Starting phenix.real_space_refine on Wed Feb 12 17:34:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7axz_11933/02_2025/7axz_11933.cif Found real_map, /net/cci-nas-00/data/ceres_data/7axz_11933/02_2025/7axz_11933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7axz_11933/02_2025/7axz_11933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7axz_11933/02_2025/7axz_11933.map" model { file = "/net/cci-nas-00/data/ceres_data/7axz_11933/02_2025/7axz_11933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7axz_11933/02_2025/7axz_11933.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 5266 2.51 5 N 1389 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8225 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4033 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4192 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 25, 'TRANS': 498} Chain breaks: 3 Time building chain proxies: 4.80, per 1000 atoms: 0.58 Number of scatterers: 8225 At special positions: 0 Unit cell: (97.464, 86.984, 119.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1529 8.00 N 1389 7.00 C 5266 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: 2.18 Conformation dependent library (CDL) restraints added in 1.2 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 34.2% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 58 through 77 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.532A pdb=" N MET A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.238A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.620A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.563A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.625A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.680A pdb=" N GLN A 484 " --> pdb=" O ASN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.631A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.540A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.539A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.707A pdb=" N LEU B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.963A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.776A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 106 removed outlier: 6.364A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP A 36 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA A 84 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 38 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 41 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 4.731A pdb=" N PHE A 410 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 345 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.459A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.232A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 253 removed outlier: 5.461A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 314 hydrogen bonds defined for protein. 855 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: 2.17 Time building geometry restraints manager: 2.39 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: 2676 1.34 - 1.46: 1370 1.46 - 1.57: 4273 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 8388 Sorted by residual: bond pdb=" CA THR A 472 " pdb=" CB THR A 472 " ideal model delta sigma weight residual 1.526 1.467 0.060 1.76e-02 3.23e+03 1.14e+01 bond pdb=" C ASP A 342 " pdb=" N PRO A 343 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.11e-02 8.12e+03 6.68e+00 bond pdb=" CA TYR A 409 " pdb=" C TYR A 409 " ideal model delta sigma weight residual 1.526 1.499 0.027 1.36e-02 5.41e+03 3.84e+00 bond pdb=" C ARG B 271 " pdb=" N VAL B 272 " ideal model delta sigma weight residual 1.334 1.310 0.024 1.24e-02 6.50e+03 3.60e+00 bond pdb=" CB PRO A 438 " pdb=" CG PRO A 438 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.56e+00 ... (remaining 8383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10428 1.49 - 2.98: 736 2.98 - 4.47: 112 4.47 - 5.96: 23 5.96 - 7.45: 7 Bond angle restraints: 11306 Sorted by residual: angle pdb=" N LEU A 337 " pdb=" CA LEU A 337 " pdb=" C LEU A 337 " ideal model delta sigma weight residual 112.72 105.91 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" N ARG A 339 " pdb=" CA ARG A 339 " pdb=" CB ARG A 339 " ideal model delta sigma weight residual 109.51 116.70 -7.19 1.58e+00 4.01e-01 2.07e+01 angle pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " pdb=" NE ARG A 339 " ideal model delta sigma weight residual 112.00 119.45 -7.45 2.20e+00 2.07e-01 1.15e+01 angle pdb=" CA LYS A 338 " pdb=" C LYS A 338 " pdb=" N ARG A 339 " ideal model delta sigma weight residual 116.84 122.56 -5.72 1.71e+00 3.42e-01 1.12e+01 angle pdb=" C GLN B 510 " pdb=" N HIS B 511 " pdb=" CA HIS B 511 " ideal model delta sigma weight residual 120.72 115.21 5.51 1.67e+00 3.59e-01 1.09e+01 ... (remaining 11301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4612 17.91 - 35.81: 468 35.81 - 53.72: 79 53.72 - 71.62: 11 71.62 - 89.53: 11 Dihedral angle restraints: 5181 sinusoidal: 2183 harmonic: 2998 Sorted by residual: dihedral pdb=" CA MET B 389 " pdb=" C MET B 389 " pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLU A 336 " pdb=" C GLU A 336 " pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 715 0.037 - 0.073: 368 0.073 - 0.110: 118 0.110 - 0.147: 43 0.147 - 0.183: 20 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CA THR B 479 " pdb=" N THR B 479 " pdb=" C THR B 479 " pdb=" CB THR B 479 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB VAL B 393 " pdb=" CA VAL B 393 " pdb=" CG1 VAL B 393 " pdb=" CG2 VAL B 393 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1261 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 165 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 166 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 450 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.18e+00 pdb=" C GLN B 450 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN B 450 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 451 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 283 " 0.041 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO A 284 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " 0.033 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 88 2.51 - 3.11: 6623 3.11 - 3.70: 12008 3.70 - 4.30: 17374 4.30 - 4.90: 29268 Nonbonded interactions: 65361 Sorted by model distance: nonbonded pdb=" OH TYR A 274 " pdb=" OE2 GLU A 371 " model vdw 1.911 3.040 nonbonded pdb=" OE1 GLU A 491 " pdb=" OH TYR B 316 " model vdw 1.987 3.040 nonbonded pdb=" OH TYR A 409 " pdb=" OE1 GLN B 269 " model vdw 2.033 3.040 nonbonded pdb=" OE1 GLN B 509 " pdb=" NE2 HIS B 511 " model vdw 2.097 3.120 nonbonded pdb=" NH2 ARG A 325 " pdb=" O ALA B 498 " model vdw 2.128 3.120 ... (remaining 65356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.009 0.094 8388 Z= 0.583 Angle : 0.871 7.448 11306 Z= 0.493 Chirality : 0.052 0.183 1264 Planarity : 0.006 0.063 1456 Dihedral : 14.876 89.529 3227 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -2.73 (0.25), residues: 1011 helix: -0.89 (0.27), residues: 315 sheet: -2.20 (0.40), residues: 155 loop : -2.29 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 276 HIS 0.006 0.002 HIS B 120 PHE 0.020 0.003 PHE A 471 TYR 0.028 0.003 TYR A 400 ARG 0.011 0.001 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.7074 (mmt) cc_final: 0.6819 (mmt) REVERT: A 265 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7168 (mmtt) REVERT: B 40 MET cc_start: 0.7512 (ttp) cc_final: 0.7291 (ttm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2426 time to fit residues: 31.5009 Evaluate side-chains 61 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 0.0670 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 33 GLN B 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.114575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.093596 restraints weight = 19242.519| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.01 r_work: 0.3551 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8388 Z= 0.182 Angle : 0.607 8.152 11306 Z= 0.312 Chirality : 0.043 0.154 1264 Planarity : 0.005 0.055 1456 Dihedral : 5.115 24.726 1094 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.76 % Allowed : 5.96 % Favored : 93.28 % 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: -1.65 (0.26), residues: 1011 helix: 0.29 (0.29), residues: 314 sheet: -1.44 (0.39), residues: 166 loop : -1.86 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 247 HIS 0.004 0.001 HIS B 188 PHE 0.016 0.001 PHE A 487 TYR 0.011 0.001 TYR A 400 ARG 0.007 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8452 (mp) cc_final: 0.8107 (mt) REVERT: A 102 ILE cc_start: 0.8721 (mm) cc_final: 0.8407 (mt) REVERT: A 265 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7252 (mmtt) REVERT: B 78 THR cc_start: 0.7619 (m) cc_final: 0.7380 (t) REVERT: B 210 MET cc_start: 0.8324 (ttm) cc_final: 0.7959 (tmm) REVERT: B 474 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5607 (pm20) outliers start: 7 outliers final: 0 residues processed: 101 average time/residue: 0.1865 time to fit residues: 27.1076 Evaluate side-chains 76 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 131 HIS B 450 GLN B 527 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.112335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091020 restraints weight = 19650.358| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.03 r_work: 0.3489 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8388 Z= 0.308 Angle : 0.617 9.251 11306 Z= 0.311 Chirality : 0.044 0.145 1264 Planarity : 0.005 0.059 1456 Dihedral : 4.953 20.015 1094 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.52 % Allowed : 9.97 % Favored : 88.52 % 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: -1.52 (0.26), residues: 1011 helix: 0.27 (0.29), residues: 316 sheet: -1.27 (0.39), residues: 166 loop : -1.74 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 247 HIS 0.004 0.001 HIS A 204 PHE 0.040 0.002 PHE B 59 TYR 0.015 0.002 TYR A 400 ARG 0.004 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8770 (mm) cc_final: 0.8451 (mt) REVERT: A 265 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7390 (mmtt) REVERT: B 15 ASP cc_start: 0.7215 (t70) cc_final: 0.6736 (t0) REVERT: B 210 MET cc_start: 0.8441 (ttm) cc_final: 0.8088 (tmm) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.1776 time to fit residues: 23.5934 Evaluate side-chains 83 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 414 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.114660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093587 restraints weight = 19094.248| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.99 r_work: 0.3536 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8388 Z= 0.178 Angle : 0.537 7.847 11306 Z= 0.271 Chirality : 0.042 0.143 1264 Planarity : 0.004 0.060 1456 Dihedral : 4.521 18.600 1094 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.73 % Allowed : 11.70 % Favored : 86.57 % 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: -1.03 (0.26), residues: 1011 helix: 0.65 (0.29), residues: 317 sheet: -0.88 (0.40), residues: 165 loop : -1.46 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 247 HIS 0.004 0.001 HIS B 188 PHE 0.024 0.001 PHE B 59 TYR 0.010 0.001 TYR A 400 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8751 (mm) cc_final: 0.8444 (mt) REVERT: A 135 MET cc_start: 0.6238 (tpp) cc_final: 0.5948 (tpp) REVERT: A 265 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7395 (mmtt) REVERT: B 15 ASP cc_start: 0.6876 (t70) cc_final: 0.6554 (t0) REVERT: B 206 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7947 (mm-30) REVERT: B 210 MET cc_start: 0.8366 (ttm) cc_final: 0.7993 (tmm) REVERT: B 450 GLN cc_start: 0.5728 (mt0) cc_final: 0.5436 (mt0) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 0.1874 time to fit residues: 25.7441 Evaluate side-chains 88 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 393 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.111125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.089813 restraints weight = 19192.322| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.94 r_work: 0.3468 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8388 Z= 0.378 Angle : 0.645 11.036 11306 Z= 0.322 Chirality : 0.044 0.142 1264 Planarity : 0.005 0.061 1456 Dihedral : 4.885 19.306 1094 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.17 % Allowed : 13.33 % Favored : 84.51 % 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: -1.32 (0.26), residues: 1011 helix: 0.32 (0.28), residues: 317 sheet: -1.20 (0.39), residues: 172 loop : -1.52 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 247 HIS 0.004 0.001 HIS B 188 PHE 0.021 0.002 PHE B 345 TYR 0.015 0.002 TYR A 400 ARG 0.004 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8858 (mm) cc_final: 0.8545 (mt) REVERT: A 265 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7479 (mmtt) REVERT: A 288 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7951 (tp) REVERT: B 15 ASP cc_start: 0.7254 (t70) cc_final: 0.6843 (t0) REVERT: B 450 GLN cc_start: 0.5803 (mt0) cc_final: 0.5382 (mt0) REVERT: B 474 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5518 (pm20) outliers start: 20 outliers final: 13 residues processed: 88 average time/residue: 0.1730 time to fit residues: 22.9068 Evaluate side-chains 89 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 87 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 overall best weight: 2.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.112960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091757 restraints weight = 18954.839| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.95 r_work: 0.3504 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8388 Z= 0.231 Angle : 0.564 10.221 11306 Z= 0.281 Chirality : 0.042 0.139 1264 Planarity : 0.005 0.061 1456 Dihedral : 4.583 18.690 1094 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 13.33 % Favored : 84.62 % 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: -1.05 (0.26), residues: 1011 helix: 0.61 (0.29), residues: 318 sheet: -1.30 (0.38), residues: 177 loop : -1.29 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.021 0.002 PHE B 345 TYR 0.012 0.001 TYR A 400 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8872 (mm) cc_final: 0.8547 (mt) REVERT: A 265 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7475 (mmtt) REVERT: B 15 ASP cc_start: 0.7036 (t70) cc_final: 0.6636 (t0) REVERT: B 206 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 210 MET cc_start: 0.8381 (ttm) cc_final: 0.8027 (tmm) REVERT: B 450 GLN cc_start: 0.5527 (mt0) cc_final: 0.5280 (mt0) outliers start: 19 outliers final: 9 residues processed: 89 average time/residue: 0.1684 time to fit residues: 22.4666 Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.111786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.090003 restraints weight = 19319.163| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.02 r_work: 0.3486 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8388 Z= 0.275 Angle : 0.588 10.673 11306 Z= 0.293 Chirality : 0.042 0.138 1264 Planarity : 0.005 0.061 1456 Dihedral : 4.598 19.854 1094 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.17 % Allowed : 14.19 % Favored : 83.64 % 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: -1.05 (0.26), residues: 1011 helix: 0.61 (0.28), residues: 319 sheet: -1.21 (0.37), residues: 184 loop : -1.33 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 247 HIS 0.003 0.001 HIS B 131 PHE 0.023 0.002 PHE B 345 TYR 0.013 0.001 TYR A 400 ARG 0.003 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8846 (mm) cc_final: 0.8551 (mt) REVERT: A 265 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7578 (mmtt) REVERT: B 15 ASP cc_start: 0.7146 (t70) cc_final: 0.6813 (t0) REVERT: B 206 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 210 MET cc_start: 0.8397 (ttm) cc_final: 0.8029 (tmm) REVERT: B 474 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.5374 (pm20) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.1861 time to fit residues: 25.4820 Evaluate side-chains 90 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.110570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.088718 restraints weight = 19614.600| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.02 r_work: 0.3463 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8388 Z= 0.357 Angle : 0.646 12.209 11306 Z= 0.319 Chirality : 0.044 0.139 1264 Planarity : 0.005 0.060 1456 Dihedral : 4.849 20.922 1094 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.38 % Allowed : 14.63 % Favored : 82.99 % 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: -1.33 (0.26), residues: 1011 helix: 0.16 (0.27), residues: 334 sheet: -1.14 (0.38), residues: 178 loop : -1.48 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 247 HIS 0.004 0.001 HIS B 131 PHE 0.025 0.002 PHE B 345 TYR 0.015 0.002 TYR A 400 ARG 0.003 0.001 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8850 (mm) cc_final: 0.8596 (mt) REVERT: A 265 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7583 (mmtt) REVERT: B 206 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 474 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5442 (pm20) outliers start: 22 outliers final: 15 residues processed: 91 average time/residue: 0.1836 time to fit residues: 24.8694 Evaluate side-chains 87 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.111715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.090045 restraints weight = 19652.924| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.01 r_work: 0.3489 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8388 Z= 0.255 Angle : 0.602 11.126 11306 Z= 0.298 Chirality : 0.043 0.138 1264 Planarity : 0.005 0.060 1456 Dihedral : 4.664 19.703 1094 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.95 % Allowed : 15.06 % Favored : 82.99 % 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: -1.13 (0.26), residues: 1011 helix: 0.46 (0.28), residues: 329 sheet: -1.27 (0.38), residues: 183 loop : -1.34 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 247 HIS 0.003 0.001 HIS A 486 PHE 0.040 0.002 PHE B 59 TYR 0.012 0.001 TYR A 400 ARG 0.003 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8829 (mm) cc_final: 0.8555 (mt) REVERT: A 265 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7566 (mmtt) REVERT: B 206 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 247 TRP cc_start: 0.7080 (t60) cc_final: 0.6751 (t60) REVERT: B 474 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5362 (pm20) outliers start: 18 outliers final: 16 residues processed: 90 average time/residue: 0.1643 time to fit residues: 22.5112 Evaluate side-chains 93 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 GLN Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 0.0020 chunk 6 optimal weight: 9.9990 chunk 65 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 overall best weight: 0.8150 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.115027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.093671 restraints weight = 19061.821| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.97 r_work: 0.3556 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8388 Z= 0.154 Angle : 0.546 10.541 11306 Z= 0.269 Chirality : 0.041 0.143 1264 Planarity : 0.004 0.063 1456 Dihedral : 4.221 18.091 1094 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.41 % Allowed : 16.25 % Favored : 82.34 % 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: -0.69 (0.27), residues: 1011 helix: 0.99 (0.29), residues: 326 sheet: -1.05 (0.38), residues: 173 loop : -1.18 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 247 HIS 0.002 0.001 HIS B 188 PHE 0.037 0.001 PHE B 59 TYR 0.010 0.001 TYR A 400 ARG 0.003 0.000 ARG A 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8828 (mm) cc_final: 0.8529 (mt) REVERT: A 265 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7503 (mmtt) REVERT: B 20 MET cc_start: 0.6894 (mtp) cc_final: 0.6665 (ptp) REVERT: B 206 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 210 MET cc_start: 0.8475 (ttm) cc_final: 0.8001 (tmm) REVERT: B 474 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5341 (pm20) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 0.1804 time to fit residues: 26.3736 Evaluate side-chains 84 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 480 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094140 restraints weight = 19182.224| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.95 r_work: 0.3546 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8388 Z= 0.179 Angle : 0.572 10.356 11306 Z= 0.283 Chirality : 0.041 0.149 1264 Planarity : 0.005 0.064 1456 Dihedral : 4.200 17.049 1094 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 16.68 % Favored : 81.80 % 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: -0.65 (0.27), residues: 1011 helix: 1.03 (0.29), residues: 324 sheet: -1.01 (0.38), residues: 173 loop : -1.17 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 247 HIS 0.003 0.001 HIS B 382 PHE 0.032 0.002 PHE B 491 TYR 0.014 0.001 TYR B 395 ARG 0.004 0.000 ARG A 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.75 seconds wall clock time: 66 minutes 5.80 seconds (3965.80 seconds total)