Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:12:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/11_2022/6x2z_22014.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/11_2022/6x2z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/11_2022/6x2z_22014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/11_2022/6x2z_22014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/11_2022/6x2z_22014.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/11_2022/6x2z_22014.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3205 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3205 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 600 "'] Classifications: {'peptide': 420, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408, None: 3} Not linked: pdbres="ASP A 600 " pdbres=" NA A 601 " Not linked: pdbres=" NA A 601 " pdbres=" NA A 602 " Not linked: pdbres=" NA A 602 " pdbres=" NA A 603 " Chain breaks: 3 Time building chain proxies: 2.51, per 1000 atoms: 0.78 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 524.7 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: 0.16 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: 0.85 Time building geometry restraints manager: 1.27 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: 99.68 - 106.54: 69 106.54 - 113.39: 1868 113.39 - 120.24: 1232 120.24 - 127.10: 1215 127.10 - 133.95: 19 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 2.440 nonbonded pdb=" OG1 THR A 370 " pdb=" OD2 ASP A 600 " model vdw 2.318 2.440 ... (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 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. 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.190 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1100 time to fit residues: 9.8723 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4751 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 3247 Z= 0.141 Angle : 0.565 7.805 4403 Z= 0.299 Chirality : 0.039 0.133 558 Planarity : 0.005 0.042 537 Dihedral : 5.114 22.266 440 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 2.27 % 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: -3.12 (0.36), residues: 413 helix: -1.94 (0.25), residues: 307 sheet: -0.67 (1.47), residues: 18 loop : -1.96 (0.59), residues: 88 *********************** 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 71 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.347 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 69 average time/residue: 0.0840 time to fit residues: 8.0997 Evaluate side-chains 53 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0320 time to fit residues: 0.5959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2454 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= 0.193 Angle : 0.556 6.145 4403 Z= 0.288 Chirality : 0.041 0.155 558 Planarity : 0.004 0.035 537 Dihedral : 4.806 19.574 440 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 1.70 % 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: -1.53 (0.40), residues: 413 helix: -0.67 (0.29), residues: 307 sheet: -0.37 (1.46), residues: 18 loop : -1.79 (0.60), residues: 88 *********************** 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 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.389 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.0880 time to fit residues: 7.1234 Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0436 time to fit residues: 0.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.0050 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 33 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3247 Z= 0.112 Angle : 0.498 7.193 4403 Z= 0.256 Chirality : 0.039 0.172 558 Planarity : 0.003 0.031 537 Dihedral : 4.398 20.291 440 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.42 % 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: -0.74 (0.42), residues: 413 helix: -0.01 (0.31), residues: 306 sheet: -0.48 (1.42), residues: 18 loop : -1.79 (0.59), residues: 89 *********************** 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 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.377 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 69 average time/residue: 0.0981 time to fit residues: 9.2119 Evaluate side-chains 55 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0330 time to fit residues: 0.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 3247 Z= 0.183 Angle : 0.535 6.823 4403 Z= 0.272 Chirality : 0.041 0.160 558 Planarity : 0.003 0.028 537 Dihedral : 4.401 16.784 440 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.42 % 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: -0.33 (0.42), residues: 413 helix: 0.28 (0.31), residues: 308 sheet: -0.32 (1.41), residues: 18 loop : -1.68 (0.61), residues: 87 *********************** 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 59 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.345 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 58 average time/residue: 0.0876 time to fit residues: 7.1808 Evaluate side-chains 58 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0410 time to fit residues: 0.7153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2936 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 9.306 4403 Z= 0.261 Chirality : 0.040 0.171 558 Planarity : 0.003 0.026 537 Dihedral : 4.270 16.661 440 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.43), residues: 413 helix: 0.55 (0.31), residues: 307 sheet: -0.30 (1.38), residues: 18 loop : -1.74 (0.60), residues: 88 *********************** 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 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.376 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.0900 time to fit residues: 7.6074 Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0446 time to fit residues: 0.6673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3247 Z= 0.168 Angle : 0.540 8.988 4403 Z= 0.271 Chirality : 0.040 0.120 558 Planarity : 0.003 0.026 537 Dihedral : 4.300 16.895 440 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 1.13 % 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: 0.15 (0.43), residues: 413 helix: 0.68 (0.31), residues: 308 sheet: -0.24 (1.38), residues: 18 loop : -1.65 (0.60), residues: 87 *********************** 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 60 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.383 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 57 average time/residue: 0.1050 time to fit residues: 8.3111 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0332 time to fit residues: 0.5699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3247 Z= 0.196 Angle : 0.552 8.486 4403 Z= 0.277 Chirality : 0.040 0.143 558 Planarity : 0.003 0.028 537 Dihedral : 4.308 17.497 440 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.57 % 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: 0.23 (0.43), residues: 413 helix: 0.73 (0.31), residues: 308 sheet: -0.28 (1.37), residues: 18 loop : -1.62 (0.61), residues: 87 *********************** 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 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.383 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 55 average time/residue: 0.0938 time to fit residues: 7.2146 Evaluate side-chains 55 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0551 time to fit residues: 0.6207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3130 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= 0.131 Angle : 0.525 8.094 4403 Z= 0.261 Chirality : 0.039 0.134 558 Planarity : 0.003 0.026 537 Dihedral : 4.161 16.190 440 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.43), residues: 413 helix: 0.97 (0.31), residues: 307 sheet: -0.19 (1.34), residues: 18 loop : -1.66 (0.59), residues: 88 *********************** 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 60 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.378 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.1176 time to fit residues: 8.8614 Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0447 time to fit residues: 0.6883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3084 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= 0.189 Angle : 0.571 8.438 4403 Z= 0.282 Chirality : 0.040 0.141 558 Planarity : 0.003 0.027 537 Dihedral : 4.225 17.260 440 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.57 % 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: 0.54 (0.42), residues: 413 helix: 0.96 (0.31), residues: 309 sheet: -0.28 (1.33), residues: 18 loop : -1.52 (0.60), residues: 86 ********************** 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 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.405 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.0948 time to fit residues: 7.1174 Evaluate side-chains 54 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0360 time to fit residues: 0.6498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 41 optimal weight: 2.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.146451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111017 restraints weight = 4563.932| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.14 r_work: 0.3260 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work: 0.3237 rms_B_bonded: 1.94 restraints_weight: 0.1250 r_work: 0.3226 rms_B_bonded: 2.00 restraints_weight: 0.0625 r_work: 0.3214 rms_B_bonded: 2.09 restraints_weight: 0.0312 r_work: 0.3201 rms_B_bonded: 2.20 restraints_weight: 0.0156 r_work: 0.3188 rms_B_bonded: 2.35 restraints_weight: 0.0078 r_work: 0.3174 rms_B_bonded: 2.52 restraints_weight: 0.0039 r_work: 0.3160 rms_B_bonded: 2.72 restraints_weight: 0.0020 r_work: 0.3144 rms_B_bonded: 2.95 restraints_weight: 0.0010 r_work: 0.3127 rms_B_bonded: 3.22 restraints_weight: 0.0005 r_work: 0.3109 rms_B_bonded: 3.52 restraints_weight: 0.0002 r_work: 0.3090 rms_B_bonded: 3.86 restraints_weight: 0.0001 r_work: 0.3069 rms_B_bonded: 4.25 restraints_weight: 0.0001 r_work: 0.3047 rms_B_bonded: 4.69 restraints_weight: 0.0000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3161 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= 0.156 Angle : 0.556 8.585 4403 Z= 0.274 Chirality : 0.039 0.142 558 Planarity : 0.003 0.026 537 Dihedral : 4.172 16.299 440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.57 % 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: 0.73 (0.42), residues: 413 helix: 1.10 (0.31), residues: 308 sheet: -0.20 (1.32), residues: 18 loop : -1.43 (0.60), residues: 87 =============================================================================== Job complete usr+sys time: 1006.31 seconds wall clock time: 18 minutes 51.05 seconds (1131.05 seconds total)