Starting phenix.real_space_refine on Mon Sep 23 23:20:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/09_2024/6pzt_20537.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/09_2024/6pzt_20537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/09_2024/6pzt_20537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/09_2024/6pzt_20537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/09_2024/6pzt_20537.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/09_2024/6pzt_20537.cif" } resolution = 3.46 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= 0.058 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 24 5.16 5 C 3914 2.51 5 N 1026 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6062 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3031 Classifications: {'peptide': 466} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 126} Link IDs: {'PTRANS': 15, 'TRANS': 450} Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 683 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 233 Restraints were copied for chains: B Time building chain proxies: 5.26, per 1000 atoms: 0.87 Number of scatterers: 6062 At special positions: 0 Unit cell: (82.95, 101.85, 87.15, 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 24 16.00 O 1098 8.00 N 1026 7.00 C 3914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 843.8 milliseconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 301 through 315 removed outlier: 4.364A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 342 removed outlier: 3.789A pdb=" N VAL B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.702A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.461A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.104A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 517 through 542 removed outlier: 3.699A pdb=" N GLY B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.790A pdb=" N LYS B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.528A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 632 removed outlier: 4.069A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 641 through 645 removed outlier: 4.510A pdb=" N GLY B 644 " --> pdb=" O PHE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 668 removed outlier: 4.130A pdb=" N ILE B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 698 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.901A pdb=" N SER B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 752 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 301 through 315 removed outlier: 4.363A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.789A pdb=" N VAL A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.702A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 removed outlier: 4.460A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 454 removed outlier: 4.104A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 517 through 542 removed outlier: 3.698A pdb=" N GLY A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.790A pdb=" N LYS A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.529A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 632 removed outlier: 4.069A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.511A pdb=" N GLY A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 4.130A pdb=" N ILE A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 698 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.901A pdb=" N SER A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 492 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1990 1.34 - 1.46: 1608 1.46 - 1.58: 2564 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6194 Sorted by residual: bond pdb=" CB TRP A 310 " pdb=" CG TRP A 310 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.09e+00 bond pdb=" CB TRP B 310 " pdb=" CG TRP B 310 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB THR B 328 " pdb=" CG2 THR B 328 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CB THR A 328 " pdb=" CG2 THR A 328 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB TYR A 468 " pdb=" CG TYR A 468 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.20e-02 2.07e+03 1.24e+00 ... (remaining 6189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 7957 1.35 - 2.70: 435 2.70 - 4.04: 65 4.04 - 5.39: 31 5.39 - 6.74: 6 Bond angle restraints: 8494 Sorted by residual: angle pdb=" C PHE B 599 " pdb=" N THR B 600 " pdb=" CA THR B 600 " ideal model delta sigma weight residual 120.58 125.14 -4.56 1.32e+00 5.74e-01 1.20e+01 angle pdb=" N VAL B 347 " pdb=" CA VAL B 347 " pdb=" C VAL B 347 " ideal model delta sigma weight residual 112.50 108.27 4.23 1.39e+00 5.18e-01 9.25e+00 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 112.50 108.35 4.15 1.39e+00 5.18e-01 8.92e+00 angle pdb=" C GLY A 585 " pdb=" N LEU A 586 " pdb=" CA LEU A 586 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 angle pdb=" C GLY B 585 " pdb=" N LEU B 586 " pdb=" CA LEU B 586 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.79e+00 ... (remaining 8489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.65: 2988 10.65 - 21.30: 326 21.30 - 31.96: 89 31.96 - 42.61: 39 42.61 - 53.26: 14 Dihedral angle restraints: 3456 sinusoidal: 882 harmonic: 2574 Sorted by residual: dihedral pdb=" CA LEU B 698 " pdb=" C LEU B 698 " pdb=" N ALA B 699 " pdb=" CA ALA B 699 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU A 698 " pdb=" C LEU A 698 " pdb=" N ALA A 699 " pdb=" CA ALA A 699 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL A 557 " pdb=" C VAL A 557 " pdb=" N THR A 558 " pdb=" CA THR A 558 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 3453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 444 0.027 - 0.054: 319 0.054 - 0.081: 165 0.081 - 0.108: 51 0.108 - 0.134: 37 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CB VAL A 673 " pdb=" CA VAL A 673 " pdb=" CG1 VAL A 673 " pdb=" CG2 VAL A 673 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CB VAL B 673 " pdb=" CA VAL B 673 " pdb=" CG1 VAL B 673 " pdb=" CG2 VAL B 673 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA PRO B 601 " pdb=" N PRO B 601 " pdb=" C PRO B 601 " pdb=" CB PRO B 601 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1013 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 600 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 601 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 601 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 601 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 600 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B 601 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 601 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 601 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 371 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C ILE B 371 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE B 371 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 372 " -0.008 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 80 2.60 - 3.18: 6456 3.18 - 3.75: 9862 3.75 - 4.33: 12445 4.33 - 4.90: 19723 Nonbonded interactions: 48566 Sorted by model distance: nonbonded pdb=" SG CYS A 563 " pdb=" SG CYS A 568 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " model vdw 2.031 3.760 nonbonded pdb=" OD2 ASP B 448 " pdb=" OG SER B 597 " model vdw 2.120 3.040 nonbonded pdb=" OD2 ASP A 448 " pdb=" OG SER A 597 " model vdw 2.121 3.040 nonbonded pdb=" O SER A 609 " pdb=" OG SER A 613 " model vdw 2.185 3.040 ... (remaining 48561 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.430 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.150 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 6194 Z= 0.473 Angle : 0.746 6.741 8494 Z= 0.425 Chirality : 0.047 0.134 1016 Planarity : 0.004 0.042 1104 Dihedral : 11.587 50.244 1826 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.43 % Allowed : 10.30 % Favored : 89.27 % 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: -3.13 (0.25), residues: 928 helix: -1.36 (0.17), residues: 628 sheet: None (None), residues: 0 loop : -3.49 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.000 HIS A 398 PHE 0.016 0.002 PHE A 488 TYR 0.018 0.002 TYR A 751 ARG 0.004 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.658 Fit side-chains REVERT: B 358 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8174 (mtm180) REVERT: B 433 LYS cc_start: 0.6335 (mmmt) cc_final: 0.5809 (tttt) REVERT: B 436 ILE cc_start: 0.8072 (mm) cc_final: 0.7690 (mt) REVERT: B 562 ASN cc_start: 0.7878 (p0) cc_final: 0.7305 (p0) REVERT: A 358 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8171 (mtm180) REVERT: A 433 LYS cc_start: 0.6590 (mmmt) cc_final: 0.6211 (tttt) REVERT: A 562 ASN cc_start: 0.7850 (p0) cc_final: 0.7338 (p0) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1575 time to fit residues: 26.4584 Evaluate side-chains 89 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 9.9990 chunk 69 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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: 0.7467 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6194 Z= 0.200 Angle : 0.623 6.764 8494 Z= 0.338 Chirality : 0.043 0.133 1016 Planarity : 0.005 0.062 1104 Dihedral : 5.135 22.415 962 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.29 % Allowed : 14.81 % Favored : 80.90 % 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 (0.28), residues: 928 helix: 0.56 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -2.68 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 733 HIS 0.001 0.000 HIS A 695 PHE 0.011 0.001 PHE B 465 TYR 0.011 0.001 TYR A 584 ARG 0.006 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.660 Fit side-chains REVERT: B 292 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7099 (tt) REVERT: B 358 ARG cc_start: 0.8419 (ttm170) cc_final: 0.7748 (mtm180) REVERT: B 429 GLU cc_start: 0.8174 (pt0) cc_final: 0.7949 (pm20) REVERT: B 433 LYS cc_start: 0.6377 (mmmt) cc_final: 0.5827 (tttt) REVERT: B 436 ILE cc_start: 0.8104 (mm) cc_final: 0.7702 (mt) REVERT: B 562 ASN cc_start: 0.7746 (p0) cc_final: 0.7156 (p0) REVERT: B 739 TYR cc_start: 0.8645 (m-80) cc_final: 0.8425 (m-80) REVERT: A 358 ARG cc_start: 0.8596 (ttm170) cc_final: 0.7991 (mtm180) REVERT: A 433 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6159 (tttt) REVERT: A 435 GLN cc_start: 0.7602 (tt0) cc_final: 0.7315 (tt0) REVERT: A 436 ILE cc_start: 0.7974 (mm) cc_final: 0.7574 (mt) REVERT: A 563 CYS cc_start: 0.7337 (t) cc_final: 0.6991 (t) outliers start: 20 outliers final: 8 residues processed: 128 average time/residue: 0.1557 time to fit residues: 26.9234 Evaluate side-chains 100 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 679 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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: 0.7453 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6194 Z= 0.181 Angle : 0.580 5.495 8494 Z= 0.314 Chirality : 0.043 0.123 1016 Planarity : 0.005 0.065 1104 Dihedral : 4.762 19.429 962 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.94 % Allowed : 17.38 % Favored : 77.68 % 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: -0.23 (0.28), residues: 928 helix: 0.83 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.63 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 733 HIS 0.002 0.001 HIS A 695 PHE 0.026 0.001 PHE B 659 TYR 0.006 0.001 TYR A 751 ARG 0.007 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.674 Fit side-chains REVERT: B 351 ARG cc_start: 0.7541 (mmp-170) cc_final: 0.7318 (mmm160) REVERT: B 358 ARG cc_start: 0.8432 (ttm170) cc_final: 0.8194 (ptm160) REVERT: B 429 GLU cc_start: 0.8198 (pt0) cc_final: 0.7958 (pm20) REVERT: B 433 LYS cc_start: 0.6419 (mmmt) cc_final: 0.5890 (tttt) REVERT: B 436 ILE cc_start: 0.8102 (mm) cc_final: 0.7702 (mt) REVERT: B 562 ASN cc_start: 0.7715 (p0) cc_final: 0.7310 (p0) REVERT: B 680 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7782 (t0) REVERT: B 739 TYR cc_start: 0.8603 (m-80) cc_final: 0.8398 (m-80) REVERT: A 358 ARG cc_start: 0.8601 (ttm170) cc_final: 0.8355 (ptm160) REVERT: A 433 LYS cc_start: 0.6612 (mmmt) cc_final: 0.6136 (tttt) REVERT: A 435 GLN cc_start: 0.7507 (tt0) cc_final: 0.7247 (tt0) REVERT: A 436 ILE cc_start: 0.7958 (mm) cc_final: 0.7540 (mt) REVERT: A 562 ASN cc_start: 0.7625 (p0) cc_final: 0.7112 (p0) REVERT: A 563 CYS cc_start: 0.6812 (t) cc_final: 0.6503 (t) outliers start: 23 outliers final: 6 residues processed: 121 average time/residue: 0.1509 time to fit residues: 24.7733 Evaluate side-chains 103 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 620 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6194 Z= 0.170 Angle : 0.569 5.808 8494 Z= 0.307 Chirality : 0.042 0.121 1016 Planarity : 0.005 0.065 1104 Dihedral : 4.547 18.540 962 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 5.36 % Allowed : 19.74 % Favored : 74.89 % 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: 0.11 (0.28), residues: 928 helix: 1.06 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.40 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.033 0.001 PHE A 659 TYR 0.006 0.001 TYR A 751 ARG 0.007 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.544 Fit side-chains REVERT: B 294 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7927 (ttm-80) REVERT: B 351 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7191 (mmm160) REVERT: B 358 ARG cc_start: 0.8476 (ttm170) cc_final: 0.8227 (ptm160) REVERT: B 433 LYS cc_start: 0.6405 (mmmt) cc_final: 0.5891 (tttt) REVERT: B 436 ILE cc_start: 0.8027 (mm) cc_final: 0.7629 (mt) REVERT: B 562 ASN cc_start: 0.7747 (p0) cc_final: 0.7095 (p0) REVERT: B 680 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7709 (t0) REVERT: B 727 MET cc_start: 0.8027 (ttp) cc_final: 0.7560 (ttp) REVERT: A 358 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8379 (ptm160) REVERT: A 429 GLU cc_start: 0.8106 (pm20) cc_final: 0.7732 (pm20) REVERT: A 433 LYS cc_start: 0.6542 (mmmt) cc_final: 0.6122 (tttt) REVERT: A 435 GLN cc_start: 0.7539 (tt0) cc_final: 0.7298 (tt0) REVERT: A 436 ILE cc_start: 0.7928 (mm) cc_final: 0.7520 (mt) REVERT: A 562 ASN cc_start: 0.7568 (p0) cc_final: 0.6901 (p0) REVERT: A 563 CYS cc_start: 0.6890 (t) cc_final: 0.6634 (t) REVERT: A 679 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.8908 (p) outliers start: 25 outliers final: 8 residues processed: 125 average time/residue: 0.1442 time to fit residues: 24.9045 Evaluate side-chains 103 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 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: 0.7444 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6194 Z= 0.179 Angle : 0.583 9.374 8494 Z= 0.309 Chirality : 0.042 0.122 1016 Planarity : 0.004 0.064 1104 Dihedral : 4.422 17.772 962 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 5.79 % Allowed : 18.45 % Favored : 75.75 % 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: 0.35 (0.28), residues: 928 helix: 1.26 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.20 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.028 0.001 PHE A 659 TYR 0.006 0.001 TYR A 751 ARG 0.008 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 0.646 Fit side-chains REVERT: B 296 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7689 (mtm) REVERT: B 351 ARG cc_start: 0.7439 (mmp-170) cc_final: 0.7210 (mmm160) REVERT: B 358 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8228 (ptm160) REVERT: B 433 LYS cc_start: 0.6424 (mmmt) cc_final: 0.5907 (tttt) REVERT: B 436 ILE cc_start: 0.8050 (mm) cc_final: 0.7656 (mt) REVERT: B 562 ASN cc_start: 0.7727 (p0) cc_final: 0.7126 (p0) REVERT: B 680 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 727 MET cc_start: 0.8043 (ttp) cc_final: 0.7575 (ttp) REVERT: A 358 ARG cc_start: 0.8678 (ttm170) cc_final: 0.8086 (mtm180) REVERT: A 433 LYS cc_start: 0.6541 (mmmt) cc_final: 0.6188 (tttt) REVERT: A 435 GLN cc_start: 0.7601 (tt0) cc_final: 0.7354 (tt0) REVERT: A 436 ILE cc_start: 0.7927 (mm) cc_final: 0.7521 (mt) REVERT: A 562 ASN cc_start: 0.7567 (p0) cc_final: 0.6931 (p0) REVERT: A 563 CYS cc_start: 0.6933 (t) cc_final: 0.6630 (t) REVERT: A 626 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6944 (t80) outliers start: 27 outliers final: 16 residues processed: 118 average time/residue: 0.1487 time to fit residues: 24.0154 Evaluate side-chains 112 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 30.0000 chunk 41 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7459 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6194 Z= 0.200 Angle : 0.577 6.201 8494 Z= 0.310 Chirality : 0.042 0.130 1016 Planarity : 0.004 0.064 1104 Dihedral : 4.403 17.785 962 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 6.22 % Allowed : 18.45 % Favored : 75.32 % 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: 0.34 (0.28), residues: 928 helix: 1.22 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.29 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.027 0.001 PHE A 659 TYR 0.005 0.001 TYR A 751 ARG 0.007 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.648 Fit side-chains REVERT: B 294 ARG cc_start: 0.8315 (ttm170) cc_final: 0.8099 (ttm-80) REVERT: B 296 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: B 358 ARG cc_start: 0.8485 (ttm170) cc_final: 0.7783 (mtp180) REVERT: B 433 LYS cc_start: 0.6429 (mmmt) cc_final: 0.5908 (tttt) REVERT: B 436 ILE cc_start: 0.8053 (mm) cc_final: 0.7660 (mt) REVERT: B 523 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8603 (mm) REVERT: B 562 ASN cc_start: 0.7686 (p0) cc_final: 0.7102 (p0) REVERT: B 626 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6996 (t80) REVERT: B 680 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8121 (t0) REVERT: A 296 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: A 358 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8121 (mtm180) REVERT: A 433 LYS cc_start: 0.6527 (mmmt) cc_final: 0.6175 (tttt) REVERT: A 435 GLN cc_start: 0.7630 (tt0) cc_final: 0.7400 (tt0) REVERT: A 436 ILE cc_start: 0.7951 (mm) cc_final: 0.7536 (mt) REVERT: A 562 ASN cc_start: 0.7511 (p0) cc_final: 0.6917 (p0) REVERT: A 679 SER cc_start: 0.9428 (OUTLIER) cc_final: 0.8854 (p) outliers start: 29 outliers final: 18 residues processed: 123 average time/residue: 0.1466 time to fit residues: 24.9337 Evaluate side-chains 113 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 PHE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7486 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6194 Z= 0.260 Angle : 0.607 5.731 8494 Z= 0.331 Chirality : 0.044 0.175 1016 Planarity : 0.005 0.063 1104 Dihedral : 4.555 17.019 962 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 6.22 % Allowed : 19.74 % Favored : 74.03 % 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: 0.07 (0.29), residues: 928 helix: 0.96 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -2.33 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.025 0.001 PHE A 659 TYR 0.006 0.001 TYR A 533 ARG 0.008 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.605 Fit side-chains REVERT: B 294 ARG cc_start: 0.8460 (ttm170) cc_final: 0.8202 (ttm-80) REVERT: B 296 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7661 (mtm) REVERT: B 358 ARG cc_start: 0.8542 (ttm170) cc_final: 0.7862 (mtm180) REVERT: B 433 LYS cc_start: 0.6437 (mmmt) cc_final: 0.6013 (tttt) REVERT: B 436 ILE cc_start: 0.8072 (mm) cc_final: 0.7675 (mt) REVERT: B 562 ASN cc_start: 0.7652 (p0) cc_final: 0.7078 (p0) REVERT: A 296 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (mtm) REVERT: A 358 ARG cc_start: 0.8720 (ttm170) cc_final: 0.8102 (mtm180) REVERT: A 429 GLU cc_start: 0.8074 (pm20) cc_final: 0.7856 (pm20) REVERT: A 433 LYS cc_start: 0.6592 (mmmt) cc_final: 0.6264 (tttt) REVERT: A 435 GLN cc_start: 0.7631 (tt0) cc_final: 0.7426 (tt0) REVERT: A 436 ILE cc_start: 0.8034 (mm) cc_final: 0.7607 (mt) REVERT: A 562 ASN cc_start: 0.7483 (p0) cc_final: 0.7030 (p0) REVERT: A 626 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7058 (t80) outliers start: 29 outliers final: 19 residues processed: 114 average time/residue: 0.1542 time to fit residues: 24.1281 Evaluate side-chains 108 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 86 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.0040 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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: 0.7444 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6194 Z= 0.173 Angle : 0.584 10.622 8494 Z= 0.310 Chirality : 0.043 0.178 1016 Planarity : 0.005 0.064 1104 Dihedral : 4.375 17.802 962 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.36 % Allowed : 21.67 % Favored : 72.96 % 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 (0.28), residues: 928 helix: 1.27 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.15 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 733 HIS 0.001 0.001 HIS B 695 PHE 0.028 0.001 PHE A 659 TYR 0.010 0.001 TYR B 686 ARG 0.007 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.598 Fit side-chains REVERT: B 294 ARG cc_start: 0.8333 (ttm170) cc_final: 0.8122 (ttm-80) REVERT: B 296 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7597 (mtm) REVERT: B 358 ARG cc_start: 0.8588 (ttm170) cc_final: 0.7915 (mtm180) REVERT: B 433 LYS cc_start: 0.6482 (mmmt) cc_final: 0.6041 (tttt) REVERT: B 436 ILE cc_start: 0.8031 (mm) cc_final: 0.7633 (mt) REVERT: B 562 ASN cc_start: 0.7734 (p0) cc_final: 0.7180 (p0) REVERT: B 680 ASN cc_start: 0.8258 (t0) cc_final: 0.7929 (t0) REVERT: A 296 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7592 (mtm) REVERT: A 358 ARG cc_start: 0.8701 (ttm170) cc_final: 0.8091 (mtm180) REVERT: A 429 GLU cc_start: 0.8030 (pm20) cc_final: 0.7824 (pm20) REVERT: A 433 LYS cc_start: 0.6618 (mmmt) cc_final: 0.6302 (tttt) REVERT: A 436 ILE cc_start: 0.7998 (mm) cc_final: 0.7579 (mt) REVERT: A 562 ASN cc_start: 0.7456 (p0) cc_final: 0.6972 (p0) REVERT: A 626 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7088 (t80) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 0.1464 time to fit residues: 23.1504 Evaluate side-chains 112 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6194 Z= 0.208 Angle : 0.635 17.639 8494 Z= 0.327 Chirality : 0.043 0.173 1016 Planarity : 0.005 0.063 1104 Dihedral : 4.353 16.579 962 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.15 % Allowed : 22.32 % Favored : 72.53 % 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: 0.28 (0.28), residues: 928 helix: 1.14 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.23 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.001 HIS B 695 PHE 0.030 0.001 PHE A 659 TYR 0.011 0.001 TYR B 686 ARG 0.008 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.866 Fit side-chains REVERT: B 294 ARG cc_start: 0.8329 (ttm170) cc_final: 0.8117 (ttm-80) REVERT: B 296 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7628 (mtm) REVERT: B 358 ARG cc_start: 0.8604 (ttm170) cc_final: 0.7963 (mtm180) REVERT: B 433 LYS cc_start: 0.6493 (mmmt) cc_final: 0.6046 (tttt) REVERT: B 436 ILE cc_start: 0.8056 (mm) cc_final: 0.7653 (mt) REVERT: B 562 ASN cc_start: 0.7744 (p0) cc_final: 0.7178 (p0) REVERT: B 626 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7085 (t80) REVERT: B 680 ASN cc_start: 0.8182 (t0) cc_final: 0.7836 (t0) REVERT: A 296 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7607 (mtm) REVERT: A 358 ARG cc_start: 0.8711 (ttm170) cc_final: 0.8097 (mtm180) REVERT: A 429 GLU cc_start: 0.8041 (pm20) cc_final: 0.7833 (pm20) REVERT: A 433 LYS cc_start: 0.6574 (mmmt) cc_final: 0.6279 (tttt) REVERT: A 436 ILE cc_start: 0.8046 (mm) cc_final: 0.7627 (mt) REVERT: A 562 ASN cc_start: 0.7427 (p0) cc_final: 0.6986 (p0) REVERT: A 626 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7096 (t80) REVERT: A 679 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.8798 (p) outliers start: 24 outliers final: 16 residues processed: 113 average time/residue: 0.1565 time to fit residues: 24.2478 Evaluate side-chains 114 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 PHE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 22 optimal weight: 0.0030 overall best weight: 0.4288 ------------------------------------------------------------------------------- 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: 0.7421 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6194 Z= 0.171 Angle : 0.632 17.831 8494 Z= 0.319 Chirality : 0.043 0.175 1016 Planarity : 0.005 0.064 1104 Dihedral : 4.238 16.132 962 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.36 % Allowed : 22.10 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 928 helix: 1.27 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.18 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.001 0.001 HIS B 695 PHE 0.028 0.001 PHE A 659 TYR 0.010 0.001 TYR B 686 ARG 0.002 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.743 Fit side-chains REVERT: B 296 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7537 (mtm) REVERT: B 358 ARG cc_start: 0.8587 (ttm170) cc_final: 0.8221 (ptm160) REVERT: B 433 LYS cc_start: 0.6465 (mmmt) cc_final: 0.6050 (tttt) REVERT: B 436 ILE cc_start: 0.8065 (mm) cc_final: 0.7694 (mt) REVERT: B 562 ASN cc_start: 0.7651 (p0) cc_final: 0.7067 (p0) REVERT: B 626 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7089 (t80) REVERT: B 680 ASN cc_start: 0.8244 (t0) cc_final: 0.7904 (t0) REVERT: A 296 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7572 (mtm) REVERT: A 358 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8087 (mtm180) REVERT: A 429 GLU cc_start: 0.8059 (pm20) cc_final: 0.7850 (pm20) REVERT: A 433 LYS cc_start: 0.6516 (mmmt) cc_final: 0.6254 (tttt) REVERT: A 436 ILE cc_start: 0.7934 (mm) cc_final: 0.7514 (mt) REVERT: A 626 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7095 (t80) REVERT: A 679 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.8825 (p) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 0.1552 time to fit residues: 24.6890 Evaluate side-chains 119 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 626 PHE Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 751 TYR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 626 PHE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107809 restraints weight = 12690.370| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.87 r_work: 0.3386 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6194 Z= 0.201 Angle : 0.636 18.288 8494 Z= 0.325 Chirality : 0.043 0.167 1016 Planarity : 0.005 0.064 1104 Dihedral : 4.232 16.283 962 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.15 % Allowed : 22.32 % Favored : 72.53 % 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: 0.35 (0.28), residues: 928 helix: 1.20 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.000 HIS A 695 PHE 0.029 0.001 PHE A 659 TYR 0.010 0.001 TYR B 686 ARG 0.007 0.001 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.16 seconds wall clock time: 26 minutes 16.66 seconds (1576.66 seconds total)