Starting phenix.real_space_refine on Sat Aug 3 01:45:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/08_2024/8wtd_37832.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/08_2024/8wtd_37832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/08_2024/8wtd_37832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/08_2024/8wtd_37832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/08_2024/8wtd_37832.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/08_2024/8wtd_37832.cif" } resolution = 3.06 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= 0.072 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 4134 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 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6456 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: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1555 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: 6456 At special positions: 0 Unit cell: (73.528, 91.304, 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 4134 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=1.99 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: 2.44 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 53.8% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 20 through 29 Processing helix chain 'A' and resid 31 through 53 removed outlier: 3.935A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.545A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 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 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.721A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.991A 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: 3.630A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.725A 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: 4.156A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.578A 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: 3.679A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.672A 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 446 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.745A 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: 4.115A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.543A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) removed outlier: 3.552A 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: 3.852A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.738A 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: 3.692A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.533A pdb=" N PHE B 371 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 removed outlier: 3.601A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.233A 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 354 through 358 removed outlier: 3.531A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.356A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454 removed outlier: 8.324A pdb=" N ASN B 450 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER B 494 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU B 452 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU B 492 " --> pdb=" O LEU B 452 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 843 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: 1.74 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1069 1.29 - 1.42: 1837 1.42 - 1.55: 3676 1.55 - 1.68: 0 1.68 - 1.81: 58 Bond restraints: 6640 Sorted by residual: bond pdb=" C PRO B 491 " pdb=" O PRO B 491 " ideal model delta sigma weight residual 1.235 1.156 0.079 1.30e-02 5.92e+03 3.70e+01 bond pdb=" CA ALA A 36 " pdb=" CB ALA A 36 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.58e-02 4.01e+03 2.50e+01 bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.532 1.454 0.077 1.59e-02 3.96e+03 2.38e+01 bond pdb=" CA SER B 490 " pdb=" CB SER B 490 " ideal model delta sigma weight residual 1.526 1.454 0.073 1.53e-02 4.27e+03 2.25e+01 bond pdb=" C PRO B 486 " pdb=" O PRO B 486 " ideal model delta sigma weight residual 1.233 1.190 0.043 9.60e-03 1.09e+04 2.03e+01 ... (remaining 6635 not shown) Histogram of bond angle deviations from ideal: 95.40 - 103.12: 62 103.12 - 110.85: 2196 110.85 - 118.57: 2959 118.57 - 126.29: 3665 126.29 - 134.01: 144 Bond angle restraints: 9026 Sorted by residual: angle pdb=" N LYS A 31 " pdb=" CA LYS A 31 " pdb=" C LYS A 31 " ideal model delta sigma weight residual 113.72 102.68 11.04 1.30e+00 5.92e-01 7.21e+01 angle pdb=" C PRO B 486 " pdb=" CA PRO B 486 " pdb=" CB PRO B 486 " ideal model delta sigma weight residual 111.40 103.78 7.62 9.10e-01 1.21e+00 7.02e+01 angle pdb=" CA ASP A 30 " pdb=" CB ASP A 30 " pdb=" CG ASP A 30 " ideal model delta sigma weight residual 112.60 120.71 -8.11 1.00e+00 1.00e+00 6.58e+01 angle pdb=" N PRO B 491 " pdb=" CA PRO B 491 " pdb=" CB PRO B 491 " ideal model delta sigma weight residual 103.25 95.40 7.85 1.05e+00 9.07e-01 5.58e+01 angle pdb=" N TYR B 489 " pdb=" CA TYR B 489 " pdb=" CB TYR B 489 " ideal model delta sigma weight residual 110.49 123.07 -12.58 1.69e+00 3.50e-01 5.54e+01 ... (remaining 9021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.48: 3455 20.48 - 40.96: 393 40.96 - 61.43: 110 61.43 - 81.91: 10 81.91 - 102.39: 10 Dihedral angle restraints: 3978 sinusoidal: 1658 harmonic: 2320 Sorted by residual: 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 38.78 54.22 1 1.00e+01 1.00e-02 3.99e+01 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 93.00 147.16 -54.16 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C PHE A 28 " pdb=" N PHE A 28 " pdb=" CA PHE A 28 " pdb=" CB PHE A 28 " ideal model delta harmonic sigma weight residual -122.60 -108.45 -14.15 0 2.50e+00 1.60e-01 3.20e+01 ... (remaining 3975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 822 0.068 - 0.135: 111 0.135 - 0.203: 12 0.203 - 0.271: 8 0.271 - 0.338: 2 Chirality restraints: 955 Sorted by residual: chirality pdb=" CA PHE A 28 " pdb=" N PHE A 28 " pdb=" C PHE A 28 " pdb=" CB PHE A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.86e+00 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 2.79 -0.28 2.00e-01 2.50e+01 2.01e+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 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 952 not shown) Planarity restraints: 1169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 81 " -0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C GLN A 81 " 0.087 2.00e-02 2.50e+03 pdb=" O GLN A 81 " -0.032 2.00e-02 2.50e+03 pdb=" N MET A 82 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 470 " -0.017 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C THR B 470 " 0.054 2.00e-02 2.50e+03 pdb=" O THR B 470 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU B 471 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 478 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.83e+00 pdb=" N PRO B 479 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.036 5.00e-02 4.00e+02 ... (remaining 1166 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1201 2.77 - 3.30: 6090 3.30 - 3.83: 11023 3.83 - 4.37: 12761 4.37 - 4.90: 22451 Nonbonded interactions: 53526 Sorted by model distance: nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 215 " pdb=" OE1 GLU A 571 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.267 3.040 nonbonded pdb=" O ASP A 499 " pdb=" OG SER A 502 " model vdw 2.268 3.040 ... (remaining 53521 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.060 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 6640 Z= 0.322 Angle : 0.901 12.584 9026 Z= 0.563 Chirality : 0.053 0.338 955 Planarity : 0.004 0.065 1165 Dihedral : 18.482 102.391 2470 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.34 % Favored : 93.89 % Rotamer: Outliers : 0.72 % Allowed : 23.34 % Favored : 75.94 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 786 helix: 0.90 (0.27), residues: 403 sheet: 1.39 (0.86), residues: 44 loop : -1.35 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.006 0.001 HIS A 34 PHE 0.017 0.001 PHE A 369 TYR 0.027 0.001 TYR B 453 ARG 0.002 0.000 ARG B 457 *********************** 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 120 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.672 Fit side-chains REVERT: A 75 GLU cc_start: 0.6860 (tt0) cc_final: 0.6326 (mt-10) REVERT: A 102 GLN cc_start: 0.7864 (mm110) cc_final: 0.7586 (mm-40) REVERT: A 168 TRP cc_start: 0.7271 (t-100) cc_final: 0.6659 (t-100) REVERT: A 224 GLU cc_start: 0.5770 (mt-10) cc_final: 0.5432 (mm-30) REVERT: A 227 GLU cc_start: 0.6494 (tt0) cc_final: 0.5957 (mt-10) REVERT: A 325 GLN cc_start: 0.7254 (tm130) cc_final: 0.7025 (tp-100) REVERT: A 402 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7198 (mt-10) REVERT: A 480 MET cc_start: 0.7646 (mtp) cc_final: 0.7376 (mtp) REVERT: A 547 SER cc_start: 0.8332 (t) cc_final: 0.7914 (p) REVERT: A 552 GLN cc_start: 0.7398 (tp40) cc_final: 0.7114 (tp40) REVERT: A 562 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7512 (mttp) REVERT: A 577 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7628 (mtpp) REVERT: A 589 GLU cc_start: 0.6757 (tp30) cc_final: 0.6483 (tp30) REVERT: B 356 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8294 (tttm) REVERT: B 471 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: B 493 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7035 (tm130) outliers start: 5 outliers final: 1 residues processed: 118 average time/residue: 0.1895 time to fit residues: 29.4466 Evaluate side-chains 93 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 493 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6640 Z= 0.217 Angle : 0.581 7.505 9026 Z= 0.292 Chirality : 0.043 0.162 955 Planarity : 0.004 0.042 1165 Dihedral : 7.706 56.747 948 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 2.45 % Allowed : 22.19 % 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: 0.15 (0.31), residues: 786 helix: 0.98 (0.27), residues: 408 sheet: 1.03 (0.79), residues: 44 loop : -1.14 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.019 0.001 PHE A 369 TYR 0.010 0.001 TYR A 237 ARG 0.002 0.000 ARG B 355 *********************** 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 104 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.738 Fit side-chains REVERT: A 35 GLU cc_start: 0.7690 (mp0) cc_final: 0.7484 (mp0) REVERT: A 75 GLU cc_start: 0.6695 (tt0) cc_final: 0.6099 (mt-10) REVERT: A 102 GLN cc_start: 0.7875 (mm110) cc_final: 0.7601 (mm-40) REVERT: A 166 GLU cc_start: 0.6812 (tp30) cc_final: 0.6576 (tp30) REVERT: A 168 TRP cc_start: 0.7192 (t-100) cc_final: 0.6834 (t-100) REVERT: A 224 GLU cc_start: 0.5885 (mt-10) cc_final: 0.5517 (mm-30) REVERT: A 227 GLU cc_start: 0.6459 (tt0) cc_final: 0.5991 (mt-10) REVERT: A 325 GLN cc_start: 0.7432 (tm130) cc_final: 0.6978 (tp-100) REVERT: A 364 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7758 (t) REVERT: A 402 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7237 (mt-10) REVERT: A 423 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 483 GLU cc_start: 0.7520 (pt0) cc_final: 0.7124 (mt-10) REVERT: A 547 SER cc_start: 0.8417 (t) cc_final: 0.8165 (t) REVERT: A 552 GLN cc_start: 0.7669 (tp40) cc_final: 0.7362 (tp40) REVERT: A 562 LYS cc_start: 0.8540 (ttpp) cc_final: 0.7762 (tttt) REVERT: A 577 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7716 (mtpp) REVERT: A 589 GLU cc_start: 0.6992 (tp30) cc_final: 0.6616 (tp30) REVERT: B 356 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8285 (tttm) REVERT: B 493 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.6940 (tm130) outliers start: 17 outliers final: 9 residues processed: 100 average time/residue: 0.1580 time to fit residues: 22.2327 Evaluate side-chains 92 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6640 Z= 0.290 Angle : 0.613 8.025 9026 Z= 0.305 Chirality : 0.044 0.146 955 Planarity : 0.004 0.040 1165 Dihedral : 6.413 55.182 945 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 3.60 % Allowed : 21.76 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.30), residues: 786 helix: 0.81 (0.26), residues: 416 sheet: 0.70 (0.76), residues: 44 loop : -1.09 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.007 0.001 HIS A 34 PHE 0.023 0.002 PHE A 369 TYR 0.013 0.002 TYR A 237 ARG 0.002 0.001 ARG B 498 *********************** 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 111 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 86 time to evaluate : 0.693 Fit side-chains REVERT: A 60 GLN cc_start: 0.6175 (mm-40) cc_final: 0.5794 (mm-40) REVERT: A 68 LYS cc_start: 0.7134 (mmpt) cc_final: 0.6386 (mptt) REVERT: A 75 GLU cc_start: 0.6743 (tt0) cc_final: 0.6051 (mt-10) REVERT: A 102 GLN cc_start: 0.7889 (mm110) cc_final: 0.7501 (mm-40) REVERT: A 168 TRP cc_start: 0.7537 (t-100) cc_final: 0.6989 (t-100) REVERT: A 215 TYR cc_start: 0.7874 (m-80) cc_final: 0.7304 (m-80) REVERT: A 224 GLU cc_start: 0.5869 (mt-10) cc_final: 0.5544 (mm-30) REVERT: A 227 GLU cc_start: 0.6552 (tt0) cc_final: 0.6119 (mt-10) REVERT: A 325 GLN cc_start: 0.7588 (tm130) cc_final: 0.7070 (tp-100) REVERT: A 402 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7218 (mt-10) REVERT: A 483 GLU cc_start: 0.7317 (pt0) cc_final: 0.6929 (mt-10) REVERT: A 547 SER cc_start: 0.8520 (t) cc_final: 0.8237 (t) REVERT: A 558 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7920 (mp) REVERT: A 562 LYS cc_start: 0.8720 (ttpp) cc_final: 0.7927 (tttt) REVERT: A 577 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7748 (mtmt) REVERT: A 589 GLU cc_start: 0.7109 (tp30) cc_final: 0.6658 (tp30) REVERT: B 356 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8174 (tttm) REVERT: B 493 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.6982 (tm130) outliers start: 25 outliers final: 11 residues processed: 105 average time/residue: 0.1497 time to fit residues: 22.4559 Evaluate side-chains 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 62 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6640 Z= 0.176 Angle : 0.521 7.052 9026 Z= 0.264 Chirality : 0.041 0.138 955 Planarity : 0.004 0.045 1165 Dihedral : 5.736 53.388 945 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 1.73 % Allowed : 23.49 % 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: 0.19 (0.30), residues: 786 helix: 1.10 (0.27), residues: 405 sheet: 0.70 (0.75), residues: 44 loop : -1.16 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A 34 PHE 0.016 0.001 PHE A 369 TYR 0.009 0.001 TYR A 237 ARG 0.001 0.000 ARG A 559 *********************** 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 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.6149 (mm-40) cc_final: 0.5788 (mm-40) REVERT: A 68 LYS cc_start: 0.7081 (mmpt) cc_final: 0.6360 (mptt) REVERT: A 75 GLU cc_start: 0.6663 (tt0) cc_final: 0.5999 (mt-10) REVERT: A 102 GLN cc_start: 0.7856 (mm110) cc_final: 0.7421 (mm-40) REVERT: A 168 TRP cc_start: 0.7520 (t-100) cc_final: 0.7102 (t-100) REVERT: A 224 GLU cc_start: 0.5866 (mt-10) cc_final: 0.5545 (mm-30) REVERT: A 227 GLU cc_start: 0.6458 (tt0) cc_final: 0.5966 (mt-10) REVERT: A 325 GLN cc_start: 0.7559 (tm130) cc_final: 0.7062 (tp-100) REVERT: A 483 GLU cc_start: 0.7293 (pt0) cc_final: 0.6891 (mt-10) REVERT: A 547 SER cc_start: 0.8519 (t) cc_final: 0.8245 (t) REVERT: A 562 LYS cc_start: 0.8636 (ttpp) cc_final: 0.7840 (tttt) REVERT: A 577 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7672 (mtmt) REVERT: B 356 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8274 (tttm) REVERT: B 493 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.6963 (tm130) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.1557 time to fit residues: 19.6391 Evaluate side-chains 91 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6640 Z= 0.207 Angle : 0.539 7.482 9026 Z= 0.273 Chirality : 0.042 0.133 955 Planarity : 0.004 0.043 1165 Dihedral : 5.553 53.903 945 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.83 % Favored : 95.04 % Rotamer: Outliers : 2.88 % Allowed : 22.77 % Favored : 74.35 % 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: 0.20 (0.30), residues: 786 helix: 1.07 (0.27), residues: 409 sheet: 0.65 (0.74), residues: 44 loop : -1.12 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.017 0.001 PHE A 369 TYR 0.010 0.001 TYR A 237 ARG 0.001 0.000 ARG A 177 *********************** 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 109 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.6184 (mm-40) cc_final: 0.5792 (mm-40) REVERT: A 68 LYS cc_start: 0.7103 (mmpt) cc_final: 0.6402 (mptt) REVERT: A 102 GLN cc_start: 0.7897 (mm110) cc_final: 0.7603 (mm-40) REVERT: A 168 TRP cc_start: 0.7641 (t-100) cc_final: 0.7274 (t-100) REVERT: A 215 TYR cc_start: 0.7871 (m-80) cc_final: 0.7343 (m-80) REVERT: A 224 GLU cc_start: 0.5845 (mt-10) cc_final: 0.5532 (mm-30) REVERT: A 227 GLU cc_start: 0.6467 (tt0) cc_final: 0.5967 (mt-10) REVERT: A 325 GLN cc_start: 0.7564 (tm130) cc_final: 0.7123 (tp-100) REVERT: A 353 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8654 (mtpt) REVERT: A 402 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7198 (mt-10) REVERT: A 476 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5708 (tptp) REVERT: A 547 SER cc_start: 0.8534 (t) cc_final: 0.8237 (t) REVERT: A 558 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 562 LYS cc_start: 0.8662 (ttpp) cc_final: 0.7873 (tttt) REVERT: A 577 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7684 (mtmt) REVERT: B 356 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8230 (tttm) REVERT: B 493 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6850 (tm130) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 0.1569 time to fit residues: 22.5881 Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR 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: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.0370 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6640 Z= 0.170 Angle : 0.514 7.112 9026 Z= 0.260 Chirality : 0.041 0.132 955 Planarity : 0.004 0.043 1165 Dihedral : 5.313 54.560 945 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 2.88 % Allowed : 22.33 % 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: 0.29 (0.30), residues: 786 helix: 1.26 (0.27), residues: 398 sheet: 0.68 (0.74), residues: 44 loop : -1.16 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.001 PHE A 369 TYR 0.009 0.001 TYR A 237 ARG 0.001 0.000 ARG A 177 *********************** 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 108 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.703 Fit side-chains REVERT: A 30 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7292 (t70) REVERT: A 60 GLN cc_start: 0.6186 (mm-40) cc_final: 0.5786 (mm-40) REVERT: A 68 LYS cc_start: 0.7089 (mmpt) cc_final: 0.6375 (mptt) REVERT: A 102 GLN cc_start: 0.7853 (mm110) cc_final: 0.7086 (mt0) REVERT: A 168 TRP cc_start: 0.7764 (t-100) cc_final: 0.7479 (t-100) REVERT: A 215 TYR cc_start: 0.7852 (m-80) cc_final: 0.7370 (m-80) REVERT: A 224 GLU cc_start: 0.5811 (mt-10) cc_final: 0.5495 (mm-30) REVERT: A 227 GLU cc_start: 0.6403 (tt0) cc_final: 0.5917 (mt-10) REVERT: A 325 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7068 (tp-100) REVERT: A 353 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8653 (mtpt) REVERT: A 364 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7673 (t) REVERT: A 402 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7177 (mt-10) REVERT: A 467 GLU cc_start: 0.4269 (OUTLIER) cc_final: 0.4042 (pm20) REVERT: A 476 LYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5724 (tptp) REVERT: A 547 SER cc_start: 0.8528 (t) cc_final: 0.8225 (t) REVERT: A 562 LYS cc_start: 0.8634 (ttpp) cc_final: 0.7845 (tttt) REVERT: A 577 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7638 (mtmt) REVERT: B 356 LYS cc_start: 0.8453 (ttmm) cc_final: 0.8246 (tttm) REVERT: B 493 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6883 (tm130) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 0.1567 time to fit residues: 22.4550 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0060 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.7745 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6640 Z= 0.162 Angle : 0.507 7.185 9026 Z= 0.257 Chirality : 0.041 0.132 955 Planarity : 0.004 0.043 1165 Dihedral : 5.213 55.187 945 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 2.59 % Allowed : 22.91 % Favored : 74.50 % 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: 0.31 (0.30), residues: 786 helix: 1.23 (0.27), residues: 403 sheet: 0.77 (0.74), residues: 44 loop : -1.13 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.001 PHE A 369 TYR 0.017 0.001 TYR B 365 ARG 0.001 0.000 ARG A 177 *********************** 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 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.6206 (mm-40) cc_final: 0.5810 (mm-40) REVERT: A 68 LYS cc_start: 0.7066 (mmpt) cc_final: 0.6358 (mptt) REVERT: A 102 GLN cc_start: 0.7841 (mm110) cc_final: 0.7061 (mt0) REVERT: A 168 TRP cc_start: 0.7805 (t-100) cc_final: 0.7559 (t-100) REVERT: A 215 TYR cc_start: 0.7874 (m-80) cc_final: 0.7411 (m-80) REVERT: A 224 GLU cc_start: 0.5845 (mt-10) cc_final: 0.5521 (mm-30) REVERT: A 227 GLU cc_start: 0.6408 (tt0) cc_final: 0.6020 (mt-10) REVERT: A 325 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7246 (tp-100) REVERT: A 353 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8640 (mtpt) REVERT: A 364 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7664 (t) REVERT: A 397 ASN cc_start: 0.8234 (p0) cc_final: 0.8030 (p0) REVERT: A 402 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7199 (mt-10) REVERT: A 408 MET cc_start: 0.7821 (mpp) cc_final: 0.7468 (mmm) REVERT: A 467 GLU cc_start: 0.4304 (OUTLIER) cc_final: 0.4081 (pm20) REVERT: A 476 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5720 (tptp) REVERT: A 547 SER cc_start: 0.8526 (t) cc_final: 0.8234 (t) REVERT: A 562 LYS cc_start: 0.8620 (ttpp) cc_final: 0.7844 (tttt) REVERT: A 577 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7614 (mtmt) REVERT: B 356 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8202 (tttm) REVERT: B 493 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.6829 (tm130) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 0.1671 time to fit residues: 22.8918 Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR 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: 0.8980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6640 Z= 0.204 Angle : 0.528 7.447 9026 Z= 0.267 Chirality : 0.042 0.132 955 Planarity : 0.004 0.043 1165 Dihedral : 4.834 54.398 943 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 2.31 % Allowed : 22.91 % 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: 0.26 (0.30), residues: 786 helix: 1.16 (0.26), residues: 403 sheet: 0.81 (0.74), residues: 44 loop : -1.13 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 34 PHE 0.016 0.001 PHE A 369 TYR 0.010 0.001 TYR A 237 ARG 0.002 0.000 ARG A 177 *********************** 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 101 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 68 LYS cc_start: 0.7091 (mmpt) cc_final: 0.6384 (mptt) REVERT: A 102 GLN cc_start: 0.7854 (mm110) cc_final: 0.7071 (mt0) REVERT: A 168 TRP cc_start: 0.7862 (t-100) cc_final: 0.7617 (t-100) REVERT: A 215 TYR cc_start: 0.7907 (m-80) cc_final: 0.7489 (m-80) REVERT: A 224 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5521 (mm-30) REVERT: A 227 GLU cc_start: 0.6426 (tt0) cc_final: 0.6049 (mt-10) REVERT: A 353 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8662 (mtpt) REVERT: A 364 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7686 (t) REVERT: A 402 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7241 (mt-10) REVERT: A 467 GLU cc_start: 0.4452 (OUTLIER) cc_final: 0.4187 (pm20) REVERT: A 476 LYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5740 (tptp) REVERT: A 547 SER cc_start: 0.8546 (t) cc_final: 0.8245 (t) REVERT: A 562 LYS cc_start: 0.8663 (ttpp) cc_final: 0.7877 (tttt) REVERT: A 577 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7622 (mtmt) REVERT: B 356 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8197 (tttm) REVERT: B 493 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.6907 (tm130) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 0.1740 time to fit residues: 23.8347 Evaluate side-chains 97 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6640 Z= 0.195 Angle : 0.525 7.344 9026 Z= 0.265 Chirality : 0.042 0.133 955 Planarity : 0.004 0.043 1165 Dihedral : 4.795 54.427 943 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 2.88 % Allowed : 22.33 % 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: 0.29 (0.30), residues: 786 helix: 1.18 (0.26), residues: 403 sheet: 0.80 (0.75), residues: 44 loop : -1.12 (0.33), residues: 339 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 0.016 0.001 PHE A 369 TYR 0.017 0.001 TYR B 365 ARG 0.002 0.000 ARG A 177 *********************** 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: 20 poor density : 83 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7649 (mp0) cc_final: 0.7161 (mp0) REVERT: A 68 LYS cc_start: 0.7047 (mmpt) cc_final: 0.6320 (mptt) REVERT: A 102 GLN cc_start: 0.7850 (mm110) cc_final: 0.7532 (mm110) REVERT: A 168 TRP cc_start: 0.7876 (t-100) cc_final: 0.7612 (t-100) REVERT: A 215 TYR cc_start: 0.7919 (m-80) cc_final: 0.7457 (m-80) REVERT: A 224 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5493 (mm-30) REVERT: A 227 GLU cc_start: 0.6398 (tt0) cc_final: 0.6040 (mt-10) REVERT: A 353 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8652 (mtpt) REVERT: A 364 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7674 (t) REVERT: A 402 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7207 (mt-10) REVERT: A 467 GLU cc_start: 0.4521 (OUTLIER) cc_final: 0.3356 (pm20) REVERT: A 476 LYS cc_start: 0.6114 (OUTLIER) cc_final: 0.5727 (tptp) REVERT: A 494 ASP cc_start: 0.7515 (m-30) cc_final: 0.7192 (t70) REVERT: A 547 SER cc_start: 0.8552 (t) cc_final: 0.8246 (t) REVERT: A 562 LYS cc_start: 0.8656 (ttpp) cc_final: 0.7873 (tttt) REVERT: A 577 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7602 (mtmt) REVERT: A 582 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6519 (mmm160) REVERT: B 356 LYS cc_start: 0.8415 (ttmm) cc_final: 0.8189 (tttm) REVERT: B 493 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.6864 (tm130) outliers start: 20 outliers final: 13 residues processed: 99 average time/residue: 0.1698 time to fit residues: 22.9947 Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0370 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6640 Z= 0.151 Angle : 0.498 7.027 9026 Z= 0.252 Chirality : 0.041 0.128 955 Planarity : 0.004 0.044 1165 Dihedral : 4.601 55.369 943 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer: Outliers : 2.16 % Allowed : 23.34 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 786 helix: 1.27 (0.27), residues: 403 sheet: 0.77 (0.74), residues: 44 loop : -1.05 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 34 PHE 0.014 0.001 PHE A 369 TYR 0.008 0.001 TYR A 237 ARG 0.001 0.000 ARG A 559 ********************** 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 96 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7636 (mp0) cc_final: 0.7182 (mp0) REVERT: A 68 LYS cc_start: 0.7104 (mmpt) cc_final: 0.6381 (mptt) REVERT: A 102 GLN cc_start: 0.7843 (mm110) cc_final: 0.7478 (mm110) REVERT: A 126 ILE cc_start: 0.6970 (mt) cc_final: 0.6286 (mt) REVERT: A 168 TRP cc_start: 0.7894 (t-100) cc_final: 0.7623 (t-100) REVERT: A 215 TYR cc_start: 0.7839 (m-80) cc_final: 0.7375 (m-80) REVERT: A 224 GLU cc_start: 0.5828 (mt-10) cc_final: 0.5513 (mm-30) REVERT: A 227 GLU cc_start: 0.6324 (tt0) cc_final: 0.5974 (mt-10) REVERT: A 364 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7557 (t) REVERT: A 366 MET cc_start: 0.7465 (tpp) cc_final: 0.7178 (ttt) REVERT: A 408 MET cc_start: 0.7814 (mpp) cc_final: 0.7332 (mmm) REVERT: A 467 GLU cc_start: 0.4381 (OUTLIER) cc_final: 0.4174 (pm20) REVERT: A 474 MET cc_start: 0.6809 (mmp) cc_final: 0.6576 (mmp) REVERT: A 476 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5599 (tptp) REVERT: A 480 MET cc_start: 0.7464 (mtp) cc_final: 0.7227 (mtp) REVERT: A 494 ASP cc_start: 0.7520 (m-30) cc_final: 0.7199 (t0) REVERT: A 547 SER cc_start: 0.8551 (t) cc_final: 0.8244 (t) REVERT: A 562 LYS cc_start: 0.8600 (ttpp) cc_final: 0.7827 (tttt) REVERT: A 577 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7543 (mtmt) REVERT: B 356 LYS cc_start: 0.8436 (ttmm) cc_final: 0.8198 (tttm) REVERT: B 493 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.6782 (tm130) outliers start: 15 outliers final: 10 residues processed: 92 average time/residue: 0.2435 time to fit residues: 31.0809 Evaluate side-chains 94 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 552 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.179281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142419 restraints weight = 6769.967| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.36 r_work: 0.3449 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6640 Z= 0.209 Angle : 0.530 7.448 9026 Z= 0.268 Chirality : 0.042 0.132 955 Planarity : 0.004 0.043 1165 Dihedral : 4.745 54.630 943 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.58 % Favored : 95.29 % Rotamer: Outliers : 2.59 % Allowed : 22.91 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 786 helix: 1.20 (0.27), residues: 403 sheet: 0.76 (0.75), residues: 44 loop : -1.06 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS A 241 PHE 0.016 0.001 PHE A 369 TYR 0.015 0.001 TYR B 365 ARG 0.002 0.000 ARG A 582 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.93 seconds wall clock time: 33 minutes 3.07 seconds (1983.07 seconds total)