Starting phenix.real_space_refine (version: dev) on Mon Feb 20 19:10:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbl_32405/02_2023/7wbl_32405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbl_32405/02_2023/7wbl_32405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbl_32405/02_2023/7wbl_32405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbl_32405/02_2023/7wbl_32405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbl_32405/02_2023/7wbl_32405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbl_32405/02_2023/7wbl_32405.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6402 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6484 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.18, per 1000 atoms: 0.64 Number of scatterers: 6484 At special positions: 0 Unit cell: (75.71, 86.43, 123.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1221 8.00 N 1073 7.00 C 4152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 103 " " NAG A 802 " - " ASN A 53 " " NAG A 803 " - " ASN A 90 " " NAG A 804 " - " ASN A 322 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 805 " - pdb=" NE2 HIS A 374 " 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 56.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.952A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.588A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.092A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.690A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.576A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.545A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.684A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.818A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.820A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.579A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.710A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.525A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 4.051A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 538 through 542' Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.633A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.733A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.938A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.816A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.893A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.563A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.143A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.299A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.563A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 846 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: 1.71 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.48: 1774 1.48 - 1.61: 2741 1.61 - 1.74: 0 1.74 - 1.87: 58 Bond restraints: 6667 Sorted by residual: bond pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 1.334 1.505 -0.171 2.34e-02 1.83e+03 5.36e+01 bond pdb=" N GLY A 352 " pdb=" CA GLY A 352 " ideal model delta sigma weight residual 1.448 1.475 -0.027 9.00e-03 1.23e+04 8.81e+00 bond pdb=" N ARG B 498 " pdb=" CA ARG B 498 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.50e-02 4.44e+03 7.56e+00 bond pdb=" N CYS B 488 " pdb=" CA CYS B 488 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.19e-02 7.06e+03 6.98e+00 bond pdb=" N GLU A 35 " pdb=" CA GLU A 35 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.28e-02 6.10e+03 6.30e+00 ... (remaining 6662 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.00: 223 107.00 - 113.74: 3542 113.74 - 120.49: 2672 120.49 - 127.24: 2528 127.24 - 133.99: 98 Bond angle restraints: 9063 Sorted by residual: angle pdb=" C ARG B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.84 132.27 -12.43 1.25e+00 6.40e-01 9.88e+01 angle pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" O GLY A 352 " ideal model delta sigma weight residual 122.45 118.18 4.27 7.20e-01 1.93e+00 3.51e+01 angle pdb=" CA ARG B 498 " pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 117.93 126.11 -8.18 1.42e+00 4.96e-01 3.32e+01 angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 126.48 -12.08 2.30e+00 1.89e-01 2.76e+01 angle pdb=" O ARG B 498 " pdb=" C ARG B 498 " pdb=" N PRO B 499 " ideal model delta sigma weight residual 121.72 117.79 3.93 9.80e-01 1.04e+00 1.61e+01 ... (remaining 9058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3421 16.79 - 33.57: 390 33.57 - 50.36: 86 50.36 - 67.14: 25 67.14 - 83.93: 8 Dihedral angle restraints: 3930 sinusoidal: 1604 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 45.60 47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 56.80 36.20 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -114.71 28.71 1 1.00e+01 1.00e-02 1.18e+01 ... (remaining 3927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 802 0.055 - 0.110: 137 0.110 - 0.164: 17 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 959 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 103 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ARG B 498 " pdb=" N ARG B 498 " pdb=" C ARG B 498 " pdb=" CB ARG B 498 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 956 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 497 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C PHE B 497 " 0.069 2.00e-02 2.50e+03 pdb=" O PHE B 497 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG B 498 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 478 " 0.013 2.00e-02 2.50e+03 1.17e-02 3.44e+00 pdb=" CG TRP A 478 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 478 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 478 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 478 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 478 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 478 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 478 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 478 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO A 583 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.020 5.00e-02 4.00e+02 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 156 2.71 - 3.26: 6280 3.26 - 3.80: 9928 3.80 - 4.35: 12420 4.35 - 4.90: 21633 Nonbonded interactions: 50417 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 805 " model vdw 2.158 2.230 nonbonded pdb=" O SER B 496 " pdb=" OH TYR B 501 " model vdw 2.175 2.440 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.183 2.440 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.235 2.440 nonbonded pdb=" O MET A 152 " pdb=" NH1 ARG A 161 " model vdw 2.302 2.520 ... (remaining 50412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4152 2.51 5 N 1073 2.21 5 O 1221 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.090 Process input model: 21.480 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.004 0.171 6667 Z= 0.221 Angle : 0.582 12.427 9063 Z= 0.339 Chirality : 0.043 0.274 959 Planarity : 0.004 0.040 1170 Dihedral : 15.296 83.928 2415 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.56 % Favored : 96.06 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.52 (0.30), residues: 787 helix: 1.27 (0.27), residues: 379 sheet: 0.20 (0.74), residues: 46 loop : -0.59 (0.32), residues: 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.720 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.1703 time to fit residues: 23.6401 Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.751 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0661 time to fit residues: 1.1825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 6667 Z= 0.169 Angle : 0.499 10.296 9063 Z= 0.259 Chirality : 0.042 0.268 959 Planarity : 0.003 0.037 1170 Dihedral : 3.936 15.223 885 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.72 (0.30), residues: 787 helix: 1.47 (0.27), residues: 383 sheet: 0.16 (0.74), residues: 46 loop : -0.55 (0.33), residues: 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.740 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 98 average time/residue: 0.1498 time to fit residues: 20.8415 Evaluate side-chains 92 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0598 time to fit residues: 1.7681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 6667 Z= 0.186 Angle : 0.501 11.820 9063 Z= 0.258 Chirality : 0.042 0.249 959 Planarity : 0.003 0.038 1170 Dihedral : 3.934 15.055 885 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.75 (0.30), residues: 787 helix: 1.44 (0.27), residues: 384 sheet: 0.09 (0.67), residues: 56 loop : -0.45 (0.34), residues: 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.742 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.1620 time to fit residues: 21.1591 Evaluate side-chains 88 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0682 time to fit residues: 1.4084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 194 ASN A 340 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 6667 Z= 0.170 Angle : 0.492 12.220 9063 Z= 0.253 Chirality : 0.041 0.222 959 Planarity : 0.003 0.037 1170 Dihedral : 3.895 15.080 885 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.83 (0.30), residues: 787 helix: 1.54 (0.27), residues: 382 sheet: 0.19 (0.68), residues: 56 loop : -0.45 (0.34), residues: 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.704 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.1555 time to fit residues: 22.1756 Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0603 time to fit residues: 1.8864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 6667 Z= 0.179 Angle : 0.503 12.080 9063 Z= 0.259 Chirality : 0.042 0.209 959 Planarity : 0.003 0.036 1170 Dihedral : 3.907 15.107 885 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.87 (0.31), residues: 787 helix: 1.51 (0.27), residues: 382 sheet: 0.32 (0.69), residues: 56 loop : -0.38 (0.34), residues: 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 0.779 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 99 average time/residue: 0.1550 time to fit residues: 21.7804 Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0637 time to fit residues: 1.4099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 6667 Z= 0.172 Angle : 0.501 11.969 9063 Z= 0.256 Chirality : 0.041 0.200 959 Planarity : 0.003 0.035 1170 Dihedral : 3.922 15.112 885 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.93 (0.31), residues: 787 helix: 1.62 (0.27), residues: 376 sheet: 0.41 (0.70), residues: 56 loop : -0.40 (0.34), residues: 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.820 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.1640 time to fit residues: 23.4172 Evaluate side-chains 97 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0616 time to fit residues: 1.6362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.0060 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.058 6667 Z= 0.139 Angle : 0.484 11.935 9063 Z= 0.246 Chirality : 0.040 0.193 959 Planarity : 0.003 0.032 1170 Dihedral : 3.808 14.758 885 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.31), residues: 787 helix: 1.69 (0.27), residues: 382 sheet: 0.25 (0.68), residues: 56 loop : -0.29 (0.35), residues: 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.678 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 94 average time/residue: 0.1811 time to fit residues: 24.0310 Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0676 time to fit residues: 1.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 51 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 6667 Z= 0.181 Angle : 0.512 11.931 9063 Z= 0.260 Chirality : 0.042 0.190 959 Planarity : 0.003 0.035 1170 Dihedral : 3.922 19.946 885 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.98 (0.31), residues: 787 helix: 1.66 (0.27), residues: 378 sheet: 0.28 (0.68), residues: 56 loop : -0.35 (0.35), residues: 353 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.753 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 93 average time/residue: 0.1619 time to fit residues: 21.5531 Evaluate side-chains 94 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.791 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0591 time to fit residues: 1.2799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.0980 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 6667 Z= 0.125 Angle : 0.484 11.731 9063 Z= 0.241 Chirality : 0.040 0.185 959 Planarity : 0.003 0.030 1170 Dihedral : 3.726 20.295 885 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.28 (0.31), residues: 787 helix: 1.93 (0.27), residues: 381 sheet: 0.37 (0.69), residues: 56 loop : -0.24 (0.35), residues: 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.663 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 95 average time/residue: 0.1674 time to fit residues: 22.2296 Evaluate side-chains 91 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0667 time to fit residues: 1.3605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 6667 Z= 0.195 Angle : 0.537 11.745 9063 Z= 0.271 Chirality : 0.043 0.375 959 Planarity : 0.004 0.040 1170 Dihedral : 3.893 20.208 885 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.32 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.10 (0.31), residues: 787 helix: 1.74 (0.27), residues: 378 sheet: 0.47 (0.69), residues: 56 loop : -0.30 (0.35), residues: 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.783 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.1482 time to fit residues: 20.5418 Evaluate side-chains 89 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0629 time to fit residues: 1.2193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.0050 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.198378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.160911 restraints weight = 7498.935| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.04 r_work: 0.3572 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 6667 Z= 0.151 Angle : 0.512 11.853 9063 Z= 0.257 Chirality : 0.042 0.345 959 Planarity : 0.003 0.041 1170 Dihedral : 3.837 20.284 885 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.12 (0.31), residues: 787 helix: 1.71 (0.27), residues: 384 sheet: 0.47 (0.69), residues: 56 loop : -0.26 (0.35), residues: 347 =============================================================================== Job complete usr+sys time: 1563.62 seconds wall clock time: 28 minutes 58.95 seconds (1738.95 seconds total)