Starting phenix.real_space_refine on Sun Mar 10 18:55:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkw_33209/03_2024/7xkw_33209_updated.pdb" } resolution = 3.1 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= 0.104 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 3 5.21 5 S 21 5.16 5 C 2632 2.51 5 N 706 2.21 5 O 768 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 561": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4132 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 499, 4097 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 14, 'TRANS': 484} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 499, 4097 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 14, 'TRANS': 484} Chain breaks: 1 bond proxies already assigned to first conformer: 4168 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Unusual residues: {' MG': 3, 'FPS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.77, per 1000 atoms: 1.15 Number of scatterers: 4132 At special positions: 0 Unit cell: (63.18, 78.57, 87.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 2 15.00 Mg 3 11.99 O 768 8.00 N 706 7.00 C 2632 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: 1.89 Conformation dependent library (CDL) restraints added in 2.2 seconds 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 0 sheets defined 69.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 56 through 73 Processing helix chain 'A' and resid 78 through 89 Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.872A pdb=" N GLU A 97 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA A 98 " --> pdb=" O HIS A 95 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 99 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 100 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.786A pdb=" N TYR A 173 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 197 Processing helix chain 'A' and resid 202 through 213 removed outlier: 4.334A pdb=" N LEU A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 240 through 270 removed outlier: 3.638A pdb=" N ASN A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 288 No H-bonds generated for 'chain 'A' and resid 285 through 288' Processing helix chain 'A' and resid 298 through 322 removed outlier: 4.861A pdb=" N GLN A 302 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 305 " --> pdb=" O GLN A 302 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 306 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A 309 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 312 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU A 313 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 314 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 316 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET A 317 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 339 removed outlier: 3.982A pdb=" N ARG A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 350 through 370 Processing helix chain 'A' and resid 376 through 402 removed outlier: 4.443A pdb=" N LYS A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 384 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 389 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 393 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 394 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 396 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA A 397 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 402 " --> pdb=" O TRP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 removed outlier: 4.178A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.578A pdb=" N LEU A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 449 through 466 removed outlier: 4.123A pdb=" N ILE A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 458 " --> pdb=" O CYS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 472 No H-bonds generated for 'chain 'A' and resid 470 through 472' Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 491 through 512 removed outlier: 3.552A pdb=" N LYS A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 4.288A pdb=" N ARG A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Proline residue: A 527 - end of helix removed outlier: 3.789A pdb=" N ILE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 535 " --> pdb=" O ALA A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 197 hydrogen bonds defined for protein. 480 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: 1.06 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 1379 1.36 - 1.54: 2731 1.54 - 1.71: 65 1.71 - 1.89: 33 1.89 - 2.07: 1 Bond restraints: 4209 Sorted by residual: bond pdb=" CA SER A 419 " pdb=" CB SER A 419 " ideal model delta sigma weight residual 1.534 1.455 0.079 1.58e-02 4.01e+03 2.49e+01 bond pdb=" CA ALA A 420 " pdb=" CB ALA A 420 " ideal model delta sigma weight residual 1.531 1.458 0.074 1.53e-02 4.27e+03 2.33e+01 bond pdb=" CA SER A 418 " pdb=" CB SER A 418 " ideal model delta sigma weight residual 1.531 1.453 0.078 1.69e-02 3.50e+03 2.12e+01 bond pdb=" N ASP A 322 " pdb=" CA ASP A 322 " ideal model delta sigma weight residual 1.457 1.508 -0.050 1.17e-02 7.31e+03 1.84e+01 bond pdb=" C LEU A 311 " pdb=" O LEU A 311 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.28e-02 6.10e+03 1.71e+01 ... (remaining 4204 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.79: 110 106.79 - 113.61: 2282 113.61 - 120.43: 1761 120.43 - 127.25: 1493 127.25 - 134.07: 41 Bond angle restraints: 5687 Sorted by residual: angle pdb=" C4 FPS A 601 " pdb=" C3 FPS A 601 " pdb=" C5 FPS A 601 " ideal model delta sigma weight residual 68.21 115.91 -47.70 3.00e+00 1.11e-01 2.53e+02 angle pdb=" C10 FPS A 601 " pdb=" C8 FPS A 601 " pdb=" C9 FPS A 601 " ideal model delta sigma weight residual 68.18 115.20 -47.02 3.00e+00 1.11e-01 2.46e+02 angle pdb=" C7 FPS A 601 " pdb=" C8 FPS A 601 " pdb=" C9 FPS A 601 " ideal model delta sigma weight residual 85.85 123.81 -37.96 3.00e+00 1.11e-01 1.60e+02 angle pdb=" C2 FPS A 601 " pdb=" C3 FPS A 601 " pdb=" C5 FPS A 601 " ideal model delta sigma weight residual 85.83 120.98 -35.15 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C10 FPS A 601 " pdb=" C8 FPS A 601 " pdb=" C7 FPS A 601 " ideal model delta sigma weight residual 152.67 120.97 31.70 3.00e+00 1.11e-01 1.12e+02 ... (remaining 5682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2318 17.28 - 34.56: 192 34.56 - 51.84: 46 51.84 - 69.12: 12 69.12 - 86.39: 3 Dihedral angle restraints: 2571 sinusoidal: 1078 harmonic: 1493 Sorted by residual: dihedral pdb=" C GLU A 328 " pdb=" N GLU A 328 " pdb=" CA GLU A 328 " pdb=" CB GLU A 328 " ideal model delta harmonic sigma weight residual -122.60 -113.51 -9.09 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C TYR A 537 " pdb=" N TYR A 537 " pdb=" CA TYR A 537 " pdb=" CB TYR A 537 " ideal model delta harmonic sigma weight residual -122.60 -113.65 -8.95 0 2.50e+00 1.60e-01 1.28e+01 dihedral pdb=" N GLU A 328 " pdb=" C GLU A 328 " pdb=" CA GLU A 328 " pdb=" CB GLU A 328 " ideal model delta harmonic sigma weight residual 122.80 114.78 8.02 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 2568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 550 0.072 - 0.144: 60 0.144 - 0.216: 16 0.216 - 0.288: 2 0.288 - 0.360: 1 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA GLU A 328 " pdb=" N GLU A 328 " pdb=" C GLU A 328 " pdb=" CB GLU A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CA ARG A 281 " pdb=" N ARG A 281 " pdb=" C ARG A 281 " pdb=" CB ARG A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TYR A 538 " pdb=" N TYR A 538 " pdb=" C TYR A 538 " pdb=" CB TYR A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 626 not shown) Planarity restraints: 727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 515 " -0.051 5.00e-02 4.00e+02 7.84e-02 9.83e+00 pdb=" N PRO A 516 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 326 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.70e+00 pdb=" C LYS A 326 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS A 326 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 327 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 309 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ILE A 309 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE A 309 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 310 " 0.015 2.00e-02 2.50e+03 ... (remaining 724 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 1 2.22 - 2.89: 1529 2.89 - 3.56: 6020 3.56 - 4.23: 9315 4.23 - 4.90: 16589 Nonbonded interactions: 33454 Sorted by model distance: nonbonded pdb=" O2B FPS A 601 " pdb="MG MG A 603 " model vdw 1.547 2.170 nonbonded pdb=" OD1 ASP A 318 " pdb="MG MG A 603 " model vdw 2.233 2.170 nonbonded pdb=" O GLU A 61 " pdb=" NE2 GLN A 65 " model vdw 2.261 2.520 nonbonded pdb=" NH2 ARG A 332 " pdb=" O GLN A 347 " model vdw 2.300 2.520 nonbonded pdb=" OD1 ASP A 272 " pdb=" NH1 ARG A 275 " model vdw 2.307 2.520 ... (remaining 33449 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=0.50 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: 0.540 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: 3.120 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 20.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 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 : 0.007 0.079 4209 Z= 0.473 Angle : 1.614 47.696 5687 Z= 0.772 Chirality : 0.055 0.360 629 Planarity : 0.006 0.078 727 Dihedral : 14.102 86.394 1599 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.61 % Allowed : 3.03 % Favored : 96.36 % Rotamer: Outliers : 1.11 % Allowed : 2.23 % Favored : 96.66 % 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: -1.01 (0.38), residues: 496 helix: -0.13 (0.28), residues: 362 sheet: None (None), residues: 0 loop : -1.93 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 290 HIS 0.009 0.001 HIS A 72 PHE 0.007 0.001 PHE A 147 TYR 0.024 0.002 TYR A 538 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 291 MET cc_start: 0.8532 (mmm) cc_final: 0.7978 (mmp) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 0.2095 time to fit residues: 16.8480 Evaluate side-chains 44 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 470 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS A 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4209 Z= 0.183 Angle : 0.720 21.266 5687 Z= 0.321 Chirality : 0.038 0.120 629 Planarity : 0.005 0.068 727 Dihedral : 5.379 51.268 567 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.11 % Allowed : 6.68 % Favored : 92.20 % 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: -0.78 (0.38), residues: 496 helix: -0.04 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 268 HIS 0.008 0.002 HIS A 72 PHE 0.007 0.001 PHE A 188 TYR 0.020 0.002 TYR A 232 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.482 Fit side-chains REVERT: A 291 MET cc_start: 0.8439 (mmm) cc_final: 0.7812 (mmp) outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.2099 time to fit residues: 14.8134 Evaluate side-chains 50 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 39 optimal weight: 0.0770 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4209 Z= 0.139 Angle : 0.639 21.659 5687 Z= 0.284 Chirality : 0.037 0.112 629 Planarity : 0.004 0.061 727 Dihedral : 5.457 53.472 563 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.11 % Allowed : 8.69 % Favored : 90.20 % 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: -0.39 (0.38), residues: 496 helix: 0.23 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.31 (0.54), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 267 HIS 0.007 0.001 HIS A 72 PHE 0.008 0.001 PHE A 188 TYR 0.019 0.001 TYR A 538 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.470 Fit side-chains REVERT: A 159 ARG cc_start: 0.7170 (mtp-110) cc_final: 0.6947 (mtp85) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.2582 time to fit residues: 15.9527 Evaluate side-chains 48 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4209 Z= 0.159 Angle : 0.654 21.783 5687 Z= 0.288 Chirality : 0.037 0.119 629 Planarity : 0.004 0.057 727 Dihedral : 5.467 55.372 563 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.11 % Allowed : 8.69 % Favored : 90.20 % 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: -0.24 (0.39), residues: 496 helix: 0.36 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.32 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 267 HIS 0.004 0.001 HIS A 378 PHE 0.008 0.001 PHE A 188 TYR 0.017 0.001 TYR A 232 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.476 Fit side-chains REVERT: A 159 ARG cc_start: 0.7195 (mtp-110) cc_final: 0.6957 (mtp85) REVERT: A 539 GLN cc_start: 0.5883 (mm-40) cc_final: 0.5681 (mm-40) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.2140 time to fit residues: 12.7077 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7500 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4209 Z= 0.207 Angle : 0.683 21.730 5687 Z= 0.305 Chirality : 0.038 0.146 629 Planarity : 0.004 0.055 727 Dihedral : 5.556 55.111 563 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.56 % Allowed : 9.35 % Favored : 89.09 % 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: -0.37 (0.38), residues: 496 helix: 0.26 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.36 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 399 HIS 0.006 0.001 HIS A 378 PHE 0.009 0.001 PHE A 188 TYR 0.019 0.002 TYR A 232 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.396 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.1779 time to fit residues: 10.1356 Evaluate side-chains 44 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7474 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4209 Z= 0.172 Angle : 0.655 21.772 5687 Z= 0.289 Chirality : 0.037 0.131 629 Planarity : 0.004 0.054 727 Dihedral : 5.475 54.824 563 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.11 % Allowed : 10.24 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.39), residues: 496 helix: 0.34 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.29 (0.56), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 267 HIS 0.004 0.001 HIS A 192 PHE 0.008 0.001 PHE A 188 TYR 0.016 0.001 TYR A 232 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.530 Fit side-chains REVERT: A 159 ARG cc_start: 0.7244 (mtp-110) cc_final: 0.6990 (mtp85) REVERT: A 331 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7331 (mt-10) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.2176 time to fit residues: 12.6058 Evaluate side-chains 48 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.0050 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4209 Z= 0.135 Angle : 0.634 21.800 5687 Z= 0.276 Chirality : 0.036 0.112 629 Planarity : 0.004 0.053 727 Dihedral : 5.315 53.962 563 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.34 % Allowed : 10.02 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.40), residues: 496 helix: 0.49 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.22 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 267 HIS 0.004 0.001 HIS A 475 PHE 0.008 0.001 PHE A 188 TYR 0.012 0.001 TYR A 232 ARG 0.001 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.477 Fit side-chains REVERT: A 110 ARG cc_start: 0.7088 (mtm180) cc_final: 0.6800 (mtm180) REVERT: A 159 ARG cc_start: 0.7220 (mtp-110) cc_final: 0.6969 (mtp85) REVERT: A 331 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7402 (mm-30) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.2083 time to fit residues: 13.1732 Evaluate side-chains 46 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4209 Z= 0.199 Angle : 0.670 21.734 5687 Z= 0.298 Chirality : 0.038 0.141 629 Planarity : 0.004 0.052 727 Dihedral : 5.349 51.953 563 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.34 % Allowed : 10.02 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.39), residues: 496 helix: 0.42 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.26 (0.57), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 399 HIS 0.005 0.001 HIS A 378 PHE 0.009 0.001 PHE A 188 TYR 0.018 0.002 TYR A 232 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6869 (mtm180) REVERT: A 331 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7352 (mm-30) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.2339 time to fit residues: 12.4644 Evaluate side-chains 44 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7485 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4209 Z= 0.193 Angle : 0.665 21.742 5687 Z= 0.296 Chirality : 0.038 0.141 629 Planarity : 0.004 0.052 727 Dihedral : 5.359 50.341 563 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.34 % Allowed : 10.02 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.39), residues: 496 helix: 0.38 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.22 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 290 HIS 0.005 0.001 HIS A 378 PHE 0.009 0.001 PHE A 188 TYR 0.016 0.002 TYR A 232 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7106 (mtm180) cc_final: 0.6879 (mtm180) REVERT: A 331 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7359 (mm-30) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.2331 time to fit residues: 13.1100 Evaluate side-chains 49 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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: 0.7416 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4209 Z= 0.133 Angle : 0.635 21.788 5687 Z= 0.277 Chirality : 0.036 0.113 629 Planarity : 0.004 0.052 727 Dihedral : 5.223 49.459 563 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.11 % Allowed : 10.47 % Favored : 88.42 % 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: 0.03 (0.40), residues: 496 helix: 0.54 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -1.15 (0.58), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 267 HIS 0.003 0.001 HIS A 475 PHE 0.008 0.001 PHE A 188 TYR 0.011 0.001 TYR A 232 ARG 0.001 0.000 ARG A 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 992 Ramachandran restraints generated. 496 Oldfield, 0 Emsley, 496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.444 Fit side-chains REVERT: A 110 ARG cc_start: 0.7084 (mtm180) cc_final: 0.6879 (mtm180) REVERT: A 159 ARG cc_start: 0.7195 (mtp-110) cc_final: 0.6928 (mtp85) REVERT: A 331 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7393 (mm-30) outliers start: 5 outliers final: 4 residues processed: 46 average time/residue: 0.2138 time to fit residues: 12.1204 Evaluate side-chains 45 residues out of total 447 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.169092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133887 restraints weight = 6237.127| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.44 r_work: 0.3315 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4209 Z= 0.180 Angle : 0.655 21.729 5687 Z= 0.290 Chirality : 0.038 0.129 629 Planarity : 0.004 0.052 727 Dihedral : 5.259 48.311 563 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.89 % Allowed : 10.47 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.40), residues: 496 helix: 0.47 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.11 (0.59), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 290 HIS 0.005 0.001 HIS A 378 PHE 0.009 0.001 PHE A 188 TYR 0.016 0.001 TYR A 232 ARG 0.002 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.32 seconds wall clock time: 25 minutes 18.05 seconds (1518.05 seconds total)