Starting phenix.real_space_refine on Thu Feb 15 12:56:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8k_15916/02_2024/8b8k_15916_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8k_15916/02_2024/8b8k_15916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8k_15916/02_2024/8b8k_15916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8k_15916/02_2024/8b8k_15916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8k_15916/02_2024/8b8k_15916_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b8k_15916/02_2024/8b8k_15916_updated.pdb" } resolution = 3.01 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 P 2 5.49 5 S 80 5.16 5 C 8098 2.51 5 N 1976 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12324 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "B" Number of atoms: 6121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6121 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 9 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 3, 'P1O': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.63, per 1000 atoms: 0.54 Number of scatterers: 12324 At special positions: 0 Unit cell: (118.482, 108.066, 113.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 6 19.99 S 80 16.00 P 2 15.00 O 2162 8.00 N 1976 7.00 C 8098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 2.1 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2824 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 6 sheets defined 59.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 294 through 330 removed outlier: 3.526A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP A 329 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 361 through 374 removed outlier: 4.862A pdb=" N GLU A 366 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 367 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 408 removed outlier: 3.934A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.694A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 487 removed outlier: 4.484A pdb=" N ILE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 538 removed outlier: 3.706A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 572 removed outlier: 5.015A pdb=" N SER A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 637 Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 665 through 680 Processing helix chain 'A' and resid 688 through 709 removed outlier: 3.982A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 746 removed outlier: 3.815A pdb=" N VAL A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 826 through 856 Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'B' and resid 90 through 108 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 206 through 219 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 294 through 330 removed outlier: 3.531A pdb=" N LEU B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASP B 329 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASN B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 361 through 374 removed outlier: 4.808A pdb=" N GLU B 366 " --> pdb=" O ILE B 363 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 408 removed outlier: 3.934A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 426 removed outlier: 3.720A pdb=" N GLN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 487 removed outlier: 4.462A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 538 removed outlier: 3.715A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 572 removed outlier: 5.019A pdb=" N SER B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 637 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 665 through 680 Processing helix chain 'B' and resid 688 through 709 removed outlier: 3.992A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 746 removed outlier: 3.811A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 759 Processing helix chain 'B' and resid 776 through 780 Processing helix chain 'B' and resid 797 through 801 Processing helix chain 'B' and resid 826 through 856 Processing helix chain 'B' and resid 862 through 874 Processing sheet with id= A, first strand: chain 'A' and resid 244 through 246 Processing sheet with id= B, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.543A pdb=" N SER A 190 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 782 through 785 Processing sheet with id= D, first strand: chain 'B' and resid 244 through 246 Processing sheet with id= E, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.554A pdb=" N SER B 190 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 782 through 785 678 hydrogen bonds defined for protein. 1956 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: 3.82 Time building geometry restraints manager: 5.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2011 1.32 - 1.45: 3570 1.45 - 1.57: 6941 1.57 - 1.69: 4 1.69 - 1.81: 120 Bond restraints: 12646 Sorted by residual: bond pdb=" CA ASP B 583 " pdb=" CB ASP B 583 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" CA ASP A 375 " pdb=" CB ASP A 375 " ideal model delta sigma weight residual 1.531 1.565 -0.034 3.28e-02 9.30e+02 1.09e+00 bond pdb=" CA ASP B 375 " pdb=" CB ASP B 375 " ideal model delta sigma weight residual 1.531 1.564 -0.033 3.28e-02 9.30e+02 1.03e+00 bond pdb=" CB VAL A 702 " pdb=" CG1 VAL A 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.17e-01 bond pdb=" CB VAL B 702 " pdb=" CG1 VAL B 702 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.15e-01 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 93.19 - 101.35: 41 101.35 - 109.50: 904 109.50 - 117.66: 8184 117.66 - 125.82: 7773 125.82 - 133.97: 216 Bond angle restraints: 17118 Sorted by residual: angle pdb=" N VAL B 578 " pdb=" CA VAL B 578 " pdb=" C VAL B 578 " ideal model delta sigma weight residual 113.71 110.39 3.32 9.50e-01 1.11e+00 1.22e+01 angle pdb=" CA GLY B 600 " pdb=" C GLY B 600 " pdb=" O GLY B 600 " ideal model delta sigma weight residual 122.45 120.32 2.13 7.20e-01 1.93e+00 8.71e+00 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.86e+00 angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 114.06 -3.36 1.22e+00 6.72e-01 7.59e+00 angle pdb=" CA GLY A 600 " pdb=" C GLY A 600 " pdb=" O GLY A 600 " ideal model delta sigma weight residual 122.37 120.37 2.00 7.30e-01 1.88e+00 7.47e+00 ... (remaining 17113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.03: 7354 32.03 - 64.06: 125 64.06 - 96.09: 5 96.09 - 128.12: 0 128.12 - 160.14: 2 Dihedral angle restraints: 7486 sinusoidal: 3104 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.81 -40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " pdb=" SG CYS B 601 " pdb=" CB CYS B 601 " ideal model delta sinusoidal sigma weight residual 93.00 133.43 -40.43 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" O5 P1O A1003 " pdb=" C7 P1O A1003 " pdb=" C8 P1O A1003 " pdb=" O7 P1O A1003 " ideal model delta sinusoidal sigma weight residual 56.91 -142.95 -160.14 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 7483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 997 0.025 - 0.050: 483 0.050 - 0.075: 255 0.075 - 0.099: 88 0.099 - 0.124: 31 Chirality restraints: 1854 Sorted by residual: chirality pdb=" CA VAL A 715 " pdb=" N VAL A 715 " pdb=" C VAL A 715 " pdb=" CB VAL A 715 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL B 715 " pdb=" N VAL B 715 " pdb=" C VAL B 715 " pdb=" CB VAL B 715 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1851 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 597 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 598 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 597 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 598 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 598 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 598 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 580 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO B 581 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 581 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 581 " -0.023 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 195 2.67 - 3.23: 12134 3.23 - 3.78: 19754 3.78 - 4.34: 26341 4.34 - 4.90: 43678 Nonbonded interactions: 102102 Sorted by model distance: nonbonded pdb=" OG SER B 190 " pdb=" OD2 ASP B 194 " model vdw 2.111 2.440 nonbonded pdb=" OG SER A 190 " pdb=" OD2 ASP A 194 " model vdw 2.121 2.440 nonbonded pdb=" OD2 ASP B 749 " pdb=" OH TYR B 776 " model vdw 2.230 2.440 nonbonded pdb=" OD2 ASP A 749 " pdb=" OH TYR A 776 " model vdw 2.245 2.440 nonbonded pdb=" OE2 GLU A 699 " pdb="CA CA A1002 " model vdw 2.256 2.510 ... (remaining 102097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.910 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: 4.340 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.040 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.003 0.034 12646 Z= 0.185 Angle : 0.500 6.111 17118 Z= 0.283 Chirality : 0.039 0.124 1854 Planarity : 0.004 0.047 2118 Dihedral : 11.832 160.144 4638 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.92 % Allowed : 4.95 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1442 helix: 2.16 (0.16), residues: 920 sheet: 0.40 (0.66), residues: 62 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 273 HIS 0.003 0.001 HIS A 275 PHE 0.012 0.001 PHE A 560 TYR 0.016 0.001 TYR A 580 ARG 0.003 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 209 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: A 196 TYR cc_start: 0.6038 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: A 236 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8725 (mp) REVERT: A 255 TYR cc_start: 0.8186 (m-80) cc_final: 0.7805 (m-10) REVERT: A 298 ILE cc_start: 0.9013 (tp) cc_final: 0.8701 (tt) REVERT: A 370 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8045 (mmtm) REVERT: A 403 GLU cc_start: 0.8060 (tt0) cc_final: 0.7610 (tm-30) REVERT: A 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8170 (tt0) REVERT: A 413 LEU cc_start: 0.8981 (tt) cc_final: 0.8723 (tt) REVERT: A 546 ASP cc_start: 0.8391 (m-30) cc_final: 0.8048 (m-30) REVERT: A 695 ASN cc_start: 0.8767 (t0) cc_final: 0.8397 (t0) REVERT: A 749 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7203 (t0) REVERT: A 770 TYR cc_start: 0.7937 (p90) cc_final: 0.7404 (t80) REVERT: A 773 MET cc_start: 0.9525 (mmm) cc_final: 0.9201 (tpp) REVERT: A 826 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (tt) REVERT: B 73 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: B 196 TYR cc_start: 0.5988 (OUTLIER) cc_final: 0.4639 (m-80) REVERT: B 289 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8111 (ttt-90) REVERT: B 298 ILE cc_start: 0.9047 (tp) cc_final: 0.8705 (tt) REVERT: B 370 LYS cc_start: 0.8262 (ptpp) cc_final: 0.8018 (mmtm) REVERT: B 403 GLU cc_start: 0.8111 (tt0) cc_final: 0.7637 (tm-30) REVERT: B 407 GLU cc_start: 0.8457 (tt0) cc_final: 0.8157 (tt0) REVERT: B 413 LEU cc_start: 0.9136 (tt) cc_final: 0.8915 (tt) REVERT: B 546 ASP cc_start: 0.8310 (m-30) cc_final: 0.7991 (m-30) REVERT: B 695 ASN cc_start: 0.8770 (t0) cc_final: 0.8395 (t0) REVERT: B 749 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7171 (t0) REVERT: B 770 TYR cc_start: 0.7884 (p90) cc_final: 0.7486 (t80) REVERT: B 773 MET cc_start: 0.9502 (mmm) cc_final: 0.9161 (tpp) outliers start: 39 outliers final: 13 residues processed: 248 average time/residue: 0.2570 time to fit residues: 90.0622 Evaluate side-chains 147 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 860 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 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 44 GLN A 99 GLN A 104 ASN A 193 ASN A 234 ASN A 525 ASN A 559 GLN A 632 ASN A 710 GLN A 730 GLN A 814 ASN B 43 ASN B 44 GLN B 104 ASN B 234 ASN B 525 ASN B 559 GLN B 632 ASN B 710 GLN B 730 GLN B 814 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12646 Z= 0.194 Angle : 0.499 7.567 17118 Z= 0.267 Chirality : 0.038 0.135 1854 Planarity : 0.004 0.046 2118 Dihedral : 9.912 158.883 1732 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.00 % Allowed : 8.77 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1442 helix: 2.16 (0.17), residues: 920 sheet: 0.47 (0.67), residues: 62 loop : -1.30 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.003 0.001 HIS A 275 PHE 0.013 0.001 PHE A 461 TYR 0.016 0.001 TYR B 580 ARG 0.005 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: A 192 MET cc_start: 0.5882 (ptt) cc_final: 0.5669 (ptt) REVERT: A 196 TYR cc_start: 0.6040 (OUTLIER) cc_final: 0.4615 (m-80) REVERT: A 255 TYR cc_start: 0.8216 (m-80) cc_final: 0.7912 (m-10) REVERT: A 298 ILE cc_start: 0.9052 (tp) cc_final: 0.8696 (tt) REVERT: A 403 GLU cc_start: 0.8059 (tt0) cc_final: 0.7621 (tm-30) REVERT: A 407 GLU cc_start: 0.8424 (tt0) cc_final: 0.8162 (tt0) REVERT: A 543 THR cc_start: 0.8725 (p) cc_final: 0.8427 (p) REVERT: A 546 ASP cc_start: 0.8374 (m-30) cc_final: 0.8138 (m-30) REVERT: A 631 MET cc_start: 0.8431 (mmm) cc_final: 0.8138 (mtp) REVERT: A 695 ASN cc_start: 0.8762 (t0) cc_final: 0.8376 (t0) REVERT: A 749 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7339 (t0) REVERT: A 770 TYR cc_start: 0.7947 (p90) cc_final: 0.7391 (t80) REVERT: A 773 MET cc_start: 0.9495 (mmm) cc_final: 0.9146 (tpp) REVERT: A 826 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8983 (tt) REVERT: B 73 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: B 142 MET cc_start: 0.8715 (ptt) cc_final: 0.8466 (ptt) REVERT: B 196 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.4469 (m-80) REVERT: B 298 ILE cc_start: 0.9060 (tp) cc_final: 0.8702 (tt) REVERT: B 403 GLU cc_start: 0.8109 (tt0) cc_final: 0.7647 (tm-30) REVERT: B 407 GLU cc_start: 0.8453 (tt0) cc_final: 0.8203 (tt0) REVERT: B 461 PHE cc_start: 0.6242 (m-80) cc_final: 0.5578 (t80) REVERT: B 543 THR cc_start: 0.8851 (p) cc_final: 0.8533 (p) REVERT: B 546 ASP cc_start: 0.8417 (m-30) cc_final: 0.8185 (m-30) REVERT: B 695 ASN cc_start: 0.8771 (t0) cc_final: 0.8380 (t0) REVERT: B 749 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7318 (t0) REVERT: B 770 TYR cc_start: 0.7897 (p90) cc_final: 0.7482 (t80) REVERT: B 773 MET cc_start: 0.9463 (mmm) cc_final: 0.8724 (mmt) outliers start: 40 outliers final: 27 residues processed: 183 average time/residue: 0.2414 time to fit residues: 64.1966 Evaluate side-chains 158 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 0.0970 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 525 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12646 Z= 0.183 Angle : 0.492 6.692 17118 Z= 0.262 Chirality : 0.038 0.162 1854 Planarity : 0.004 0.044 2118 Dihedral : 9.658 160.761 1724 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.45 % Allowed : 8.70 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1442 helix: 2.20 (0.16), residues: 920 sheet: 0.52 (0.69), residues: 62 loop : -1.28 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.003 0.001 HIS A 143 PHE 0.020 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.004 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 134 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: A 196 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.4624 (m-80) REVERT: A 255 TYR cc_start: 0.8205 (m-80) cc_final: 0.7932 (m-10) REVERT: A 298 ILE cc_start: 0.9019 (tp) cc_final: 0.8688 (tt) REVERT: A 334 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 403 GLU cc_start: 0.8066 (tt0) cc_final: 0.7627 (tm-30) REVERT: A 407 GLU cc_start: 0.8393 (tt0) cc_final: 0.8156 (tt0) REVERT: A 481 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8741 (p) REVERT: A 543 THR cc_start: 0.8787 (p) cc_final: 0.8447 (p) REVERT: A 546 ASP cc_start: 0.8400 (m-30) cc_final: 0.8142 (m-30) REVERT: A 631 MET cc_start: 0.8481 (mmm) cc_final: 0.8134 (mtp) REVERT: A 695 ASN cc_start: 0.8763 (t0) cc_final: 0.8350 (t0) REVERT: A 749 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7378 (t0) REVERT: A 770 TYR cc_start: 0.7952 (p90) cc_final: 0.7381 (t80) REVERT: A 773 MET cc_start: 0.9473 (mmm) cc_final: 0.8666 (mmt) REVERT: A 826 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9114 (tt) REVERT: B 73 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: B 142 MET cc_start: 0.8673 (ptt) cc_final: 0.8436 (ptt) REVERT: B 196 TYR cc_start: 0.5921 (OUTLIER) cc_final: 0.4419 (m-80) REVERT: B 298 ILE cc_start: 0.9062 (tp) cc_final: 0.8705 (tt) REVERT: B 334 SER cc_start: 0.8656 (OUTLIER) cc_final: 0.8370 (p) REVERT: B 403 GLU cc_start: 0.8108 (tt0) cc_final: 0.7652 (tm-30) REVERT: B 407 GLU cc_start: 0.8433 (tt0) cc_final: 0.8203 (tt0) REVERT: B 461 PHE cc_start: 0.6440 (m-80) cc_final: 0.6100 (t80) REVERT: B 481 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 543 THR cc_start: 0.8885 (p) cc_final: 0.8576 (p) REVERT: B 546 ASP cc_start: 0.8445 (m-30) cc_final: 0.8196 (m-30) REVERT: B 695 ASN cc_start: 0.8785 (t0) cc_final: 0.8395 (t0) REVERT: B 749 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7353 (t0) REVERT: B 770 TYR cc_start: 0.7997 (p90) cc_final: 0.7513 (t80) REVERT: B 773 MET cc_start: 0.9438 (mmm) cc_final: 0.8693 (mmt) outliers start: 46 outliers final: 26 residues processed: 173 average time/residue: 0.2454 time to fit residues: 62.5522 Evaluate side-chains 160 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN B 143 HIS B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12646 Z= 0.195 Angle : 0.487 6.516 17118 Z= 0.259 Chirality : 0.038 0.143 1854 Planarity : 0.004 0.042 2118 Dihedral : 9.374 160.734 1721 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.52 % Allowed : 8.85 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1442 helix: 2.20 (0.16), residues: 920 sheet: 0.52 (0.68), residues: 62 loop : -1.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS B 275 PHE 0.024 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 128 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: A 196 TYR cc_start: 0.6003 (OUTLIER) cc_final: 0.4542 (m-80) REVERT: A 255 TYR cc_start: 0.8208 (m-80) cc_final: 0.7969 (m-10) REVERT: A 298 ILE cc_start: 0.9007 (tp) cc_final: 0.8677 (tt) REVERT: A 334 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 403 GLU cc_start: 0.8071 (tt0) cc_final: 0.7628 (tm-30) REVERT: A 407 GLU cc_start: 0.8398 (tt0) cc_final: 0.8160 (tt0) REVERT: A 481 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8745 (p) REVERT: A 543 THR cc_start: 0.8815 (p) cc_final: 0.8480 (p) REVERT: A 546 ASP cc_start: 0.8414 (m-30) cc_final: 0.8152 (m-30) REVERT: A 695 ASN cc_start: 0.8778 (t0) cc_final: 0.8367 (t0) REVERT: A 749 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7404 (t0) REVERT: A 770 TYR cc_start: 0.7954 (p90) cc_final: 0.7355 (t80) REVERT: A 773 MET cc_start: 0.9461 (mmm) cc_final: 0.8666 (mmt) REVERT: A 826 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9124 (tt) REVERT: B 73 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: B 142 MET cc_start: 0.8633 (ptt) cc_final: 0.8423 (ptt) REVERT: B 196 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.4408 (m-80) REVERT: B 298 ILE cc_start: 0.8988 (tp) cc_final: 0.8645 (tt) REVERT: B 334 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8377 (p) REVERT: B 403 GLU cc_start: 0.8112 (tt0) cc_final: 0.7653 (tm-30) REVERT: B 407 GLU cc_start: 0.8437 (tt0) cc_final: 0.8217 (tt0) REVERT: B 461 PHE cc_start: 0.6387 (m-80) cc_final: 0.6022 (t80) REVERT: B 543 THR cc_start: 0.8906 (p) cc_final: 0.8604 (p) REVERT: B 546 ASP cc_start: 0.8398 (m-30) cc_final: 0.8166 (m-30) REVERT: B 631 MET cc_start: 0.8418 (mmm) cc_final: 0.8109 (mmm) REVERT: B 695 ASN cc_start: 0.8785 (t0) cc_final: 0.8372 (t0) REVERT: B 749 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7365 (t0) REVERT: B 770 TYR cc_start: 0.8034 (p90) cc_final: 0.7512 (t80) REVERT: B 773 MET cc_start: 0.9412 (mmm) cc_final: 0.8682 (mmt) outliers start: 47 outliers final: 31 residues processed: 169 average time/residue: 0.2361 time to fit residues: 58.5652 Evaluate side-chains 162 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.0070 chunk 81 optimal weight: 0.0970 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 98 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12646 Z= 0.185 Angle : 0.480 6.434 17118 Z= 0.256 Chirality : 0.038 0.134 1854 Planarity : 0.004 0.042 2118 Dihedral : 9.199 162.400 1721 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.82 % Allowed : 9.15 % Favored : 87.03 % 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: 1.61 (0.22), residues: 1442 helix: 2.21 (0.16), residues: 920 sheet: 0.55 (0.68), residues: 62 loop : -1.32 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS B 275 PHE 0.020 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: A 196 TYR cc_start: 0.5929 (OUTLIER) cc_final: 0.4432 (m-80) REVERT: A 255 TYR cc_start: 0.8182 (m-80) cc_final: 0.7948 (m-10) REVERT: A 298 ILE cc_start: 0.8976 (tp) cc_final: 0.8644 (tt) REVERT: A 334 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 403 GLU cc_start: 0.8114 (tt0) cc_final: 0.7680 (tm-30) REVERT: A 407 GLU cc_start: 0.8379 (tt0) cc_final: 0.8146 (tt0) REVERT: A 481 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (p) REVERT: A 543 THR cc_start: 0.8803 (p) cc_final: 0.8469 (p) REVERT: A 546 ASP cc_start: 0.8421 (m-30) cc_final: 0.8157 (m-30) REVERT: A 631 MET cc_start: 0.8361 (mmm) cc_final: 0.8102 (mmm) REVERT: A 659 MET cc_start: 0.8758 (ttm) cc_final: 0.8428 (ttm) REVERT: A 661 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8754 (mppt) REVERT: A 695 ASN cc_start: 0.8773 (t0) cc_final: 0.8340 (t0) REVERT: A 749 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7428 (t0) REVERT: A 770 TYR cc_start: 0.7960 (p90) cc_final: 0.7360 (t80) REVERT: A 773 MET cc_start: 0.9447 (mmm) cc_final: 0.8658 (mmt) REVERT: B 73 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7360 (m-80) REVERT: B 142 MET cc_start: 0.8627 (ptt) cc_final: 0.8100 (ptt) REVERT: B 196 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4222 (m-80) REVERT: B 298 ILE cc_start: 0.8973 (tp) cc_final: 0.8632 (tt) REVERT: B 334 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8326 (p) REVERT: B 403 GLU cc_start: 0.8111 (tt0) cc_final: 0.7656 (tm-30) REVERT: B 407 GLU cc_start: 0.8436 (tt0) cc_final: 0.8226 (tt0) REVERT: B 461 PHE cc_start: 0.6329 (m-80) cc_final: 0.6080 (t80) REVERT: B 543 THR cc_start: 0.8815 (p) cc_final: 0.8504 (p) REVERT: B 546 ASP cc_start: 0.8406 (m-30) cc_final: 0.8151 (m-30) REVERT: B 695 ASN cc_start: 0.8755 (t0) cc_final: 0.8317 (t0) REVERT: B 749 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7422 (t0) REVERT: B 770 TYR cc_start: 0.8027 (p90) cc_final: 0.7489 (t80) REVERT: B 773 MET cc_start: 0.9407 (mmm) cc_final: 0.8561 (mmt) outliers start: 51 outliers final: 34 residues processed: 171 average time/residue: 0.2465 time to fit residues: 61.2700 Evaluate side-chains 164 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 121 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN B 525 ASN B 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12646 Z= 0.246 Angle : 0.505 6.483 17118 Z= 0.270 Chirality : 0.039 0.134 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.140 161.916 1719 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.67 % Allowed : 9.67 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1442 helix: 2.16 (0.17), residues: 920 sheet: 0.48 (0.67), residues: 62 loop : -1.31 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.002 0.001 HIS A 844 PHE 0.018 0.001 PHE A 461 TYR 0.015 0.001 TYR B 580 ARG 0.003 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 1.497 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: A 196 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4519 (m-80) REVERT: A 255 TYR cc_start: 0.8210 (m-80) cc_final: 0.8007 (m-10) REVERT: A 298 ILE cc_start: 0.8973 (tp) cc_final: 0.8560 (tt) REVERT: A 334 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8433 (p) REVERT: A 403 GLU cc_start: 0.8136 (tt0) cc_final: 0.7700 (tm-30) REVERT: A 407 GLU cc_start: 0.8383 (tt0) cc_final: 0.8151 (tt0) REVERT: A 418 GLN cc_start: 0.8380 (tt0) cc_final: 0.8104 (tt0) REVERT: A 481 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8753 (p) REVERT: A 543 THR cc_start: 0.8792 (p) cc_final: 0.8474 (p) REVERT: A 546 ASP cc_start: 0.8432 (m-30) cc_final: 0.8182 (m-30) REVERT: A 631 MET cc_start: 0.8425 (mmm) cc_final: 0.8134 (mmm) REVERT: A 659 MET cc_start: 0.8794 (ttm) cc_final: 0.8460 (ttm) REVERT: A 661 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8768 (mppt) REVERT: A 695 ASN cc_start: 0.8800 (t0) cc_final: 0.8397 (t0) REVERT: A 714 MET cc_start: 0.8903 (mtp) cc_final: 0.8622 (mtp) REVERT: A 749 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.7452 (t0) REVERT: A 770 TYR cc_start: 0.8009 (p90) cc_final: 0.7466 (t80) REVERT: A 773 MET cc_start: 0.9417 (mmm) cc_final: 0.8621 (mmt) REVERT: B 73 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: B 196 TYR cc_start: 0.5874 (OUTLIER) cc_final: 0.4846 (m-80) REVERT: B 298 ILE cc_start: 0.8947 (tp) cc_final: 0.8557 (tt) REVERT: B 334 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8327 (p) REVERT: B 403 GLU cc_start: 0.8119 (tt0) cc_final: 0.7651 (tm-30) REVERT: B 407 GLU cc_start: 0.8445 (tt0) cc_final: 0.8229 (tt0) REVERT: B 461 PHE cc_start: 0.6448 (m-80) cc_final: 0.6214 (t80) REVERT: B 543 THR cc_start: 0.8800 (p) cc_final: 0.8487 (p) REVERT: B 546 ASP cc_start: 0.8422 (m-30) cc_final: 0.8157 (m-30) REVERT: B 631 MET cc_start: 0.8440 (mmm) cc_final: 0.8151 (mmm) REVERT: B 695 ASN cc_start: 0.8809 (t0) cc_final: 0.8404 (t0) REVERT: B 749 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.7429 (t0) REVERT: B 770 TYR cc_start: 0.8047 (p90) cc_final: 0.7484 (t80) REVERT: B 773 MET cc_start: 0.9393 (mmm) cc_final: 0.8574 (mmt) outliers start: 49 outliers final: 35 residues processed: 166 average time/residue: 0.2314 time to fit residues: 56.8247 Evaluate side-chains 160 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 116 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 549 ASN A 710 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12646 Z= 0.271 Angle : 0.520 6.491 17118 Z= 0.280 Chirality : 0.040 0.133 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.203 164.134 1719 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.52 % Allowed : 9.52 % Favored : 86.96 % 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: 1.49 (0.22), residues: 1442 helix: 2.12 (0.17), residues: 920 sheet: 0.44 (0.67), residues: 62 loop : -1.35 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 273 HIS 0.001 0.001 HIS B 108 PHE 0.016 0.002 PHE A 461 TYR 0.016 0.001 TYR B 580 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 121 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: A 196 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4748 (m-80) REVERT: A 298 ILE cc_start: 0.8971 (tp) cc_final: 0.8546 (tt) REVERT: A 334 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8434 (p) REVERT: A 403 GLU cc_start: 0.8150 (tt0) cc_final: 0.7762 (tm-30) REVERT: A 418 GLN cc_start: 0.8348 (tt0) cc_final: 0.8095 (tt0) REVERT: A 481 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8779 (p) REVERT: A 543 THR cc_start: 0.8776 (p) cc_final: 0.8490 (p) REVERT: A 546 ASP cc_start: 0.8362 (m-30) cc_final: 0.8141 (m-30) REVERT: A 659 MET cc_start: 0.8809 (ttm) cc_final: 0.8473 (ttm) REVERT: A 661 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8746 (mppt) REVERT: A 695 ASN cc_start: 0.8837 (t0) cc_final: 0.8450 (t0) REVERT: A 714 MET cc_start: 0.8932 (mtp) cc_final: 0.8663 (mtp) REVERT: A 749 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.7605 (t0) REVERT: A 770 TYR cc_start: 0.8013 (p90) cc_final: 0.7467 (t80) REVERT: A 773 MET cc_start: 0.9407 (mmm) cc_final: 0.8620 (mmt) REVERT: B 73 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: B 142 MET cc_start: 0.8575 (ptt) cc_final: 0.8257 (ptt) REVERT: B 196 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.4836 (m-80) REVERT: B 298 ILE cc_start: 0.8968 (tp) cc_final: 0.8534 (tt) REVERT: B 334 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8327 (p) REVERT: B 403 GLU cc_start: 0.8168 (tt0) cc_final: 0.7702 (tm-30) REVERT: B 407 GLU cc_start: 0.8443 (tt0) cc_final: 0.8227 (tt0) REVERT: B 543 THR cc_start: 0.8806 (p) cc_final: 0.8534 (p) REVERT: B 546 ASP cc_start: 0.8435 (m-30) cc_final: 0.8203 (m-30) REVERT: B 661 LYS cc_start: 0.9055 (mmtp) cc_final: 0.8762 (mppt) REVERT: B 695 ASN cc_start: 0.8845 (t0) cc_final: 0.8454 (t0) REVERT: B 770 TYR cc_start: 0.8063 (p90) cc_final: 0.7495 (t80) REVERT: B 773 MET cc_start: 0.9402 (mmm) cc_final: 0.8578 (mmt) outliers start: 47 outliers final: 34 residues processed: 161 average time/residue: 0.2300 time to fit residues: 55.1071 Evaluate side-chains 154 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Chi-restraints excluded: chain B residue 874 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN A 710 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 12646 Z= 0.228 Angle : 0.505 6.507 17118 Z= 0.272 Chirality : 0.039 0.132 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.127 164.413 1717 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.30 % Allowed : 9.90 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1442 helix: 2.18 (0.17), residues: 916 sheet: 0.45 (0.67), residues: 62 loop : -1.29 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS B 844 PHE 0.015 0.001 PHE A 461 TYR 0.018 0.001 TYR A 580 ARG 0.002 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: A 196 TYR cc_start: 0.6045 (OUTLIER) cc_final: 0.4819 (m-80) REVERT: A 298 ILE cc_start: 0.8970 (tp) cc_final: 0.8544 (tt) REVERT: A 334 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 403 GLU cc_start: 0.8143 (tt0) cc_final: 0.7764 (tm-30) REVERT: A 418 GLN cc_start: 0.8325 (tt0) cc_final: 0.8068 (tt0) REVERT: A 481 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8776 (p) REVERT: A 543 THR cc_start: 0.8783 (p) cc_final: 0.8497 (p) REVERT: A 546 ASP cc_start: 0.8375 (m-30) cc_final: 0.8154 (m-30) REVERT: A 631 MET cc_start: 0.8421 (mmm) cc_final: 0.8161 (mmm) REVERT: A 659 MET cc_start: 0.8764 (ttm) cc_final: 0.8455 (ttm) REVERT: A 661 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8741 (mppt) REVERT: A 695 ASN cc_start: 0.8797 (t0) cc_final: 0.8397 (t0) REVERT: A 714 MET cc_start: 0.8926 (mtp) cc_final: 0.8653 (mtp) REVERT: A 770 TYR cc_start: 0.8002 (p90) cc_final: 0.7357 (t80) REVERT: A 773 MET cc_start: 0.9414 (mmm) cc_final: 0.8622 (mmt) REVERT: B 73 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: B 196 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.4839 (m-80) REVERT: B 298 ILE cc_start: 0.8978 (tp) cc_final: 0.8552 (tt) REVERT: B 334 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8342 (p) REVERT: B 403 GLU cc_start: 0.8170 (tt0) cc_final: 0.7699 (tm-30) REVERT: B 407 GLU cc_start: 0.8426 (tt0) cc_final: 0.8167 (tt0) REVERT: B 543 THR cc_start: 0.8806 (p) cc_final: 0.8536 (p) REVERT: B 546 ASP cc_start: 0.8357 (m-30) cc_final: 0.8119 (m-30) REVERT: B 631 MET cc_start: 0.8455 (mmm) cc_final: 0.8184 (mmm) REVERT: B 661 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8781 (mppt) REVERT: B 695 ASN cc_start: 0.8805 (t0) cc_final: 0.8403 (t0) REVERT: B 770 TYR cc_start: 0.8052 (p90) cc_final: 0.7483 (t80) REVERT: B 773 MET cc_start: 0.9412 (mmm) cc_final: 0.8593 (mmt) outliers start: 44 outliers final: 34 residues processed: 158 average time/residue: 0.2319 time to fit residues: 54.3657 Evaluate side-chains 157 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.0030 chunk 124 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 12646 Z= 0.189 Angle : 0.492 7.401 17118 Z= 0.264 Chirality : 0.038 0.133 1854 Planarity : 0.004 0.044 2118 Dihedral : 9.012 165.405 1715 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.07 % Allowed : 10.34 % Favored : 86.58 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.22), residues: 1442 helix: 2.25 (0.17), residues: 916 sheet: 0.50 (0.68), residues: 62 loop : -1.28 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 397 HIS 0.002 0.001 HIS B 844 PHE 0.015 0.001 PHE A 461 TYR 0.014 0.001 TYR B 580 ARG 0.002 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 123 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: A 196 TYR cc_start: 0.5898 (OUTLIER) cc_final: 0.4705 (m-80) REVERT: A 298 ILE cc_start: 0.8966 (tp) cc_final: 0.8564 (tt) REVERT: A 334 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8208 (p) REVERT: A 403 GLU cc_start: 0.8131 (tt0) cc_final: 0.7772 (tm-30) REVERT: A 418 GLN cc_start: 0.8292 (tt0) cc_final: 0.8072 (tt0) REVERT: A 481 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (p) REVERT: A 543 THR cc_start: 0.8788 (p) cc_final: 0.8492 (p) REVERT: A 546 ASP cc_start: 0.8369 (m-30) cc_final: 0.8137 (m-30) REVERT: A 631 MET cc_start: 0.8395 (mmm) cc_final: 0.8165 (mmm) REVERT: A 659 MET cc_start: 0.8725 (ttm) cc_final: 0.8442 (ttm) REVERT: A 661 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8765 (mppt) REVERT: A 695 ASN cc_start: 0.8745 (t0) cc_final: 0.8314 (t0) REVERT: A 714 MET cc_start: 0.8921 (mtp) cc_final: 0.8653 (mtp) REVERT: A 770 TYR cc_start: 0.7958 (p90) cc_final: 0.7352 (t80) REVERT: A 773 MET cc_start: 0.9424 (mmm) cc_final: 0.9107 (tpp) REVERT: B 73 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: B 196 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.5179 (m-80) REVERT: B 298 ILE cc_start: 0.8974 (tp) cc_final: 0.8572 (tt) REVERT: B 334 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 403 GLU cc_start: 0.8117 (tt0) cc_final: 0.7665 (tm-30) REVERT: B 543 THR cc_start: 0.8807 (p) cc_final: 0.8526 (p) REVERT: B 546 ASP cc_start: 0.8361 (m-30) cc_final: 0.8105 (m-30) REVERT: B 631 MET cc_start: 0.8471 (mmm) cc_final: 0.8233 (mmm) REVERT: B 661 LYS cc_start: 0.9105 (mmtp) cc_final: 0.8781 (mppt) REVERT: B 695 ASN cc_start: 0.8751 (t0) cc_final: 0.8317 (t0) REVERT: B 749 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.7573 (t0) REVERT: B 770 TYR cc_start: 0.8044 (p90) cc_final: 0.7473 (t80) REVERT: B 773 MET cc_start: 0.9423 (mmm) cc_final: 0.8604 (mmt) outliers start: 41 outliers final: 31 residues processed: 159 average time/residue: 0.2408 time to fit residues: 56.2631 Evaluate side-chains 155 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN B 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 12646 Z= 0.236 Angle : 0.511 8.287 17118 Z= 0.275 Chirality : 0.039 0.166 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.030 164.735 1715 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.30 % Allowed : 10.04 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1442 helix: 2.19 (0.17), residues: 916 sheet: 0.46 (0.67), residues: 62 loop : -1.28 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.001 0.001 HIS B 108 PHE 0.015 0.001 PHE A 461 TYR 0.018 0.001 TYR A 580 ARG 0.005 0.000 ARG B 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 115 time to evaluate : 1.485 Fit side-chains revert: symmetry clash REVERT: A 73 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: A 196 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.4697 (m-80) REVERT: A 298 ILE cc_start: 0.8968 (tp) cc_final: 0.8558 (tt) REVERT: A 334 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 403 GLU cc_start: 0.8135 (tt0) cc_final: 0.7766 (tm-30) REVERT: A 418 GLN cc_start: 0.8323 (tt0) cc_final: 0.8085 (tt0) REVERT: A 481 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8773 (p) REVERT: A 543 THR cc_start: 0.8778 (p) cc_final: 0.8493 (p) REVERT: A 546 ASP cc_start: 0.8379 (m-30) cc_final: 0.8163 (m-30) REVERT: A 631 MET cc_start: 0.8408 (mmm) cc_final: 0.8171 (mmm) REVERT: A 659 MET cc_start: 0.8778 (ttm) cc_final: 0.8444 (ttm) REVERT: A 661 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8765 (mppt) REVERT: A 695 ASN cc_start: 0.8799 (t0) cc_final: 0.8376 (t0) REVERT: A 714 MET cc_start: 0.8938 (mtp) cc_final: 0.8664 (mtp) REVERT: A 749 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.7624 (t0) REVERT: A 770 TYR cc_start: 0.8005 (p90) cc_final: 0.7352 (t80) REVERT: A 773 MET cc_start: 0.9417 (mmm) cc_final: 0.8529 (mmt) REVERT: B 73 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: B 196 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.5274 (m-80) REVERT: B 298 ILE cc_start: 0.8978 (tp) cc_final: 0.8566 (tt) REVERT: B 334 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8146 (p) REVERT: B 403 GLU cc_start: 0.8155 (tt0) cc_final: 0.7709 (tm-30) REVERT: B 543 THR cc_start: 0.8843 (p) cc_final: 0.8525 (p) REVERT: B 546 ASP cc_start: 0.8365 (m-30) cc_final: 0.8125 (m-30) REVERT: B 631 MET cc_start: 0.8446 (mmm) cc_final: 0.8190 (mmm) REVERT: B 661 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8780 (mppt) REVERT: B 695 ASN cc_start: 0.8807 (t0) cc_final: 0.8381 (t0) REVERT: B 749 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.7602 (t0) REVERT: B 770 TYR cc_start: 0.8062 (p90) cc_final: 0.7483 (t80) REVERT: B 773 MET cc_start: 0.9406 (mmm) cc_final: 0.8577 (mmt) outliers start: 44 outliers final: 33 residues processed: 153 average time/residue: 0.2411 time to fit residues: 54.8707 Evaluate side-chains 157 residues out of total 1334 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain B residue 48 ARG Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 458 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 772 THR Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 848 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 868 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 117 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081435 restraints weight = 22218.220| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.57 r_work: 0.2954 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12646 Z= 0.216 Angle : 0.501 8.632 17118 Z= 0.268 Chirality : 0.038 0.148 1854 Planarity : 0.004 0.043 2118 Dihedral : 9.047 165.525 1715 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.37 % Allowed : 10.04 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1442 helix: 2.21 (0.17), residues: 916 sheet: 0.47 (0.67), residues: 62 loop : -1.26 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS A 844 PHE 0.034 0.001 PHE B 461 TYR 0.015 0.001 TYR A 580 ARG 0.004 0.000 ARG B 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.22 seconds wall clock time: 46 minutes 55.79 seconds (2815.79 seconds total)