399.267| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.91 r_work: 0.3273 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6235 Z= 0.187 Angle : 0.536 7.135 8445 Z= 0.273 Chirality : 0.043 0.137 928 Planarity : 0.006 0.132 1069 Dihedral : 5.925 85.446 835 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.08 % Allowed : 21.79 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.32), residues: 739 helix: 1.87 (0.28), residues: 358 sheet: -0.27 (0.75), residues: 53 loop : 0.17 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 437 TYR 0.014 0.001 TYR B 411 PHE 0.015 0.002 PHE A 152 TRP 0.009 0.001 TRP B 370 HIS 0.005 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 ( 6234) covalent geometry : angle 0.53645 / 0.27 ( 8445) hydrogen bonds : bond 0.04192 / 2.67 ( 279) hydrogen bonds : angle 4.30435 / 3.00 ( 792) Misc. bond : bond 0.00455 / 0.24 ( 1) *********************** 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 to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7344 (p) REVERT: A 237 LYS cc_start: 0.7690 (mttt) cc_final: 0.6984 (mmtt) REVERT: A 261 SER cc_start: 0.8463 (OUTLIER) cc_final: 0.8047 (m) REVERT: B 175 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: B 194 LYS cc_start: 0.7826 (mttt) cc_final: 0.6964 (mptt) REVERT: B 291 ARG cc_start: 0.7906 (tpt170) cc_final: 0.7076 (mtt90) REVERT: B 303 ASP cc_start: 0.8458 (m-30) cc_final: 0.8134 (m-30) REVERT: B 346 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7819 (mp) REVERT: B 372 GLU cc_start: 0.7923 (tp30) cc_final: 0.7610 (tm-30) REVERT: C 372 LYS cc_start: 0.7895 (mmtp) cc_final: 0.7532 (mmtp) REVERT: C 406 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: C 502 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7154 (mtp180) REVERT: C 506 ARG cc_start: 0.6960 (ttm110) cc_final: 0.6534 (ttp-110) REVERT: C 519 SER cc_start: 0.7706 (m) cc_final: 0.7486 (m) outliers start: 27 outliers final: 14 residues processed: 99 average time/residue: 0.5219 time to fit residues: 54.0622 Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain 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 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 489 MET 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 47 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3851 r_free = 0.3851 target = 0.162216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.119538 restraints weight = 6230.968| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.99 r_work: 0.3273 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6235 Z= 0.140 Angle : 0.502 7.392 8445 Z= 0.257 Chirality : 0.042 0.128 928 Planarity : 0.005 0.061 1069 Dihedral : 5.739 85.596 835 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.93 % Allowed : 21.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.32), residues: 739 helix: 1.95 (0.28), residues: 358 sheet: -0.18 (0.76), residues: 53 loop : 0.20 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 437 TYR 0.011 0.001 TYR B 411 PHE 0.012 0.001 PHE A 152 TRP 0.010 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 6234) covalent geometry : angle 0.50227 / 0.26 ( 8445) hydrogen bonds : bond 0.03705 / 2.34 ( 279) hydrogen bonds : angle 4.21914 / 2.95 ( 792) Misc. bond : bond 0.00407 / 0.21 ( 1) *********************** 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 109 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7331 (p) REVERT: A 237 LYS cc_start: 0.7698 (mttt) cc_final: 0.6989 (mmtt) REVERT: A 261 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8127 (m) REVERT: A 265 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8663 (mt0) REVERT: B 175 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: B 194 LYS cc_start: 0.7835 (mttt) cc_final: 0.6975 (mptt) REVERT: B 272 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6868 (mm-30) REVERT: B 291 ARG cc_start: 0.7918 (tpt170) cc_final: 0.7100 (mtt90) REVERT: B 303 ASP cc_start: 0.8486 (m-30) cc_final: 0.8170 (m-30) REVERT: B 346 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7802 (mp) REVERT: B 372 GLU cc_start: 0.7945 (tp30) cc_final: 0.7635 (tm-30) REVERT: C 372 LYS cc_start: 0.7914 (mmtp) cc_final: 0.7577 (mmtp) REVERT: C 406 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: C 485 SER cc_start: 0.8137 (t) cc_final: 0.7768 (p) REVERT: C 502 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7130 (mtp180) REVERT: C 506 ARG cc_start: 0.6969 (ttm110) cc_final: 0.6604 (ttp-110) REVERT: C 519 SER cc_start: 0.7682 (m) cc_final: 0.7463 (m) outliers start: 26 outliers final: 13 residues processed: 99 average time/residue: 0.5375 time to fit residues: 55.4724 Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 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 23 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 0.0060 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3901 r_free = 0.3901 target = 0.166238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124686 restraints weight = 6285.625| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.97 r_work: 0.3326 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6235 Z= 0.108 Angle : 0.489 12.027 8445 Z= 0.251 Chirality : 0.040 0.123 928 Planarity : 0.006 0.136 1069 Dihedral : 5.618 85.408 835 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.32), residues: 739 helix: 2.14 (0.29), residues: 357 sheet: -0.15 (0.76), residues: 53 loop : 0.24 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 437 TYR 0.009 0.001 TYR B 411 PHE 0.010 0.001 PHE A 152 TRP 0.010 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 6234) covalent geometry : angle 0.48924 / 0.25 ( 8445) hydrogen bonds : bond 0.03307 / 2.08 ( 279) hydrogen bonds : angle 4.13118 / 2.90 ( 792) Misc. bond : bond 0.00435 / 0.23 ( 1) *********************** 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 to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.214 Fit side-chains REVERT: A 177 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7243 (p) REVERT: A 237 LYS cc_start: 0.7715 (mttt) cc_final: 0.7026 (mmtt) REVERT: A 261 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8060 (m) REVERT: B 175 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 194 LYS cc_start: 0.7837 (mttt) cc_final: 0.6992 (mptt) REVERT: B 272 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6863 (mm-30) REVERT: B 291 ARG cc_start: 0.7911 (tpt170) cc_final: 0.7118 (mtt90) REVERT: B 303 ASP cc_start: 0.8459 (m-30) cc_final: 0.8162 (m-30) REVERT: B 372 GLU cc_start: 0.7881 (tp30) cc_final: 0.7599 (tm-30) REVERT: C 372 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7657 (mmtp) REVERT: C 406 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: C 415 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.6905 (tmtm) REVERT: C 485 SER cc_start: 0.8134 (t) cc_final: 0.7773 (p) REVERT: C 502 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7138 (mtp180) REVERT: C 506 ARG cc_start: 0.6943 (ttm110) cc_final: 0.6608 (ttp-110) REVERT: C 519 SER cc_start: 0.7620 (m) cc_final: 0.7401 (m) outliers start: 25 outliers final: 13 residues processed: 98 average time/residue: 0.5259 time to fit residues: 53.9191 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 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 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 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.125259 restraints weight = 6212.067| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.96 r_work: 0.3342 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6235 Z= 0.111 Angle : 0.501 12.680 8445 Z= 0.256 Chirality : 0.041 0.141 928 Planarity : 0.006 0.125 1069 Dihedral : 5.588 85.648 835 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 23.00 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.32), residues: 739 helix: 2.23 (0.29), residues: 356 sheet: -0.08 (0.76), residues: 53 loop : 0.19 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 437 TYR 0.009 0.001 TYR B 411 PHE 0.010 0.001 PHE A 152 TRP 0.009 0.001 TRP B 370 HIS 0.003 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 ( 6234) covalent geometry : angle 0.50073 / 0.26 ( 8445) hydrogen bonds : bond 0.03313 / 2.08 ( 279) hydrogen bonds : angle 4.09601 / 2.88 ( 792) Misc. bond : bond 0.00433 / 0.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7261 (p) REVERT: A 233 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: A 237 LYS cc_start: 0.7688 (mttt) cc_final: 0.6969 (mmtt) REVERT: A 261 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8061 (m) REVERT: B 175 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: B 194 LYS cc_start: 0.7827 (mttt) cc_final: 0.6965 (mptt) REVERT: B 272 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 291 ARG cc_start: 0.7868 (tpt170) cc_final: 0.7085 (mtt90) REVERT: B 303 ASP cc_start: 0.8447 (m-30) cc_final: 0.8146 (m-30) REVERT: B 372 GLU cc_start: 0.7878 (tp30) cc_final: 0.7580 (tm-30) REVERT: C 406 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: C 485 SER cc_start: 0.8136 (t) cc_final: 0.7770 (p) REVERT: C 502 ARG cc_start: 0.7756 (mmt90) cc_final: 0.7110 (mtp180) REVERT: C 506 ARG cc_start: 0.6902 (ttm110) cc_final: 0.6561 (ttp-110) REVERT: C 519 SER cc_start: 0.7577 (m) cc_final: 0.7347 (m) outliers start: 22 outliers final: 13 residues processed: 94 average time/residue: 0.4875 time to fit residues: 47.8113 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain C residue 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 61 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.0000 chunk 10 optimal weight: 0.8980 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3900 r_free = 0.3900 target = 0.166081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124493 restraints weight = 6268.850| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.98 r_work: 0.3326 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6235 Z= 0.128 Angle : 0.569 18.506 8445 Z= 0.279 Chirality : 0.041 0.127 928 Planarity : 0.007 0.171 1069 Dihedral : 5.595 85.332 835 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.32), residues: 739 helix: 2.19 (0.29), residues: 356 sheet: -0.04 (0.76), residues: 53 loop : 0.15 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 437 TYR 0.011 0.001 TYR B 411 PHE 0.011 0.001 PHE A 152 TRP 0.009 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 6234) covalent geometry : angle 0.56857 / 0.28 ( 8445) hydrogen bonds : bond 0.03513 / 2.22 ( 279) hydrogen bonds : angle 4.11835 / 2.89 ( 792) Misc. bond : bond 0.00574 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7251 (p) REVERT: A 237 LYS cc_start: 0.7762 (mttt) cc_final: 0.7069 (mmtt) REVERT: A 261 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8104 (m) REVERT: B 175 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: B 194 LYS cc_start: 0.7837 (mttt) cc_final: 0.6991 (mptt) REVERT: B 272 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 291 ARG cc_start: 0.7894 (tpt170) cc_final: 0.7125 (mtt90) REVERT: B 303 ASP cc_start: 0.8450 (m-30) cc_final: 0.8140 (m-30) REVERT: B 372 GLU cc_start: 0.7895 (tp30) cc_final: 0.7581 (tm-30) REVERT: C 372 LYS cc_start: 0.7800 (mmtp) cc_final: 0.7562 (mmtp) REVERT: C 406 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: C 485 SER cc_start: 0.8141 (t) cc_final: 0.7781 (p) REVERT: C 502 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7167 (mtp180) REVERT: C 506 ARG cc_start: 0.6951 (ttm110) cc_final: 0.6603 (ttp-110) REVERT: C 519 SER cc_start: 0.7607 (m) cc_final: 0.7383 (m) outliers start: 22 outliers final: 14 residues processed: 95 average time/residue: 0.4947 time to fit residues: 48.9709 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 70 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.3665 > 50:) chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124545 restraints weight = 6183.250| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.97 r_work: 0.3302 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6235 Z= 0.138 Angle : 0.615 20.682 8445 Z= 0.301 Chirality : 0.042 0.220 928 Planarity : 0.008 0.191 1069 Dihedral : 7.726 155.292 834 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.87 % Allowed : 22.84 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.32), residues: 739 helix: 2.16 (0.29), residues: 356 sheet: -0.06 (0.76), residues: 53 loop : 0.14 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 199 TYR 0.011 0.001 TYR B 411 PHE 0.012 0.001 PHE A 152 TRP 0.009 0.001 TRP B 370 HIS 0.004 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 6234) covalent geometry : angle 0.61462 / 0.30 ( 8445) hydrogen bonds : bond 0.03617 / 2.26 ( 279) hydrogen bonds : angle 4.15031 / 2.91 ( 792) Misc. bond : bond 0.00803 / 0.42 ( 1) ********************** 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 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7223 (p) REVERT: A 237 LYS cc_start: 0.7739 (mttt) cc_final: 0.7024 (mmtt) REVERT: A 261 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8060 (m) REVERT: B 175 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: B 194 LYS cc_start: 0.7825 (mttt) cc_final: 0.6956 (mptt) REVERT: B 272 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6784 (mm-30) REVERT: B 291 ARG cc_start: 0.7842 (tpt170) cc_final: 0.7030 (mtt90) REVERT: B 303 ASP cc_start: 0.8448 (m-30) cc_final: 0.8125 (m-30) REVERT: B 372 GLU cc_start: 0.7897 (tp30) cc_final: 0.7551 (tm-30) REVERT: C 372 LYS cc_start: 0.7787 (mmtp) cc_final: 0.7554 (mmtp) REVERT: C 406 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: C 485 SER cc_start: 0.8130 (t) cc_final: 0.7768 (p) REVERT: C 502 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7131 (mtp180) REVERT: C 506 ARG cc_start: 0.6850 (ttm110) cc_final: 0.6554 (ttp-110) REVERT: C 519 SER cc_start: 0.7570 (m) cc_final: 0.7349 (m) REVERT: C 522 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6184 (tppt) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.4902 time to fit residues: 48.7558 Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 397 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 522 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 52 optimal weight: 0.0020 chunk 71 optimal weight: 2.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3888 r_free = 0.3888 target = 0.164802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123595 restraints weight = 6174.581| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.93 r_work: 0.3314 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6235 Z= 0.167 Angle : 0.601 17.446 8445 Z= 0.304 Chirality : 0.043 0.155 928 Planarity : 0.009 0.228 1069 Dihedral : 7.623 149.873 834 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.33 % Allowed : 22.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.32), residues: 739 helix: 2.04 (0.28), residues: 356 sheet: -0.07 (0.76), residues: 53 loop : 0.11 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 199 TYR 0.013 0.001 TYR B 411 PHE 0.013 0.001 PHE A 152 TRP 0.008 0.001 TRP B 370 HIS 0.006 0.001 HIS C 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 6234) covalent geometry : angle 0.60126 / 0.30 ( 8445) hydrogen bonds : bond 0.03975 / 2.50 ( 279) hydrogen bonds : angle 4.22682 / 2.95 ( 792) Misc. bond : bond 0.00883 / 0.46 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2045.14 seconds wall clock time: 35 minutes 24.90 seconds (2124.90 seconds total)