Starting phenix.real_space_refine on Fri Apr 5 17:54:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wfk_37494/04_2024/8wfk_37494_updated.pdb" } resolution = 3.22 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= 0.044 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: 7 Type Number sf(0) Gaussians S 35 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 2918 2.51 5 N 683 2.21 5 O 728 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 4371 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4341 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 25, 'TRANS': 520} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CL': 1, ' NA': 2, 'W5O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.03, per 1000 atoms: 0.69 Number of scatterers: 4371 At special positions: 0 Unit cell: (84.15, 73.1, 86.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 2 17.00 S 35 16.00 Na 2 11.00 F 3 9.00 O 728 8.00 N 683 7.00 C 2918 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 239 " distance=1.13 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 175 " distance=1.09 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: 1.65 Conformation dependent library (CDL) restraints added in 796.2 milliseconds 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 994 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 0 sheets defined 62.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.885A pdb=" N ILE A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 122 through 140 removed outlier: 4.124A pdb=" N GLY A 126 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 132 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 134 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 138 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.698A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.544A pdb=" N CYS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 removed outlier: 4.093A pdb=" N SER A 258 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLY A 259 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.539A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.955A pdb=" N ALA A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.711A pdb=" N SER A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.800A pdb=" N SER A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.784A pdb=" N ILE A 363 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 386 No H-bonds generated for 'chain 'A' and resid 383 through 386' Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.631A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 434 removed outlier: 3.638A pdb=" N LEU A 405 " --> pdb=" O PRO A 401 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N CYS A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 441 No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 443 through 458 removed outlier: 3.548A pdb=" N ALA A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 457 " --> pdb=" O ALA A 453 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 473 removed outlier: 4.746A pdb=" N ILE A 467 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR A 468 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 471 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 472 " --> pdb=" O TRP A 469 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 473 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 removed outlier: 4.341A pdb=" N SER A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 482 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N VAL A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 3.840A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 525 through 539 removed outlier: 3.641A pdb=" N VAL A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 578 Processing helix chain 'A' and resid 586 through 591 175 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 637 1.31 - 1.44: 1397 1.44 - 1.56: 2421 1.56 - 1.69: 0 1.69 - 1.82: 54 Bond restraints: 4509 Sorted by residual: bond pdb=" C PRO A 296 " pdb=" O PRO A 296 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.06e-02 8.90e+03 6.89e+00 bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.35e-02 5.49e+03 4.89e+00 bond pdb=" N PRO A 296 " pdb=" CA PRO A 296 " ideal model delta sigma weight residual 1.470 1.443 0.027 1.23e-02 6.61e+03 4.86e+00 bond pdb=" N CYS A 239 " pdb=" CA CYS A 239 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.21e-02 6.83e+03 4.09e+00 bond pdb=" C CYS A 147 " pdb=" O CYS A 147 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.16e-02 7.43e+03 3.79e+00 ... (remaining 4504 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 135 106.37 - 113.29: 2303 113.29 - 120.20: 1753 120.20 - 127.12: 1894 127.12 - 134.04: 65 Bond angle restraints: 6150 Sorted by residual: angle pdb=" N PRO A 296 " pdb=" CA PRO A 296 " pdb=" C PRO A 296 " ideal model delta sigma weight residual 110.55 117.00 -6.45 1.63e+00 3.76e-01 1.57e+01 angle pdb=" CA CYS A 147 " pdb=" C CYS A 147 " pdb=" N ILE A 148 " ideal model delta sigma weight residual 117.17 121.08 -3.91 1.18e+00 7.18e-01 1.10e+01 angle pdb=" CA CYS A 147 " pdb=" C CYS A 147 " pdb=" O CYS A 147 " ideal model delta sigma weight residual 120.70 117.40 3.30 1.03e+00 9.43e-01 1.03e+01 angle pdb=" CA CYS A 239 " pdb=" C CYS A 239 " pdb=" O CYS A 239 " ideal model delta sigma weight residual 120.55 117.22 3.33 1.06e+00 8.90e-01 9.88e+00 angle pdb=" N CYS A 239 " pdb=" CA CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sigma weight residual 110.12 114.69 -4.57 1.47e+00 4.63e-01 9.66e+00 ... (remaining 6145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 2178 17.64 - 35.28: 276 35.28 - 52.92: 66 52.92 - 70.55: 13 70.55 - 88.19: 9 Dihedral angle restraints: 2542 sinusoidal: 970 harmonic: 1572 Sorted by residual: dihedral pdb=" CB CYS A 147 " pdb=" SG CYS A 147 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 6.64 86.36 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CB CYS A 166 " pdb=" SG CYS A 166 " pdb=" SG CYS A 175 " pdb=" CB CYS A 175 " ideal model delta sinusoidal sigma weight residual 93.00 159.25 -66.25 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CA TRP A 322 " pdb=" C TRP A 322 " pdb=" N GLY A 323 " pdb=" CA GLY A 323 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 465 0.038 - 0.075: 165 0.075 - 0.113: 40 0.113 - 0.150: 4 0.150 - 0.188: 2 Chirality restraints: 676 Sorted by residual: chirality pdb=" CA CYS A 147 " pdb=" N CYS A 147 " pdb=" C CYS A 147 " pdb=" CB CYS A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ASP A 474 " pdb=" N ASP A 474 " pdb=" C ASP A 474 " pdb=" CB ASP A 474 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 673 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 209 " 0.040 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO A 210 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 146 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.77e+00 pdb=" C ILE A 146 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 146 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 238 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C GLY A 238 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 238 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS A 239 " -0.011 2.00e-02 2.50e+03 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 83 2.69 - 3.24: 4076 3.24 - 3.79: 6423 3.79 - 4.35: 8514 4.35 - 4.90: 14445 Nonbonded interactions: 33541 Sorted by model distance: nonbonded pdb=" O VAL A 64 " pdb="NA NA A 704 " model vdw 2.137 2.470 nonbonded pdb=" OH TYR A 316 " pdb=" O SER A 479 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR A 172 " pdb=" OE2 GLU A 213 " model vdw 2.262 2.440 nonbonded pdb=" O LEU A 414 " pdb="NA NA A 704 " model vdw 2.297 2.470 nonbonded pdb=" O TYR A 218 " pdb=" NH1 ARG A 233 " model vdw 2.312 2.520 ... (remaining 33536 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: 1.410 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: 3.820 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.130 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.003 0.046 4509 Z= 0.167 Angle : 0.606 7.229 6150 Z= 0.340 Chirality : 0.041 0.188 676 Planarity : 0.005 0.059 753 Dihedral : 16.995 88.191 1542 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 26.90 % Favored : 73.10 % 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: -1.97 (0.35), residues: 542 helix: -0.85 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.005 0.001 HIS A 381 PHE 0.014 0.001 PHE A 366 TYR 0.016 0.001 TYR A 77 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8355 (mttt) cc_final: 0.7203 (tttt) REVERT: A 367 MET cc_start: 0.7052 (tpt) cc_final: 0.6670 (tpt) REVERT: A 452 VAL cc_start: 0.8345 (p) cc_final: 0.8096 (t) REVERT: A 475 ASN cc_start: 0.8647 (m-40) cc_final: 0.8325 (t0) REVERT: A 531 PHE cc_start: 0.7916 (t80) cc_final: 0.7625 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1777 time to fit residues: 16.1658 Evaluate side-chains 61 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4509 Z= 0.163 Angle : 0.558 6.600 6150 Z= 0.275 Chirality : 0.040 0.112 676 Planarity : 0.005 0.052 753 Dihedral : 6.786 83.143 608 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.60 % Allowed : 27.11 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.36), residues: 542 helix: -0.48 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -1.98 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.005 0.001 HIS A 381 PHE 0.008 0.001 PHE A 153 TYR 0.009 0.001 TYR A 141 ARG 0.001 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.517 Fit side-chains REVERT: A 165 TYR cc_start: 0.8485 (m-80) cc_final: 0.8173 (m-80) REVERT: A 399 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6865 (mt) REVERT: A 475 ASN cc_start: 0.8666 (m-40) cc_final: 0.8230 (t0) REVERT: A 531 PHE cc_start: 0.7988 (t80) cc_final: 0.7694 (t80) outliers start: 12 outliers final: 6 residues processed: 67 average time/residue: 0.1359 time to fit residues: 12.2271 Evaluate side-chains 65 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 594 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0050 chunk 43 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4509 Z= 0.140 Angle : 0.519 10.986 6150 Z= 0.254 Chirality : 0.039 0.112 676 Planarity : 0.004 0.046 753 Dihedral : 6.717 82.967 608 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.47 % Allowed : 24.73 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.36), residues: 542 helix: -0.04 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.004 0.001 HIS A 381 PHE 0.008 0.001 PHE A 366 TYR 0.009 0.001 TYR A 141 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.547 Fit side-chains REVERT: A 350 CYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8074 (m) REVERT: A 399 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6879 (mt) REVERT: A 475 ASN cc_start: 0.8583 (m-40) cc_final: 0.8081 (t0) REVERT: A 531 PHE cc_start: 0.8027 (t80) cc_final: 0.7677 (t80) outliers start: 16 outliers final: 7 residues processed: 67 average time/residue: 0.1474 time to fit residues: 13.4140 Evaluate side-chains 66 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 350 CYS Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.0040 chunk 5 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.4170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4509 Z= 0.127 Angle : 0.491 6.129 6150 Z= 0.238 Chirality : 0.038 0.114 676 Planarity : 0.004 0.044 753 Dihedral : 6.661 82.616 608 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 26.25 % Favored : 70.93 % 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: -0.64 (0.37), residues: 542 helix: 0.32 (0.30), residues: 349 sheet: None (None), residues: 0 loop : -1.75 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.004 0.001 HIS A 381 PHE 0.007 0.001 PHE A 366 TYR 0.007 0.001 TYR A 141 ARG 0.001 0.000 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.510 Fit side-chains REVERT: A 475 ASN cc_start: 0.8552 (m-40) cc_final: 0.8027 (t0) REVERT: A 531 PHE cc_start: 0.8002 (t80) cc_final: 0.7667 (t80) outliers start: 13 outliers final: 6 residues processed: 66 average time/residue: 0.1479 time to fit residues: 12.9621 Evaluate side-chains 60 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 594 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4509 Z= 0.165 Angle : 0.501 6.062 6150 Z= 0.245 Chirality : 0.039 0.112 676 Planarity : 0.004 0.042 753 Dihedral : 6.742 86.807 608 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.04 % Allowed : 25.81 % Favored : 71.15 % 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: -0.62 (0.37), residues: 542 helix: 0.37 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.009 0.001 PHE A 361 TYR 0.011 0.001 TYR A 141 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.508 Fit side-chains REVERT: A 399 ILE cc_start: 0.7168 (OUTLIER) cc_final: 0.6940 (mt) REVERT: A 475 ASN cc_start: 0.8550 (m-40) cc_final: 0.8022 (t0) REVERT: A 531 PHE cc_start: 0.8068 (t80) cc_final: 0.7737 (t80) outliers start: 14 outliers final: 8 residues processed: 64 average time/residue: 0.1316 time to fit residues: 11.5608 Evaluate side-chains 63 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.1980 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4509 Z= 0.185 Angle : 0.512 6.942 6150 Z= 0.250 Chirality : 0.040 0.112 676 Planarity : 0.004 0.039 753 Dihedral : 6.841 89.591 608 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.60 % Allowed : 25.60 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.37), residues: 542 helix: 0.32 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.74 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.009 0.001 PHE A 150 TYR 0.010 0.001 TYR A 141 ARG 0.001 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.388 Fit side-chains REVERT: A 399 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6923 (mt) REVERT: A 475 ASN cc_start: 0.8545 (m-40) cc_final: 0.8026 (t0) REVERT: A 531 PHE cc_start: 0.8082 (t80) cc_final: 0.7738 (t80) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.1316 time to fit residues: 10.6413 Evaluate side-chains 64 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 594 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4509 Z= 0.168 Angle : 0.501 6.459 6150 Z= 0.245 Chirality : 0.039 0.111 676 Planarity : 0.004 0.039 753 Dihedral : 6.708 85.191 608 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.17 % Allowed : 26.03 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.37), residues: 542 helix: 0.36 (0.29), residues: 352 sheet: None (None), residues: 0 loop : -1.74 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.008 0.001 PHE A 361 TYR 0.011 0.001 TYR A 165 ARG 0.001 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.452 Fit side-chains REVERT: A 399 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7037 (mt) REVERT: A 475 ASN cc_start: 0.8535 (m-40) cc_final: 0.8015 (t0) REVERT: A 531 PHE cc_start: 0.8105 (t80) cc_final: 0.7766 (t80) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.1335 time to fit residues: 10.9984 Evaluate side-chains 63 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4509 Z= 0.129 Angle : 0.478 6.128 6150 Z= 0.233 Chirality : 0.038 0.113 676 Planarity : 0.004 0.040 753 Dihedral : 6.549 83.103 608 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.04 % Allowed : 25.16 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.37), residues: 542 helix: 0.47 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.67 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.007 0.001 PHE A 229 TYR 0.011 0.001 TYR A 165 ARG 0.001 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.521 Fit side-chains REVERT: A 399 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6943 (mt) REVERT: A 475 ASN cc_start: 0.8497 (m-40) cc_final: 0.7991 (t0) REVERT: A 531 PHE cc_start: 0.8082 (t80) cc_final: 0.7743 (t80) outliers start: 14 outliers final: 8 residues processed: 61 average time/residue: 0.1403 time to fit residues: 11.6468 Evaluate side-chains 61 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 594 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4509 Z= 0.166 Angle : 0.503 6.238 6150 Z= 0.247 Chirality : 0.039 0.147 676 Planarity : 0.004 0.042 753 Dihedral : 6.530 82.935 608 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.95 % Allowed : 26.25 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.37), residues: 542 helix: 0.45 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.011 0.001 PHE A 150 TYR 0.010 0.001 TYR A 165 ARG 0.001 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.485 Fit side-chains REVERT: A 399 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7055 (mt) REVERT: A 475 ASN cc_start: 0.8501 (m-40) cc_final: 0.7977 (t0) REVERT: A 531 PHE cc_start: 0.8133 (t80) cc_final: 0.7803 (t80) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1442 time to fit residues: 11.1084 Evaluate side-chains 59 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 594 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4509 Z= 0.177 Angle : 0.509 6.278 6150 Z= 0.250 Chirality : 0.039 0.128 676 Planarity : 0.004 0.041 753 Dihedral : 6.534 83.073 608 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.74 % Allowed : 26.25 % Favored : 72.02 % 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: -0.42 (0.37), residues: 542 helix: 0.45 (0.29), residues: 354 sheet: None (None), residues: 0 loop : -1.62 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.010 0.001 PHE A 109 TYR 0.010 0.001 TYR A 165 ARG 0.001 0.000 ARG A 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1084 Ramachandran restraints generated. 542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.487 Fit side-chains REVERT: A 399 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.7020 (mt) REVERT: A 475 ASN cc_start: 0.8487 (m-40) cc_final: 0.7972 (t0) REVERT: A 531 PHE cc_start: 0.8139 (t80) cc_final: 0.7796 (t80) outliers start: 8 outliers final: 6 residues processed: 57 average time/residue: 0.1386 time to fit residues: 10.7621 Evaluate side-chains 57 residues out of total 461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 548 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0270 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114598 restraints weight = 5459.076| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.99 r_work: 0.3204 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4509 Z= 0.171 Angle : 0.503 6.293 6150 Z= 0.246 Chirality : 0.039 0.117 676 Planarity : 0.004 0.041 753 Dihedral : 6.502 83.295 608 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.52 % Allowed : 26.90 % Favored : 71.58 % 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: -0.38 (0.37), residues: 542 helix: 0.50 (0.29), residues: 353 sheet: None (None), residues: 0 loop : -1.64 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 554 HIS 0.003 0.001 HIS A 381 PHE 0.011 0.001 PHE A 109 TYR 0.009 0.001 TYR A 141 ARG 0.001 0.000 ARG A 253 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1338.75 seconds wall clock time: 24 minutes 45.20 seconds (1485.20 seconds total)