Starting phenix.real_space_refine on Mon Feb 10 23:05:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2z_22014/02_2025/6x2z_22014.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2z_22014/02_2025/6x2z_22014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x2z_22014/02_2025/6x2z_22014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2z_22014/02_2025/6x2z_22014.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2z_22014/02_2025/6x2z_22014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2z_22014/02_2025/6x2z_22014.cif" } resolution = 3.03 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= 0.003 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 S 23 5.16 5 Na 3 4.78 5 C 2094 2.51 5 N 511 2.21 5 O 574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3205 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3202 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408} Chain breaks: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.80, per 1000 atoms: 0.87 Number of scatterers: 3205 At special positions: 0 Unit cell: (67.392, 67.392, 82.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 Na 3 11.00 O 574 8.00 N 511 7.00 C 2094 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: 0.70 Conformation dependent library (CDL) restraints added in 367.1 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 79.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.778A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.798A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.887A pdb=" N VAL A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.525A pdb=" N LEU A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.694A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.572A pdb=" N CYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.621A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.584A pdb=" N MET A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.092A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.894A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.679A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 4.204A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.503A pdb=" N TYR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.725A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.560A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.555A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.889A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 4.054A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.871A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.714A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.519A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.674A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 192 hydrogen bonds defined for protein. 567 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: 0.82 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 638 1.33 - 1.45: 651 1.45 - 1.57: 1917 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 3247 Sorted by residual: bond pdb=" N GLN A 122 " pdb=" CA GLN A 122 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 8.97e+00 bond pdb=" N VAL A 124 " pdb=" CA VAL A 124 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.10e+00 bond pdb=" C ASN A 451 " pdb=" O ASN A 451 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.23e+00 bond pdb=" N VAL A 450 " pdb=" CA VAL A 450 " ideal model delta sigma weight residual 1.460 1.433 0.026 1.21e-02 6.83e+03 4.73e+00 bond pdb=" C LEU A 453 " pdb=" O LEU A 453 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.17e-02 7.31e+03 4.67e+00 ... (remaining 3242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 4201 1.72 - 3.44: 164 3.44 - 5.15: 26 5.15 - 6.87: 7 6.87 - 8.59: 5 Bond angle restraints: 4403 Sorted by residual: angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 113.16 104.57 8.59 1.24e+00 6.50e-01 4.80e+01 angle pdb=" C GLY A 283 " pdb=" N LEU A 284 " pdb=" CA LEU A 284 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N ILE A 271 " pdb=" CA ILE A 271 " pdb=" C ILE A 271 " ideal model delta sigma weight residual 112.29 108.77 3.52 9.40e-01 1.13e+00 1.40e+01 angle pdb=" N GLN A 122 " pdb=" CA GLN A 122 " pdb=" C GLN A 122 " ideal model delta sigma weight residual 113.50 107.77 5.73 1.65e+00 3.67e-01 1.21e+01 angle pdb=" C THR A 121 " pdb=" N GLN A 122 " pdb=" CA GLN A 122 " ideal model delta sigma weight residual 120.17 125.31 -5.14 1.54e+00 4.22e-01 1.11e+01 ... (remaining 4398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 1671 15.57 - 31.13: 198 31.13 - 46.69: 58 46.69 - 62.25: 12 62.25 - 77.82: 7 Dihedral angle restraints: 1946 sinusoidal: 744 harmonic: 1202 Sorted by residual: dihedral pdb=" CA GLU A 272 " pdb=" C GLU A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR A 247 " pdb=" C THR A 247 " pdb=" N MET A 248 " pdb=" CA MET A 248 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 83 " pdb=" C ASP A 83 " pdb=" N SER A 84 " pdb=" CA SER A 84 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 468 0.067 - 0.135: 79 0.135 - 0.202: 7 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA ASP A 440 " pdb=" N ASP A 440 " pdb=" C ASP A 440 " pdb=" CB ASP A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN A 413 " pdb=" N GLN A 413 " pdb=" C GLN A 413 " pdb=" CB GLN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ASP A 368 " pdb=" N ASP A 368 " pdb=" C ASP A 368 " pdb=" CB ASP A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 555 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.08e+00 pdb=" N PRO A 302 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 121 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C THR A 121 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 121 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 122 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 337 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 338 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.031 5.00e-02 4.00e+02 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 78 2.69 - 3.24: 3006 3.24 - 3.79: 4910 3.79 - 4.35: 6687 4.35 - 4.90: 10760 Nonbonded interactions: 25441 Sorted by model distance: nonbonded pdb=" O ASN A 366 " pdb="NA NA A 601 " model vdw 2.131 2.470 nonbonded pdb=" O LYS A 16 " pdb=" OD1 ASN A 17 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.242 2.470 nonbonded pdb=" O ASP A 444 " pdb=" OG1 THR A 448 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR A 370 " pdb=" OD2 ASP A 600 " model vdw 2.318 3.040 ... (remaining 25436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3247 Z= 0.294 Angle : 0.835 8.589 4403 Z= 0.502 Chirality : 0.054 0.336 558 Planarity : 0.006 0.062 537 Dihedral : 15.506 77.817 1170 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 20.68 % Favored : 79.32 % 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: -5.65 (0.28), residues: 413 helix: -4.09 (0.16), residues: 296 sheet: -1.37 (1.46), residues: 18 loop : -1.95 (0.52), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.011 0.001 PHE A 159 TYR 0.011 0.001 TYR A 257 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.307 Fit side-chains REVERT: A 255 MET cc_start: 0.8606 (tpp) cc_final: 0.8163 (mmp) REVERT: A 352 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7944 (ttpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1211 time to fit residues: 10.7791 Evaluate side-chains 55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108700 restraints weight = 4666.867| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.21 r_work: 0.3114 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.153 Angle : 0.578 7.779 4403 Z= 0.306 Chirality : 0.039 0.133 558 Planarity : 0.005 0.040 537 Dihedral : 5.170 21.106 440 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.55 % Allowed : 20.96 % Favored : 76.49 % 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: -3.00 (0.36), residues: 413 helix: -1.85 (0.26), residues: 307 sheet: -0.66 (1.46), residues: 18 loop : -1.91 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 276 HIS 0.010 0.003 HIS A 296 PHE 0.013 0.001 PHE A 218 TYR 0.009 0.001 TYR A 51 ARG 0.004 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8215 (pmm) REVERT: A 255 MET cc_start: 0.9151 (tpp) cc_final: 0.8638 (mmp) REVERT: A 277 GLU cc_start: 0.8633 (tp30) cc_final: 0.8357 (tp30) REVERT: A 455 ASP cc_start: 0.8361 (m-30) cc_final: 0.7968 (m-30) outliers start: 9 outliers final: 2 residues processed: 65 average time/residue: 0.0880 time to fit residues: 8.1270 Evaluate side-chains 53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103370 restraints weight = 4652.271| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.30 r_work: 0.3114 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.153 Angle : 0.530 6.638 4403 Z= 0.278 Chirality : 0.040 0.154 558 Planarity : 0.004 0.033 537 Dihedral : 4.739 17.124 440 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.27 % Allowed : 24.08 % Favored : 73.65 % 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: -1.37 (0.41), residues: 413 helix: -0.56 (0.30), residues: 307 sheet: -0.33 (1.45), residues: 18 loop : -1.74 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.006 0.002 HIS A 296 PHE 0.014 0.001 PHE A 316 TYR 0.006 0.001 TYR A 285 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.383 Fit side-chains REVERT: A 205 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8233 (pmm) REVERT: A 255 MET cc_start: 0.9038 (tpp) cc_final: 0.8511 (mmp) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.0832 time to fit residues: 7.5552 Evaluate side-chains 60 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.103389 restraints weight = 4705.347| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.33 r_work: 0.3114 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3247 Z= 0.160 Angle : 0.515 6.971 4403 Z= 0.267 Chirality : 0.040 0.166 558 Planarity : 0.004 0.030 537 Dihedral : 4.511 16.199 440 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.40 % Allowed : 24.08 % Favored : 72.52 % 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: -0.71 (0.43), residues: 413 helix: -0.03 (0.31), residues: 308 sheet: -0.23 (1.46), residues: 18 loop : -1.70 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.005 0.002 HIS A 296 PHE 0.011 0.001 PHE A 218 TYR 0.005 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.398 Fit side-chains REVERT: A 205 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8247 (pmm) REVERT: A 248 MET cc_start: 0.9128 (tpp) cc_final: 0.8912 (mmm) REVERT: A 255 MET cc_start: 0.9002 (tpp) cc_final: 0.8497 (mmp) REVERT: A 277 GLU cc_start: 0.8789 (tp30) cc_final: 0.8319 (tp30) REVERT: A 284 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 286 MET cc_start: 0.7121 (mtp) cc_final: 0.6871 (mtp) outliers start: 12 outliers final: 5 residues processed: 68 average time/residue: 0.0846 time to fit residues: 8.1114 Evaluate side-chains 63 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 0.0670 chunk 9 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107612 restraints weight = 4655.120| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.18 r_work: 0.3196 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3247 Z= 0.164 Angle : 0.545 9.382 4403 Z= 0.271 Chirality : 0.040 0.170 558 Planarity : 0.003 0.028 537 Dihedral : 4.561 27.220 440 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.83 % Allowed : 24.93 % Favored : 72.24 % 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: -0.35 (0.43), residues: 413 helix: 0.27 (0.31), residues: 309 sheet: -0.25 (1.43), residues: 18 loop : -1.70 (0.62), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.004 0.001 HIS A 296 PHE 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.364 Fit side-chains REVERT: A 205 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8364 (pmm) REVERT: A 255 MET cc_start: 0.9016 (tpp) cc_final: 0.8571 (mmp) REVERT: A 284 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8100 (tt) REVERT: A 286 MET cc_start: 0.7303 (mtp) cc_final: 0.7042 (mtp) REVERT: A 372 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7980 (tp) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.0880 time to fit residues: 7.7146 Evaluate side-chains 66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109823 restraints weight = 4706.797| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.17 r_work: 0.3120 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3247 Z= 0.153 Angle : 0.534 8.583 4403 Z= 0.266 Chirality : 0.040 0.170 558 Planarity : 0.003 0.027 537 Dihedral : 4.470 28.104 440 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.83 % Allowed : 25.50 % Favored : 71.67 % 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: -0.06 (0.43), residues: 413 helix: 0.51 (0.32), residues: 308 sheet: -0.08 (1.44), residues: 18 loop : -1.77 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.004 0.001 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.008 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.294 Fit side-chains REVERT: A 255 MET cc_start: 0.8933 (tpp) cc_final: 0.8454 (mmp) REVERT: A 284 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7917 (tt) REVERT: A 419 MET cc_start: 0.9124 (tpt) cc_final: 0.8311 (tpt) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.0817 time to fit residues: 7.4101 Evaluate side-chains 61 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 9 optimal weight: 10.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110817 restraints weight = 4615.740| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.17 r_work: 0.3218 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.137 Angle : 0.525 7.561 4403 Z= 0.265 Chirality : 0.039 0.134 558 Planarity : 0.003 0.027 537 Dihedral : 4.428 30.051 440 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.12 % Allowed : 24.93 % Favored : 71.95 % 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: 0.17 (0.43), residues: 413 helix: 0.69 (0.31), residues: 308 sheet: 0.00 (1.43), residues: 18 loop : -1.71 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.009 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.345 Fit side-chains REVERT: A 255 MET cc_start: 0.8943 (tpp) cc_final: 0.8479 (mmp) REVERT: A 277 GLU cc_start: 0.8696 (tp30) cc_final: 0.8328 (tp30) REVERT: A 284 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7989 (tt) REVERT: A 316 PHE cc_start: 0.8039 (t80) cc_final: 0.7836 (t80) REVERT: A 329 MET cc_start: 0.8274 (mmt) cc_final: 0.8021 (mmp) REVERT: A 384 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7751 (mp) REVERT: A 419 MET cc_start: 0.9149 (tpt) cc_final: 0.8301 (tpt) REVERT: A 600 ASP cc_start: 0.8446 (t0) cc_final: 0.8211 (t70) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.0859 time to fit residues: 8.1031 Evaluate side-chains 68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 10 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112417 restraints weight = 4594.249| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.17 r_work: 0.3263 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3247 Z= 0.124 Angle : 0.516 7.249 4403 Z= 0.260 Chirality : 0.039 0.131 558 Planarity : 0.003 0.026 537 Dihedral : 4.350 30.818 440 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.27 % Allowed : 26.35 % Favored : 71.39 % 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: 0.40 (0.43), residues: 413 helix: 0.88 (0.31), residues: 308 sheet: -0.05 (1.35), residues: 18 loop : -1.71 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.010 0.001 PHE A 316 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.376 Fit side-chains REVERT: A 255 MET cc_start: 0.8907 (tpp) cc_final: 0.8489 (mmp) REVERT: A 277 GLU cc_start: 0.8641 (tp30) cc_final: 0.8243 (tp30) REVERT: A 284 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 329 MET cc_start: 0.8257 (mmt) cc_final: 0.8018 (mmp) REVERT: A 384 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7764 (mp) REVERT: A 419 MET cc_start: 0.9080 (tpt) cc_final: 0.8261 (tpt) REVERT: A 600 ASP cc_start: 0.8425 (t0) cc_final: 0.8196 (t70) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.0922 time to fit residues: 8.1421 Evaluate side-chains 63 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.110950 restraints weight = 4624.956| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.18 r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.139 Angle : 0.524 7.055 4403 Z= 0.264 Chirality : 0.039 0.133 558 Planarity : 0.003 0.025 537 Dihedral : 4.337 31.459 440 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.27 % Allowed : 25.21 % Favored : 72.52 % 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: 0.53 (0.42), residues: 413 helix: 0.97 (0.31), residues: 309 sheet: -0.37 (1.29), residues: 18 loop : -1.60 (0.59), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.017 0.001 PHE A 316 TYR 0.013 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.524 Fit side-chains REVERT: A 255 MET cc_start: 0.8938 (tpp) cc_final: 0.8541 (mmp) REVERT: A 277 GLU cc_start: 0.8601 (tp30) cc_final: 0.8166 (tp30) REVERT: A 284 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7982 (tt) REVERT: A 329 MET cc_start: 0.8241 (mmt) cc_final: 0.8027 (mmp) REVERT: A 384 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 419 MET cc_start: 0.9119 (tpt) cc_final: 0.8307 (tpt) REVERT: A 600 ASP cc_start: 0.8425 (t0) cc_final: 0.8223 (t70) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.0979 time to fit residues: 8.5242 Evaluate side-chains 63 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108805 restraints weight = 4559.695| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.15 r_work: 0.3146 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3247 Z= 0.183 Angle : 0.555 8.145 4403 Z= 0.278 Chirality : 0.040 0.132 558 Planarity : 0.003 0.027 537 Dihedral : 4.404 31.141 440 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.55 % Allowed : 24.93 % Favored : 72.52 % 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: 0.48 (0.42), residues: 413 helix: 0.94 (0.31), residues: 309 sheet: -0.61 (1.27), residues: 18 loop : -1.59 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.018 0.001 PHE A 316 TYR 0.012 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.342 Fit side-chains REVERT: A 277 GLU cc_start: 0.8590 (tp30) cc_final: 0.8092 (tp30) REVERT: A 284 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 384 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (mp) REVERT: A 419 MET cc_start: 0.9162 (tpt) cc_final: 0.8226 (tpt) outliers start: 9 outliers final: 5 residues processed: 61 average time/residue: 0.0909 time to fit residues: 7.6978 Evaluate side-chains 62 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109937 restraints weight = 4651.881| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.15 r_work: 0.3130 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3247 Z= 0.182 Angle : 0.582 8.499 4403 Z= 0.291 Chirality : 0.040 0.139 558 Planarity : 0.003 0.028 537 Dihedral : 4.421 30.503 440 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.27 % Allowed : 25.50 % Favored : 72.24 % 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: 0.63 (0.43), residues: 413 helix: 1.06 (0.31), residues: 309 sheet: -0.58 (1.27), residues: 18 loop : -1.54 (0.60), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.018 0.001 PHE A 316 TYR 0.007 0.001 TYR A 97 ARG 0.002 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2227.98 seconds wall clock time: 40 minutes 14.18 seconds (2414.18 seconds total)