Starting phenix.real_space_refine on Sat Aug 3 01:36:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrh_37776/08_2024/8wrh_37776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrh_37776/08_2024/8wrh_37776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrh_37776/08_2024/8wrh_37776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrh_37776/08_2024/8wrh_37776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrh_37776/08_2024/8wrh_37776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wrh_37776/08_2024/8wrh_37776.cif" } resolution = 3.08 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= 0.001 sd= 0.065 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4137 2.51 5 N 1069 2.21 5 O 1216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6459 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4845 Classifications: {'peptide': 594} Link IDs: {'PTRANS': 27, 'TRANS': 566} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1558 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 14, 'TRANS': 181} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.27, per 1000 atoms: 0.66 Number of scatterers: 6459 At special positions: 0 Unit cell: (71.912, 89.688, 117.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1216 8.00 N 1069 7.00 C 4137 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 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 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 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 901 " - " ASN A 546 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 53 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 54.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.620A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.568A pdb=" N ASN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.517A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.871A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix removed outlier: 3.794A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) 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 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.837A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.504A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.672A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.547A pdb=" N GLU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.141A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.570A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.774A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.723A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.655A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.554A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.669A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.537A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.571A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.527A 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 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.757A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.406A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454 removed outlier: 8.338A pdb=" N ASN B 450 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER B 494 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU B 452 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU B 492 " --> pdb=" O LEU B 452 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 858 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: 1.63 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1257 1.33 - 1.45: 1774 1.45 - 1.57: 3555 1.57 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6644 Sorted by residual: bond pdb=" N TYR B 489 " pdb=" CA TYR B 489 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" CA ALA A 80 " pdb=" CB ALA A 80 " ideal model delta sigma weight residual 1.534 1.483 0.050 1.58e-02 4.01e+03 1.02e+01 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.19e-02 7.06e+03 8.06e+00 bond pdb=" CA TYR B 489 " pdb=" C TYR B 489 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.34e-02 5.57e+03 7.11e+00 bond pdb=" N PRO B 486 " pdb=" CA PRO B 486 " ideal model delta sigma weight residual 1.473 1.440 0.033 1.32e-02 5.74e+03 6.22e+00 ... (remaining 6639 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.90: 127 104.90 - 112.19: 3173 112.19 - 119.49: 2265 119.49 - 126.79: 3338 126.79 - 134.09: 128 Bond angle restraints: 9031 Sorted by residual: angle pdb=" N TYR B 489 " pdb=" CA TYR B 489 " pdb=" CB TYR B 489 " ideal model delta sigma weight residual 110.49 123.59 -13.10 1.69e+00 3.50e-01 6.01e+01 angle pdb=" CA PHE B 455 " pdb=" CB PHE B 455 " pdb=" CG PHE B 455 " ideal model delta sigma weight residual 113.80 121.46 -7.66 1.00e+00 1.00e+00 5.87e+01 angle pdb=" N ALA A 80 " pdb=" CA ALA A 80 " pdb=" C ALA A 80 " ideal model delta sigma weight residual 113.50 105.68 7.82 1.23e+00 6.61e-01 4.04e+01 angle pdb=" N LEU A 79 " pdb=" CA LEU A 79 " pdb=" C LEU A 79 " ideal model delta sigma weight residual 113.30 106.59 6.71 1.34e+00 5.57e-01 2.50e+01 angle pdb=" N VAL B 483 " pdb=" CA VAL B 483 " pdb=" C VAL B 483 " ideal model delta sigma weight residual 109.34 119.45 -10.11 2.08e+00 2.31e-01 2.36e+01 ... (remaining 9026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.80: 3457 20.80 - 41.59: 394 41.59 - 62.39: 103 62.39 - 83.18: 13 83.18 - 103.98: 11 Dihedral angle restraints: 3978 sinusoidal: 1658 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.28 -48.28 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 44.98 48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 153.39 26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 3975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 749 0.050 - 0.099: 164 0.099 - 0.149: 36 0.149 - 0.198: 2 0.198 - 0.248: 3 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA CYS B 488 " pdb=" N CYS B 488 " pdb=" C CYS B 488 " pdb=" CB CYS B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA TYR B 489 " pdb=" N TYR B 489 " pdb=" C TYR B 489 " pdb=" CB TYR B 489 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA LEU A 79 " pdb=" N LEU A 79 " pdb=" C LEU A 79 " pdb=" CB LEU A 79 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 951 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 482 " 0.023 2.00e-02 2.50e+03 4.54e-02 2.07e+01 pdb=" C GLY B 482 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY B 482 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL B 483 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 483 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C VAL B 483 " -0.045 2.00e-02 2.50e+03 pdb=" O VAL B 483 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 484 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 455 " 0.019 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE B 455 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 455 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 455 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 455 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 455 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 455 " 0.004 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 172 2.70 - 3.25: 6326 3.25 - 3.80: 10667 3.80 - 4.35: 13447 4.35 - 4.90: 22970 Nonbonded interactions: 53582 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.151 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.172 3.040 nonbonded pdb=" OE1 GLN A 102 " pdb=" OH TYR A 202 " model vdw 2.193 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.210 3.120 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.216 3.040 ... (remaining 53577 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 21.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 0.050 6644 Z= 0.259 Angle : 0.676 13.100 9031 Z= 0.375 Chirality : 0.045 0.248 954 Planarity : 0.004 0.045 1166 Dihedral : 18.702 103.977 2470 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.83 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 24.64 % Favored : 75.36 % Cbeta Deviations : 0.13 % 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: 0.28 (0.30), residues: 786 helix: 1.21 (0.26), residues: 396 sheet: 0.89 (0.81), residues: 44 loop : -1.13 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.004 0.001 HIS A 241 PHE 0.040 0.002 PHE B 455 TYR 0.021 0.002 TYR A 279 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8023 (mtp) cc_final: 0.7782 (mtp) REVERT: A 478 TRP cc_start: 0.6722 (m100) cc_final: 0.6478 (m100) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1491 time to fit residues: 17.8691 Evaluate side-chains 83 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6644 Z= 0.180 Angle : 0.537 7.254 9031 Z= 0.268 Chirality : 0.042 0.185 954 Planarity : 0.004 0.043 1166 Dihedral : 7.150 57.633 940 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.44 % Allowed : 22.91 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.30), residues: 786 helix: 1.46 (0.26), residues: 396 sheet: 0.96 (0.78), residues: 44 loop : -1.22 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.001 PHE B 455 TYR 0.010 0.001 TYR A 385 ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8804 (p) REVERT: A 360 MET cc_start: 0.6786 (ptm) cc_final: 0.6502 (ptm) REVERT: A 364 VAL cc_start: 0.7825 (t) cc_final: 0.7510 (t) REVERT: A 478 TRP cc_start: 0.6619 (m100) cc_final: 0.6399 (m100) REVERT: A 544 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7332 (mt) REVERT: B 500 THR cc_start: 0.8789 (p) cc_final: 0.8579 (p) outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.1656 time to fit residues: 21.7100 Evaluate side-chains 89 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6644 Z= 0.220 Angle : 0.539 7.197 9031 Z= 0.269 Chirality : 0.042 0.152 954 Planarity : 0.004 0.042 1166 Dihedral : 5.117 32.039 940 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.31 % Allowed : 22.33 % Favored : 75.36 % 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: 0.43 (0.30), residues: 786 helix: 1.45 (0.26), residues: 396 sheet: 0.86 (0.78), residues: 44 loop : -1.21 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE B 455 TYR 0.018 0.001 TYR A 279 ARG 0.004 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 347 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8766 (p) REVERT: A 360 MET cc_start: 0.7089 (ptm) cc_final: 0.6814 (ptm) REVERT: A 364 VAL cc_start: 0.7916 (t) cc_final: 0.7568 (t) REVERT: A 544 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7345 (mt) outliers start: 16 outliers final: 8 residues processed: 95 average time/residue: 0.1620 time to fit residues: 21.7336 Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 508 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6644 Z= 0.329 Angle : 0.593 7.711 9031 Z= 0.300 Chirality : 0.044 0.156 954 Planarity : 0.004 0.043 1166 Dihedral : 5.005 27.456 940 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.31 % Allowed : 21.90 % Favored : 74.78 % 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 (0.30), residues: 786 helix: 1.17 (0.26), residues: 403 sheet: 0.52 (0.74), residues: 42 loop : -1.22 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 477 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.002 PHE B 455 TYR 0.019 0.002 TYR A 385 ARG 0.007 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: A 166 GLU cc_start: 0.7811 (tp30) cc_final: 0.6873 (tp30) REVERT: A 347 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8726 (p) REVERT: A 360 MET cc_start: 0.7455 (ptm) cc_final: 0.7193 (ptm) REVERT: A 364 VAL cc_start: 0.8000 (t) cc_final: 0.7711 (t) REVERT: A 467 GLU cc_start: 0.4332 (OUTLIER) cc_final: 0.3866 (pm20) REVERT: A 544 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7301 (mt) REVERT: B 508 TYR cc_start: 0.9102 (m-80) cc_final: 0.8773 (m-80) outliers start: 23 outliers final: 14 residues processed: 109 average time/residue: 0.1701 time to fit residues: 26.0004 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.0670 chunk 14 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6644 Z= 0.197 Angle : 0.523 7.505 9031 Z= 0.261 Chirality : 0.042 0.141 954 Planarity : 0.004 0.043 1166 Dihedral : 4.533 25.728 940 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.59 % Allowed : 22.62 % Favored : 74.78 % 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: 0.41 (0.30), residues: 786 helix: 1.44 (0.26), residues: 397 sheet: 0.58 (0.77), residues: 44 loop : -1.20 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 566 HIS 0.003 0.001 HIS A 34 PHE 0.012 0.001 PHE B 455 TYR 0.020 0.001 TYR A 279 ARG 0.005 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7798 (tp30) cc_final: 0.6859 (tp30) REVERT: A 259 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6671 (pt) REVERT: A 347 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8731 (p) REVERT: A 364 VAL cc_start: 0.7974 (t) cc_final: 0.7704 (t) REVERT: A 467 GLU cc_start: 0.4345 (OUTLIER) cc_final: 0.3230 (pt0) REVERT: A 544 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7383 (mt) REVERT: B 466 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5019 (ttm170) REVERT: B 478 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6727 (mtpp) outliers start: 18 outliers final: 8 residues processed: 100 average time/residue: 0.1703 time to fit residues: 23.2972 Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS 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: 2.9990 chunk 75 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6644 Z= 0.174 Angle : 0.507 7.381 9031 Z= 0.252 Chirality : 0.041 0.137 954 Planarity : 0.003 0.043 1166 Dihedral : 4.222 24.282 940 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.31 % Allowed : 24.06 % Favored : 73.63 % 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: 0.55 (0.30), residues: 786 helix: 1.70 (0.27), residues: 390 sheet: 0.59 (0.78), residues: 44 loop : -1.25 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE B 455 TYR 0.021 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.716 Fit side-chains REVERT: A 166 GLU cc_start: 0.7723 (tp30) cc_final: 0.6829 (tp30) REVERT: A 347 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8769 (p) REVERT: A 360 MET cc_start: 0.6912 (ptm) cc_final: 0.6608 (ptm) REVERT: A 364 VAL cc_start: 0.8007 (t) cc_final: 0.7727 (t) REVERT: A 435 GLU cc_start: 0.7032 (pt0) cc_final: 0.6814 (pt0) REVERT: A 467 GLU cc_start: 0.4276 (OUTLIER) cc_final: 0.3294 (pt0) REVERT: A 544 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7367 (mt) REVERT: B 466 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.4881 (ttm170) REVERT: B 478 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6740 (mtpp) REVERT: B 508 TYR cc_start: 0.8993 (m-80) cc_final: 0.8541 (m-80) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 0.1625 time to fit residues: 23.3878 Evaluate side-chains 105 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7990 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6644 Z= 0.176 Angle : 0.507 7.430 9031 Z= 0.252 Chirality : 0.041 0.141 954 Planarity : 0.003 0.043 1166 Dihedral : 4.069 23.459 940 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.16 % Allowed : 24.35 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.30), residues: 786 helix: 1.76 (0.27), residues: 390 sheet: 0.57 (0.77), residues: 44 loop : -1.19 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 PHE 0.009 0.001 PHE B 455 TYR 0.021 0.001 TYR A 279 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 166 GLU cc_start: 0.7725 (tp30) cc_final: 0.6856 (tp30) REVERT: A 347 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 360 MET cc_start: 0.6974 (ptm) cc_final: 0.6670 (ptm) REVERT: A 467 GLU cc_start: 0.4317 (OUTLIER) cc_final: 0.3357 (pt0) REVERT: A 544 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7358 (mt) REVERT: B 466 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.4891 (ttm170) REVERT: B 478 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6746 (mtpp) outliers start: 15 outliers final: 10 residues processed: 100 average time/residue: 0.1607 time to fit residues: 22.2358 Evaluate side-chains 100 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8017 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6644 Z= 0.212 Angle : 0.522 7.479 9031 Z= 0.262 Chirality : 0.042 0.137 954 Planarity : 0.004 0.043 1166 Dihedral : 4.156 23.825 940 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.03 % Allowed : 23.78 % Favored : 73.20 % 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: 0.68 (0.30), residues: 786 helix: 1.83 (0.27), residues: 382 sheet: 0.53 (0.76), residues: 42 loop : -1.13 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE B 455 TYR 0.021 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 259 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6796 (pt) REVERT: A 347 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8747 (p) REVERT: A 360 MET cc_start: 0.7094 (ptm) cc_final: 0.6817 (ptm) REVERT: A 467 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.3414 (pt0) REVERT: A 544 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7388 (mt) REVERT: B 466 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.4992 (ttm170) REVERT: B 478 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6818 (mtpp) REVERT: B 508 TYR cc_start: 0.9022 (m-80) cc_final: 0.8586 (m-80) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 0.1653 time to fit residues: 24.1972 Evaluate side-chains 106 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 467 ASP Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6644 Z= 0.213 Angle : 0.530 7.446 9031 Z= 0.266 Chirality : 0.042 0.138 954 Planarity : 0.004 0.044 1166 Dihedral : 4.190 23.573 940 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.45 % Allowed : 24.21 % Favored : 73.34 % 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: 0.59 (0.30), residues: 786 helix: 1.71 (0.27), residues: 390 sheet: 0.47 (0.76), residues: 42 loop : -1.17 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE B 455 TYR 0.021 0.001 TYR A 279 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 259 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6884 (pt) REVERT: A 347 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8747 (p) REVERT: A 360 MET cc_start: 0.7135 (ptm) cc_final: 0.6830 (ptm) REVERT: A 467 GLU cc_start: 0.4411 (OUTLIER) cc_final: 0.3488 (pt0) REVERT: A 544 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7386 (mt) REVERT: B 466 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.4963 (ttm170) REVERT: B 478 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6615 (mtpp) REVERT: B 508 TYR cc_start: 0.9048 (m-80) cc_final: 0.8625 (m-80) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.1608 time to fit residues: 22.1161 Evaluate side-chains 101 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6644 Z= 0.171 Angle : 0.516 7.406 9031 Z= 0.258 Chirality : 0.041 0.135 954 Planarity : 0.004 0.045 1166 Dihedral : 4.060 22.636 940 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.02 % Allowed : 24.64 % Favored : 73.34 % 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: 0.65 (0.30), residues: 786 helix: 1.76 (0.26), residues: 390 sheet: 0.53 (0.77), residues: 44 loop : -1.16 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE B 455 TYR 0.014 0.001 TYR A 207 ARG 0.003 0.000 ARG A 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 259 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.6853 (pt) REVERT: A 343 VAL cc_start: 0.6812 (p) cc_final: 0.6610 (m) REVERT: A 347 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8780 (p) REVERT: A 467 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.3488 (pt0) REVERT: A 510 TYR cc_start: 0.8367 (m-80) cc_final: 0.7951 (m-80) REVERT: A 544 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7377 (mt) REVERT: B 466 ARG cc_start: 0.6659 (OUTLIER) cc_final: 0.4856 (ttm170) REVERT: B 478 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6532 (mtpp) REVERT: B 508 TYR cc_start: 0.9004 (m-80) cc_final: 0.8515 (m-80) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.1637 time to fit residues: 22.0126 Evaluate side-chains 98 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 466 ARG Chi-restraints excluded: chain B residue 478 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.0030 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.184117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143227 restraints weight = 7302.050| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.24 r_work: 0.3443 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6644 Z= 0.177 Angle : 0.524 7.450 9031 Z= 0.260 Chirality : 0.041 0.135 954 Planarity : 0.004 0.045 1166 Dihedral : 4.030 22.006 940 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.73 % Allowed : 24.78 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 786 helix: 1.90 (0.27), residues: 382 sheet: -0.22 (0.71), residues: 56 loop : -1.10 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.001 PHE B 455 TYR 0.017 0.001 TYR A 279 ARG 0.003 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1725.71 seconds wall clock time: 31 minutes 34.26 seconds (1894.26 seconds total)