Starting phenix.real_space_refine on Thu Mar 13 12:13:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3k_10092/03_2025/6s3k_10092.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3k_10092/03_2025/6s3k_10092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2025/6s3k_10092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2025/6s3k_10092.map" model { file = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2025/6s3k_10092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3k_10092/03_2025/6s3k_10092.cif" } resolution = 3.7 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= 0.005 sd= 0.093 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 K 6 8.98 5 S 34 5.16 5 C 5906 2.51 5 N 1436 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8902 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4448 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 25, 'TRANS': 547} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 7.97, per 1000 atoms: 0.90 Number of scatterers: 8902 At special positions: 0 Unit cell: (67.851, 119.547, 109.854, 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) K 6 19.00 S 34 16.00 O 1520 8.00 N 1436 7.00 C 5906 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=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.2 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 67.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 30 through 38 removed outlier: 4.955A pdb=" N ASP B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 107 through 132 removed outlier: 3.701A pdb=" N GLY B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 4.321A pdb=" N ASP B 142 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.645A pdb=" N ALA B 148 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 193 removed outlier: 4.292A pdb=" N TYR B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 226 through 229 Processing helix chain 'B' and resid 231 through 238 removed outlier: 3.962A pdb=" N ILE B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 275 Processing helix chain 'B' and resid 284 through 294 removed outlier: 3.890A pdb=" N GLN B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 331 removed outlier: 3.782A pdb=" N ILE B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Proline residue: B 323 - end of helix removed outlier: 3.564A pdb=" N ARG B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.753A pdb=" N PHE B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 341 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG B 342 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 367 Processing helix chain 'B' and resid 372 through 399 removed outlier: 4.243A pdb=" N LEU B 376 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Proline residue: B 384 - end of helix removed outlier: 3.835A pdb=" N GLN B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 428 removed outlier: 3.559A pdb=" N LYS B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 461 removed outlier: 3.669A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 484 through 498 Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.973A pdb=" N LYS B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'A' and resid 30 through 38 removed outlier: 4.955A pdb=" N ASP A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 62 through 88 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 107 through 132 removed outlier: 3.700A pdb=" N GLY A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.646A pdb=" N ALA A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 193 removed outlier: 4.292A pdb=" N TYR A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 226 through 229 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.962A pdb=" N ILE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 275 Processing helix chain 'A' and resid 284 through 294 removed outlier: 3.890A pdb=" N GLN A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 331 removed outlier: 3.783A pdb=" N ILE A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 3.564A pdb=" N ARG A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.753A pdb=" N PHE A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 341 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 342 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 Processing helix chain 'A' and resid 372 through 399 removed outlier: 4.244A pdb=" N LEU A 376 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.836A pdb=" N GLN A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.559A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 461 removed outlier: 3.669A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.972A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 Processing helix chain 'A' and resid 582 through 591 Processing sheet with id=AA1, first strand: chain 'B' and resid 502 through 503 removed outlier: 8.423A pdb=" N ILE B 502 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 476 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL B 475 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU B 564 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE B 477 " --> pdb=" O LEU B 564 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET B 597 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 597 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL A 475 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 564 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 477 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ILE A 502 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 476 " --> pdb=" O ILE A 502 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1650 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: 2.32 Time building geometry restraints manager: 2.56 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: 2583 1.34 - 1.46: 1572 1.46 - 1.57: 4889 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9106 Sorted by residual: bond pdb=" C ILE B 239 " pdb=" N PRO B 240 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.39e+00 bond pdb=" C ILE A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.23e+00 bond pdb=" C VAL A 145 " pdb=" N PRO A 146 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" CG LEU B 120 " pdb=" CD1 LEU B 120 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 bond pdb=" C VAL B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 ... (remaining 9101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12004 2.83 - 5.66: 324 5.66 - 8.49: 44 8.49 - 11.31: 4 11.31 - 14.14: 6 Bond angle restraints: 12382 Sorted by residual: angle pdb=" C PHE B 508 " pdb=" N ASP B 509 " pdb=" CA ASP B 509 " ideal model delta sigma weight residual 123.91 131.06 -7.15 1.66e+00 3.63e-01 1.85e+01 angle pdb=" C PHE A 508 " pdb=" N ASP A 509 " pdb=" CA ASP A 509 " ideal model delta sigma weight residual 123.91 131.06 -7.15 1.66e+00 3.63e-01 1.85e+01 angle pdb=" C MET B 193 " pdb=" N THR B 194 " pdb=" CA THR B 194 " ideal model delta sigma weight residual 121.54 129.75 -8.21 1.91e+00 2.74e-01 1.85e+01 angle pdb=" C MET A 193 " pdb=" N THR A 194 " pdb=" CA THR A 194 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" CA LEU A 461 " pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 116.30 130.44 -14.14 3.50e+00 8.16e-02 1.63e+01 ... (remaining 12377 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4680 16.82 - 33.64: 528 33.64 - 50.46: 120 50.46 - 67.28: 14 67.28 - 84.10: 14 Dihedral angle restraints: 5356 sinusoidal: 2042 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE B 382 " pdb=" C PHE B 382 " pdb=" N ILE B 383 " pdb=" CA ILE B 383 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA PHE A 382 " pdb=" C PHE A 382 " pdb=" N ILE A 383 " pdb=" CA ILE A 383 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LYS A 105 " pdb=" C LYS A 105 " pdb=" N PRO A 106 " pdb=" CA PRO A 106 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 944 0.050 - 0.101: 379 0.101 - 0.151: 130 0.151 - 0.201: 28 0.201 - 0.251: 11 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA ASP A 509 " pdb=" N ASP A 509 " pdb=" C ASP A 509 " pdb=" CB ASP A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ASP B 509 " pdb=" N ASP B 509 " pdb=" C ASP B 509 " pdb=" CB ASP B 509 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE B 239 " pdb=" CA ILE B 239 " pdb=" CG1 ILE B 239 " pdb=" CG2 ILE B 239 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1489 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 434 " 0.048 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO A 435 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 435 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 435 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 434 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO B 435 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 435 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 435 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 335 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO B 336 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 336 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 336 " -0.038 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 3024 2.85 - 3.42: 9854 3.42 - 3.99: 15718 3.99 - 4.57: 21472 4.57 - 5.14: 31348 Nonbonded interactions: 81416 Sorted by model distance: nonbonded pdb=" OG SER B 507 " pdb=" O LEU B 532 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 507 " pdb=" O LEU A 532 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 88 " pdb=" OE2 GLU A 100 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR B 88 " pdb=" OE2 GLU B 100 " model vdw 2.284 3.040 nonbonded pdb=" OG SER B 80 " pdb=" OE1 GLN B 389 " model vdw 2.309 3.040 ... (remaining 81411 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.140 Find NCS groups from input model: 0.150 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.008 0.079 9106 Z= 0.498 Angle : 1.124 14.143 12382 Z= 0.594 Chirality : 0.063 0.251 1492 Planarity : 0.009 0.071 1508 Dihedral : 15.380 84.105 3220 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.62 % Allowed : 12.29 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.54 (0.19), residues: 1134 helix: -2.35 (0.14), residues: 748 sheet: -2.40 (0.57), residues: 66 loop : -4.38 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 520 HIS 0.004 0.002 HIS A 492 PHE 0.020 0.002 PHE A 299 TYR 0.030 0.003 TYR A 377 ARG 0.004 0.001 ARG B 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5486 (mtt) cc_final: 0.5204 (ptp) REVERT: B 52 LEU cc_start: 0.8590 (tp) cc_final: 0.8333 (tp) REVERT: B 75 LEU cc_start: 0.8518 (tp) cc_final: 0.8316 (tp) REVERT: B 229 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8665 (pp) REVERT: B 294 PHE cc_start: 0.5568 (t80) cc_final: 0.5358 (t80) REVERT: B 573 ARG cc_start: 0.7709 (ptt180) cc_final: 0.7075 (mmm160) REVERT: A 32 MET cc_start: 0.5624 (mtt) cc_final: 0.5358 (ptp) REVERT: A 51 ILE cc_start: 0.7893 (mt) cc_final: 0.7616 (mt) REVERT: A 229 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8539 (pp) REVERT: A 393 CYS cc_start: 0.8647 (t) cc_final: 0.8423 (t) REVERT: A 404 TRP cc_start: 0.7490 (t60) cc_final: 0.7196 (t60) REVERT: A 551 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7920 (mt-10) REVERT: A 573 ARG cc_start: 0.7620 (ptt180) cc_final: 0.6988 (mmm160) outliers start: 6 outliers final: 2 residues processed: 177 average time/residue: 0.1936 time to fit residues: 48.3632 Evaluate side-chains 125 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 501 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 GLN B 203 HIS B 316 ASN B 558 GLN B 575 HIS A 47 GLN A 203 HIS A 316 ASN A 558 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.170943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.130305 restraints weight = 12666.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134470 restraints weight = 7600.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137097 restraints weight = 5518.675| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9106 Z= 0.182 Angle : 0.687 9.210 12382 Z= 0.351 Chirality : 0.044 0.171 1492 Planarity : 0.006 0.053 1508 Dihedral : 5.604 31.091 1216 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.50 % Allowed : 18.33 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.24), residues: 1134 helix: -0.13 (0.18), residues: 754 sheet: -1.13 (0.71), residues: 48 loop : -3.86 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 520 HIS 0.003 0.001 HIS B 144 PHE 0.019 0.001 PHE A 448 TYR 0.017 0.002 TYR B 377 ARG 0.002 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5488 (mtt) cc_final: 0.5191 (ptp) REVERT: B 75 LEU cc_start: 0.8426 (tp) cc_final: 0.7920 (tt) REVERT: B 229 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 573 ARG cc_start: 0.7459 (ptt180) cc_final: 0.7073 (mmm160) REVERT: B 579 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.6291 (t-90) REVERT: A 32 MET cc_start: 0.5753 (mtt) cc_final: 0.5490 (ptp) REVERT: A 229 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8423 (pp) REVERT: A 440 MET cc_start: 0.7829 (tpp) cc_final: 0.7213 (mmt) REVERT: A 573 ARG cc_start: 0.7436 (ptt180) cc_final: 0.7078 (mmm160) REVERT: A 579 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.7118 (m-70) outliers start: 24 outliers final: 12 residues processed: 164 average time/residue: 0.1640 time to fit residues: 40.2562 Evaluate side-chains 143 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 579 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 84 optimal weight: 0.0770 chunk 105 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129148 restraints weight = 13074.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133303 restraints weight = 7741.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.135991 restraints weight = 5613.277| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9106 Z= 0.196 Angle : 0.676 11.189 12382 Z= 0.341 Chirality : 0.044 0.178 1492 Planarity : 0.005 0.049 1508 Dihedral : 5.101 22.892 1216 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.85 % Allowed : 20.52 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.25), residues: 1134 helix: 0.66 (0.19), residues: 752 sheet: -0.19 (0.80), residues: 46 loop : -3.48 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.002 0.001 HIS A 144 PHE 0.021 0.001 PHE A 448 TYR 0.016 0.002 TYR A 377 ARG 0.001 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5653 (mtt) cc_final: 0.5341 (ptp) REVERT: B 51 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7023 (mt) REVERT: B 52 LEU cc_start: 0.8215 (tp) cc_final: 0.7905 (tp) REVERT: B 229 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 440 MET cc_start: 0.7944 (tpt) cc_final: 0.7633 (tpp) REVERT: B 573 ARG cc_start: 0.7409 (ptt180) cc_final: 0.7053 (mmm160) REVERT: B 579 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6253 (t-90) REVERT: A 32 MET cc_start: 0.5647 (mtt) cc_final: 0.5349 (ptp) REVERT: A 51 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7064 (mt) REVERT: A 229 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8390 (pp) REVERT: A 282 ASP cc_start: 0.8363 (p0) cc_final: 0.8129 (p0) REVERT: A 292 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: A 294 PHE cc_start: 0.5379 (OUTLIER) cc_final: 0.5139 (t80) REVERT: A 440 MET cc_start: 0.7785 (tpp) cc_final: 0.7231 (mmt) REVERT: A 573 ARG cc_start: 0.7395 (ptt180) cc_final: 0.7054 (mmm160) REVERT: A 579 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6170 (t-90) outliers start: 37 outliers final: 19 residues processed: 166 average time/residue: 0.1687 time to fit residues: 41.3704 Evaluate side-chains 159 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.169788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.129478 restraints weight = 12970.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133546 restraints weight = 7663.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135946 restraints weight = 5593.100| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9106 Z= 0.199 Angle : 0.658 9.894 12382 Z= 0.330 Chirality : 0.043 0.162 1492 Planarity : 0.005 0.046 1508 Dihedral : 4.893 22.858 1216 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.38 % Allowed : 21.77 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.26), residues: 1134 helix: 1.02 (0.19), residues: 756 sheet: 0.22 (0.84), residues: 46 loop : -3.35 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 520 HIS 0.002 0.001 HIS B 144 PHE 0.021 0.001 PHE B 448 TYR 0.016 0.001 TYR A 377 ARG 0.001 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5850 (mtt) cc_final: 0.5468 (ptp) REVERT: B 229 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 440 MET cc_start: 0.7948 (tpt) cc_final: 0.7613 (tpp) REVERT: B 573 ARG cc_start: 0.7445 (ptt180) cc_final: 0.6415 (tmt170) REVERT: B 579 HIS cc_start: 0.7421 (OUTLIER) cc_final: 0.6477 (t-90) REVERT: A 32 MET cc_start: 0.5729 (mtt) cc_final: 0.5389 (ptp) REVERT: A 51 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7000 (mt) REVERT: A 229 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8402 (pp) REVERT: A 294 PHE cc_start: 0.5413 (OUTLIER) cc_final: 0.5090 (t80) REVERT: A 440 MET cc_start: 0.7757 (tpp) cc_final: 0.7187 (mmt) REVERT: A 573 ARG cc_start: 0.7439 (ptt180) cc_final: 0.7041 (mmm160) REVERT: A 579 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6242 (t-90) outliers start: 42 outliers final: 24 residues processed: 166 average time/residue: 0.1611 time to fit residues: 39.8921 Evaluate side-chains 161 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 324 GLN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.167976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127582 restraints weight = 13042.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131757 restraints weight = 7690.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134445 restraints weight = 5545.655| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9106 Z= 0.231 Angle : 0.678 9.609 12382 Z= 0.341 Chirality : 0.044 0.162 1492 Planarity : 0.005 0.048 1508 Dihedral : 4.848 22.812 1214 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.00 % Allowed : 23.12 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.26), residues: 1134 helix: 1.17 (0.19), residues: 754 sheet: 0.36 (0.85), residues: 46 loop : -3.26 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 520 HIS 0.002 0.001 HIS A 492 PHE 0.022 0.001 PHE B 448 TYR 0.017 0.002 TYR A 377 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.5676 (mtt) cc_final: 0.5362 (ptp) REVERT: B 51 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7124 (mt) REVERT: B 52 LEU cc_start: 0.8173 (tp) cc_final: 0.7914 (tp) REVERT: B 133 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8049 (tp) REVERT: B 229 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8433 (pp) REVERT: B 259 ILE cc_start: 0.7915 (tt) cc_final: 0.7613 (tp) REVERT: B 440 MET cc_start: 0.7991 (tpt) cc_final: 0.7581 (tpp) REVERT: B 573 ARG cc_start: 0.7430 (ptt180) cc_final: 0.6438 (tmt170) REVERT: B 579 HIS cc_start: 0.7429 (OUTLIER) cc_final: 0.6489 (t-90) REVERT: A 32 MET cc_start: 0.5729 (mtt) cc_final: 0.5469 (ptp) REVERT: A 51 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7094 (mt) REVERT: A 133 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8084 (tp) REVERT: A 143 TYR cc_start: 0.7316 (p90) cc_final: 0.7081 (p90) REVERT: A 229 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8425 (pp) REVERT: A 292 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.5847 (mp0) REVERT: A 294 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5202 (t80) REVERT: A 335 MET cc_start: 0.7705 (mmm) cc_final: 0.6709 (mtp) REVERT: A 440 MET cc_start: 0.7729 (tpp) cc_final: 0.7134 (mmt) REVERT: A 573 ARG cc_start: 0.7376 (ptt180) cc_final: 0.7028 (mmm160) REVERT: A 579 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.6403 (t-90) outliers start: 48 outliers final: 30 residues processed: 173 average time/residue: 0.1683 time to fit residues: 43.4139 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 489 LYS Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.170016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.129804 restraints weight = 12972.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133900 restraints weight = 7633.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136607 restraints weight = 5546.826| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9106 Z= 0.192 Angle : 0.650 9.429 12382 Z= 0.325 Chirality : 0.043 0.159 1492 Planarity : 0.005 0.048 1508 Dihedral : 4.701 22.621 1214 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.21 % Allowed : 24.06 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.26), residues: 1134 helix: 1.29 (0.19), residues: 766 sheet: 0.42 (0.85), residues: 46 loop : -3.22 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 520 HIS 0.002 0.000 HIS B 144 PHE 0.023 0.001 PHE B 448 TYR 0.015 0.001 TYR A 377 ARG 0.001 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: B 32 MET cc_start: 0.5629 (mtt) cc_final: 0.5339 (ptp) REVERT: B 51 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7062 (mt) REVERT: B 52 LEU cc_start: 0.8197 (tp) cc_final: 0.7944 (tp) REVERT: B 133 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8036 (tp) REVERT: B 229 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8421 (pp) REVERT: B 259 ILE cc_start: 0.7888 (tt) cc_final: 0.7543 (tp) REVERT: B 335 MET cc_start: 0.7650 (mmm) cc_final: 0.6678 (mtp) REVERT: B 440 MET cc_start: 0.7879 (tpt) cc_final: 0.7461 (tpp) REVERT: B 573 ARG cc_start: 0.7378 (ptt180) cc_final: 0.6431 (tmt170) REVERT: B 579 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6454 (t-90) REVERT: A 32 MET cc_start: 0.5637 (mtt) cc_final: 0.5413 (ptp) REVERT: A 51 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6995 (mt) REVERT: A 143 TYR cc_start: 0.7326 (p90) cc_final: 0.7054 (p90) REVERT: A 229 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8369 (pp) REVERT: A 292 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.5775 (mp0) REVERT: A 294 PHE cc_start: 0.5479 (OUTLIER) cc_final: 0.5043 (t80) REVERT: A 335 MET cc_start: 0.7551 (mmm) cc_final: 0.6579 (mtp) REVERT: A 440 MET cc_start: 0.7724 (tpp) cc_final: 0.7146 (mmt) REVERT: A 520 TRP cc_start: 0.7033 (t60) cc_final: 0.6828 (t60) REVERT: A 573 ARG cc_start: 0.7358 (ptt180) cc_final: 0.6952 (mmm160) REVERT: A 579 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6218 (t-90) outliers start: 50 outliers final: 30 residues processed: 182 average time/residue: 0.1628 time to fit residues: 44.2667 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.169382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129148 restraints weight = 13267.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133300 restraints weight = 7792.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.136003 restraints weight = 5622.055| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9106 Z= 0.216 Angle : 0.684 12.420 12382 Z= 0.339 Chirality : 0.044 0.208 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.696 22.676 1214 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.79 % Allowed : 25.21 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.26), residues: 1134 helix: 1.23 (0.19), residues: 776 sheet: 0.53 (0.84), residues: 46 loop : -3.47 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 520 HIS 0.002 0.001 HIS B 144 PHE 0.023 0.001 PHE A 448 TYR 0.016 0.001 TYR B 377 ARG 0.011 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: B 32 MET cc_start: 0.5674 (mtt) cc_final: 0.5438 (ptp) REVERT: B 51 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7105 (mt) REVERT: B 52 LEU cc_start: 0.8235 (tp) cc_final: 0.7981 (tp) REVERT: B 133 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8054 (tp) REVERT: B 229 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8444 (pp) REVERT: B 259 ILE cc_start: 0.7907 (tt) cc_final: 0.7593 (tp) REVERT: B 335 MET cc_start: 0.7673 (mmm) cc_final: 0.6674 (mtp) REVERT: B 440 MET cc_start: 0.7906 (tpt) cc_final: 0.7485 (tpp) REVERT: B 573 ARG cc_start: 0.7381 (ptt180) cc_final: 0.6446 (tmt170) REVERT: B 579 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.6457 (t-90) REVERT: A 32 MET cc_start: 0.5667 (mtt) cc_final: 0.5434 (ptp) REVERT: A 51 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7028 (mt) REVERT: A 133 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 143 TYR cc_start: 0.7277 (p90) cc_final: 0.7031 (p90) REVERT: A 229 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8376 (pp) REVERT: A 292 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.5814 (mp0) REVERT: A 294 PHE cc_start: 0.5638 (OUTLIER) cc_final: 0.5164 (t80) REVERT: A 335 MET cc_start: 0.7575 (mmm) cc_final: 0.6584 (mtp) REVERT: A 440 MET cc_start: 0.7716 (tpp) cc_final: 0.7099 (mmt) REVERT: A 520 TRP cc_start: 0.7010 (t60) cc_final: 0.6780 (t60) REVERT: A 573 ARG cc_start: 0.7370 (ptt180) cc_final: 0.6946 (mmm160) REVERT: A 579 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6413 (t-90) outliers start: 46 outliers final: 30 residues processed: 168 average time/residue: 0.1663 time to fit residues: 41.8563 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 75 optimal weight: 0.0050 chunk 63 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.171645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131999 restraints weight = 13270.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136092 restraints weight = 7910.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138707 restraints weight = 5755.781| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9106 Z= 0.179 Angle : 0.659 11.792 12382 Z= 0.325 Chirality : 0.043 0.175 1492 Planarity : 0.005 0.046 1508 Dihedral : 4.583 22.087 1214 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.00 % Allowed : 25.00 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.26), residues: 1134 helix: 1.37 (0.19), residues: 764 sheet: 0.58 (0.84), residues: 46 loop : -3.11 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 520 HIS 0.002 0.000 HIS B 144 PHE 0.023 0.001 PHE B 448 TYR 0.013 0.001 TYR B 377 ARG 0.004 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: B 51 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6973 (mt) REVERT: B 52 LEU cc_start: 0.8046 (tp) cc_final: 0.7810 (tp) REVERT: B 133 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8033 (tp) REVERT: B 229 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B 259 ILE cc_start: 0.7854 (tt) cc_final: 0.7526 (tp) REVERT: B 294 PHE cc_start: 0.5342 (OUTLIER) cc_final: 0.4758 (t80) REVERT: B 335 MET cc_start: 0.7589 (mmm) cc_final: 0.6604 (mtp) REVERT: B 440 MET cc_start: 0.7870 (tpt) cc_final: 0.7436 (tpp) REVERT: B 573 ARG cc_start: 0.7373 (ptt180) cc_final: 0.6397 (tmt170) REVERT: B 579 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6415 (t-90) REVERT: A 51 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6935 (mt) REVERT: A 133 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 143 TYR cc_start: 0.7265 (p90) cc_final: 0.7063 (p90) REVERT: A 229 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8292 (pp) REVERT: A 292 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: A 294 PHE cc_start: 0.5588 (OUTLIER) cc_final: 0.5115 (t80) REVERT: A 335 MET cc_start: 0.7520 (mmm) cc_final: 0.6533 (mtp) REVERT: A 440 MET cc_start: 0.7744 (tpp) cc_final: 0.7152 (mmt) REVERT: A 573 ARG cc_start: 0.7346 (ptt180) cc_final: 0.6954 (mmm160) REVERT: A 579 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6262 (t-90) outliers start: 48 outliers final: 31 residues processed: 176 average time/residue: 0.1596 time to fit residues: 42.2378 Evaluate side-chains 170 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.0040 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131712 restraints weight = 13160.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.135727 restraints weight = 7819.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.137971 restraints weight = 5702.931| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9106 Z= 0.193 Angle : 0.669 11.322 12382 Z= 0.330 Chirality : 0.044 0.171 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.546 22.021 1214 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.69 % Allowed : 25.31 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.26), residues: 1134 helix: 1.33 (0.19), residues: 772 sheet: 0.56 (0.84), residues: 46 loop : -3.38 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 520 HIS 0.002 0.001 HIS A 144 PHE 0.023 0.001 PHE B 448 TYR 0.015 0.001 TYR B 95 ARG 0.001 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: B 51 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6997 (mt) REVERT: B 52 LEU cc_start: 0.8056 (tp) cc_final: 0.7820 (tp) REVERT: B 133 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8010 (tp) REVERT: B 229 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8360 (pp) REVERT: B 259 ILE cc_start: 0.7877 (tt) cc_final: 0.7538 (tp) REVERT: B 294 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.4897 (t80) REVERT: B 335 MET cc_start: 0.7628 (mmm) cc_final: 0.6697 (mtp) REVERT: B 440 MET cc_start: 0.7894 (tpt) cc_final: 0.7450 (tpp) REVERT: B 573 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6403 (tmt170) REVERT: B 579 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6464 (t-90) REVERT: A 51 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6934 (mt) REVERT: A 133 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 143 TYR cc_start: 0.7252 (p90) cc_final: 0.6987 (p90) REVERT: A 229 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8283 (pp) REVERT: A 259 ILE cc_start: 0.7847 (tt) cc_final: 0.7524 (tp) REVERT: A 292 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: A 294 PHE cc_start: 0.5697 (OUTLIER) cc_final: 0.5220 (t80) REVERT: A 335 MET cc_start: 0.7496 (mmm) cc_final: 0.6501 (mtp) REVERT: A 440 MET cc_start: 0.7674 (tpp) cc_final: 0.7071 (mmt) REVERT: A 445 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7487 (tt) REVERT: A 573 ARG cc_start: 0.7357 (ptt180) cc_final: 0.6919 (mmm160) REVERT: A 579 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.6473 (t-90) outliers start: 45 outliers final: 32 residues processed: 172 average time/residue: 0.1630 time to fit residues: 42.2835 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 68 optimal weight: 0.0050 chunk 52 optimal weight: 30.0000 chunk 100 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127187 restraints weight = 12458.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131460 restraints weight = 7226.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134272 restraints weight = 5157.983| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9106 Z= 0.177 Angle : 0.651 11.333 12382 Z= 0.320 Chirality : 0.043 0.159 1492 Planarity : 0.005 0.046 1508 Dihedral : 4.443 21.956 1214 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.10 % Allowed : 25.10 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.26), residues: 1134 helix: 1.43 (0.19), residues: 770 sheet: 0.62 (0.84), residues: 46 loop : -3.39 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 520 HIS 0.002 0.000 HIS A 144 PHE 0.023 0.001 PHE B 448 TYR 0.012 0.001 TYR A 377 ARG 0.000 0.000 ARG A 587 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: B 133 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.7851 (tp) REVERT: B 229 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8472 (pp) REVERT: B 259 ILE cc_start: 0.7840 (tt) cc_final: 0.7506 (tp) REVERT: B 294 PHE cc_start: 0.5561 (OUTLIER) cc_final: 0.4885 (t80) REVERT: B 335 MET cc_start: 0.7658 (mmm) cc_final: 0.6653 (mtp) REVERT: B 404 TRP cc_start: 0.6550 (t60) cc_final: 0.6345 (t60) REVERT: B 440 MET cc_start: 0.7799 (tpt) cc_final: 0.7354 (tpp) REVERT: B 573 ARG cc_start: 0.7421 (ptt180) cc_final: 0.6418 (tmt170) REVERT: B 579 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.6413 (t-90) REVERT: A 51 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6782 (mt) REVERT: A 133 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.7915 (tp) REVERT: A 143 TYR cc_start: 0.7383 (p90) cc_final: 0.7107 (p90) REVERT: A 229 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8418 (pp) REVERT: A 292 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: A 294 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5279 (t80) REVERT: A 335 MET cc_start: 0.7619 (mmm) cc_final: 0.6594 (mtp) REVERT: A 404 TRP cc_start: 0.6671 (t60) cc_final: 0.6417 (t60) REVERT: A 440 MET cc_start: 0.7613 (tpp) cc_final: 0.7031 (mmt) REVERT: A 445 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7493 (tt) REVERT: A 520 TRP cc_start: 0.7074 (t60) cc_final: 0.6866 (t60) REVERT: A 573 ARG cc_start: 0.7403 (ptt180) cc_final: 0.6916 (mmm160) REVERT: A 579 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6330 (t-90) REVERT: A 597 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7828 (ttm) outliers start: 49 outliers final: 29 residues processed: 174 average time/residue: 0.1560 time to fit residues: 41.2680 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 TYR Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 579 HIS Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 294 PHE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 598 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 102 optimal weight: 0.0030 chunk 99 optimal weight: 0.9980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.172001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132310 restraints weight = 13122.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136423 restraints weight = 7609.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139113 restraints weight = 5466.808| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9106 Z= 0.189 Angle : 0.666 11.058 12382 Z= 0.325 Chirality : 0.043 0.164 1492 Planarity : 0.005 0.047 1508 Dihedral : 4.435 21.864 1214 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.69 % Allowed : 25.94 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.26), residues: 1134 helix: 1.43 (0.19), residues: 768 sheet: 0.76 (0.84), residues: 46 loop : -3.41 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 520 HIS 0.002 0.001 HIS A 144 PHE 0.024 0.001 PHE B 448 TYR 0.013 0.001 TYR B 377 ARG 0.001 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.36 seconds wall clock time: 46 minutes 39.66 seconds (2799.66 seconds total)