Starting phenix.real_space_refine on Wed Jan 17 21:20:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/01_2024/8teo_41193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/01_2024/8teo_41193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/01_2024/8teo_41193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/01_2024/8teo_41193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/01_2024/8teo_41193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teo_41193/01_2024/8teo_41193_updated.pdb" } resolution = 2.39 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= -0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 28 5.16 5 C 4488 2.51 5 N 960 2.21 5 O 1029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1536 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 90 Unusual residues: {' K': 2, 'POV': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 6, 'POV:plan-1': 7} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.21, per 1000 atoms: 0.65 Number of scatterers: 6507 At special positions: 0 Unit cell: (105.41, 105.41, 64.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 28 16.00 O 1029 8.00 N 960 7.00 C 4488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 227 through 247 Processing helix chain 'A' and resid 279 through 297 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.926A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 358 through 376 removed outlier: 3.983A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 418 removed outlier: 5.709A pdb=" N ARG A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 4.666A pdb=" N TRP A 434 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 440 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 488 Proline residue: A 473 - end of helix removed outlier: 5.570A pdb=" N VAL A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 247 Processing helix chain 'B' and resid 279 through 297 Processing helix chain 'B' and resid 311 through 325 removed outlier: 3.927A pdb=" N ILE B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 358 through 376 removed outlier: 3.983A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 418 removed outlier: 5.708A pdb=" N ARG B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 removed outlier: 4.666A pdb=" N TRP B 434 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 440 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 488 Proline residue: B 473 - end of helix removed outlier: 5.571A pdb=" N VAL B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 247 Processing helix chain 'C' and resid 279 through 297 Processing helix chain 'C' and resid 311 through 325 removed outlier: 3.927A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Proline residue: C 322 - end of helix Processing helix chain 'C' and resid 358 through 376 removed outlier: 3.983A pdb=" N VAL C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ARG C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 418 removed outlier: 5.708A pdb=" N ARG C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 440 removed outlier: 4.666A pdb=" N TRP C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET C 440 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 488 Proline residue: C 473 - end of helix removed outlier: 5.572A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 247 Processing helix chain 'D' and resid 279 through 297 Processing helix chain 'D' and resid 311 through 325 removed outlier: 3.928A pdb=" N ILE D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Proline residue: D 322 - end of helix Processing helix chain 'D' and resid 358 through 376 removed outlier: 3.983A pdb=" N VAL D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ARG D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 374 " --> pdb=" O PHE D 370 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 418 removed outlier: 5.709A pdb=" N ARG D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 440 removed outlier: 4.666A pdb=" N TRP D 434 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 440 " --> pdb=" O VAL D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 488 Proline residue: D 473 - end of helix removed outlier: 5.571A pdb=" N VAL D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 888 1.31 - 1.43: 1808 1.43 - 1.56: 3788 1.56 - 1.68: 84 1.68 - 1.81: 44 Bond restraints: 6612 Sorted by residual: bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.440 -0.113 2.00e-02 2.50e+03 3.17e+01 ... (remaining 6607 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.17: 160 107.17 - 113.88: 4026 113.88 - 120.58: 2570 120.58 - 127.29: 2056 127.29 - 133.99: 56 Bond angle restraints: 8868 Sorted by residual: angle pdb=" C32 POV B 708 " pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 110.66 120.30 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV D 703 " pdb=" C31 POV D 703 " pdb=" O31 POV D 703 " ideal model delta sigma weight residual 110.66 120.30 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV C 701 " pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C32 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C32 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 110.66 120.26 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 8863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 3524 23.01 - 46.02: 256 46.02 - 69.03: 60 69.03 - 92.04: 0 92.04 - 115.05: 4 Dihedral angle restraints: 3844 sinusoidal: 1576 harmonic: 2268 Sorted by residual: dihedral pdb=" C3 POV C 702 " pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " pdb=" C32 POV C 702 " ideal model delta sinusoidal sigma weight residual 172.61 57.56 115.05 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 POV B 703 " pdb=" C31 POV B 703 " pdb=" O31 POV B 703 " pdb=" C32 POV B 703 " ideal model delta sinusoidal sigma weight residual 172.61 57.58 115.03 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" C3 POV D 704 " pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " pdb=" C32 POV D 704 " ideal model delta sinusoidal sigma weight residual 172.61 57.58 115.03 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 776 0.038 - 0.075: 226 0.075 - 0.113: 52 0.113 - 0.151: 13 0.151 - 0.188: 5 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA LEU B 472 " pdb=" N LEU B 472 " pdb=" C LEU B 472 " pdb=" CB LEU B 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA LEU C 472 " pdb=" N LEU C 472 " pdb=" C LEU C 472 " pdb=" CB LEU C 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA LEU D 472 " pdb=" N LEU D 472 " pdb=" C LEU D 472 " pdb=" CB LEU D 472 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 1069 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 472 " -0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO D 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 473 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 472 " 0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 473 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 472 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 473 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.046 5.00e-02 4.00e+02 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.84: 2061 2.84 - 3.41: 7279 3.41 - 3.99: 12398 3.99 - 4.56: 17938 4.56 - 5.14: 25563 Nonbonded interactions: 65239 Sorted by model distance: nonbonded pdb=" OE2 GLU A 283 " pdb=" NH2 ARG A 371 " model vdw 2.259 2.520 nonbonded pdb=" OE2 GLU B 283 " pdb=" NH2 ARG B 371 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU D 283 " pdb=" NH2 ARG D 371 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU C 283 " pdb=" NH2 ARG C 371 " model vdw 2.260 2.520 nonbonded pdb=" OE2 GLU C 283 " pdb=" NH1 ARG C 368 " model vdw 2.272 2.520 ... (remaining 65234 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' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'B' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'C' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) selection = (chain 'D' and (resid 226 through 489 or (resid 702 and (name C31 or name C32 or \ name C33 or name C34 or name C35)) or (resid 703 through 704 and (name C32 or n \ ame C33 or name C34 or name C35)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 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: 6.030 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 22.250 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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:15.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.009 0.115 6612 Z= 0.589 Angle : 0.967 9.640 8868 Z= 0.399 Chirality : 0.041 0.188 1072 Planarity : 0.008 0.083 1020 Dihedral : 16.683 115.049 2364 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.60 % Allowed : 5.42 % Favored : 93.98 % 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: 2.20 (0.31), residues: 752 helix: 1.79 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -0.48 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 289 HIS 0.002 0.001 HIS B 486 PHE 0.033 0.002 PHE A 433 TYR 0.008 0.001 TYR B 415 ARG 0.008 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.730 Fit side-chains outliers start: 4 outliers final: 8 residues processed: 114 average time/residue: 1.4794 time to fit residues: 176.2879 Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6612 Z= 0.191 Angle : 0.503 4.740 8868 Z= 0.265 Chirality : 0.039 0.136 1072 Planarity : 0.005 0.059 1020 Dihedral : 12.952 71.349 1072 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 8.58 % Favored : 90.66 % 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: 3.23 (0.30), residues: 752 helix: 2.59 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.18 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 289 HIS 0.002 0.001 HIS B 378 PHE 0.029 0.002 PHE A 433 TYR 0.007 0.001 TYR B 323 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 0.734 Fit side-chains REVERT: A 316 ASP cc_start: 0.7428 (m-30) cc_final: 0.7070 (m-30) REVERT: A 487 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6985 (ttp-170) REVERT: B 487 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6963 (ttp-170) REVERT: C 487 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6989 (ttp-170) REVERT: D 487 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6965 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 119 average time/residue: 1.5271 time to fit residues: 188.8618 Evaluate side-chains 112 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.0020 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6612 Z= 0.150 Angle : 0.448 4.851 8868 Z= 0.233 Chirality : 0.038 0.130 1072 Planarity : 0.004 0.039 1020 Dihedral : 10.360 60.025 1068 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.60 % Allowed : 9.34 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.31), residues: 752 helix: 2.54 (0.21), residues: 620 sheet: None (None), residues: 0 loop : 0.16 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 289 HIS 0.001 0.001 HIS D 486 PHE 0.015 0.001 PHE C 433 TYR 0.005 0.001 TYR A 415 ARG 0.005 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 0.727 Fit side-chains REVERT: A 487 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6958 (ttp-170) REVERT: B 487 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6957 (ttp-170) REVERT: C 316 ASP cc_start: 0.7530 (m-30) cc_final: 0.7161 (m-30) REVERT: C 487 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6978 (ttp-170) REVERT: D 316 ASP cc_start: 0.7533 (m-30) cc_final: 0.7170 (m-30) REVERT: D 487 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.6971 (ttp-170) outliers start: 4 outliers final: 4 residues processed: 115 average time/residue: 1.5722 time to fit residues: 189.0896 Evaluate side-chains 113 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.0670 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 0.021 6612 Z= 0.163 Angle : 0.454 4.809 8868 Z= 0.235 Chirality : 0.038 0.133 1072 Planarity : 0.004 0.034 1020 Dihedral : 8.986 55.331 1068 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.36 % Allowed : 11.45 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.32), residues: 752 helix: 2.53 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.34 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 289 HIS 0.002 0.001 HIS B 378 PHE 0.015 0.001 PHE C 235 TYR 0.006 0.001 TYR D 483 ARG 0.004 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.767 Fit side-chains REVERT: A 380 LYS cc_start: 0.8360 (tppp) cc_final: 0.8085 (mmtp) REVERT: A 485 TYR cc_start: 0.8817 (t80) cc_final: 0.8586 (t80) REVERT: A 487 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6948 (ttp-170) REVERT: B 487 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6953 (ttp-170) REVERT: C 316 ASP cc_start: 0.7533 (m-30) cc_final: 0.7218 (m-30) REVERT: C 485 TYR cc_start: 0.8833 (t80) cc_final: 0.8619 (t80) REVERT: C 487 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6964 (ttp-170) REVERT: D 487 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6956 (ttp-170) outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 1.3328 time to fit residues: 165.8675 Evaluate side-chains 117 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6612 Z= 0.264 Angle : 0.510 5.136 8868 Z= 0.266 Chirality : 0.040 0.151 1072 Planarity : 0.004 0.027 1020 Dihedral : 9.354 55.779 1068 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.96 % Allowed : 11.90 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.32), residues: 752 helix: 2.45 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.40 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 454 HIS 0.003 0.002 HIS C 378 PHE 0.011 0.001 PHE D 416 TYR 0.008 0.001 TYR D 485 ARG 0.005 0.001 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.667 Fit side-chains REVERT: A 380 LYS cc_start: 0.8355 (tppp) cc_final: 0.8088 (mmtp) REVERT: A 487 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6965 (ttp-170) REVERT: B 487 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6959 (ttp-170) REVERT: C 380 LYS cc_start: 0.8345 (tppp) cc_final: 0.8063 (mmtp) REVERT: C 487 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: D 380 LYS cc_start: 0.8343 (tppp) cc_final: 0.8061 (mmtp) REVERT: D 487 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6956 (ttp-170) outliers start: 13 outliers final: 5 residues processed: 121 average time/residue: 1.3211 time to fit residues: 167.1689 Evaluate side-chains 119 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.0050 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6612 Z= 0.144 Angle : 0.435 4.949 8868 Z= 0.226 Chirality : 0.037 0.135 1072 Planarity : 0.004 0.028 1020 Dihedral : 8.213 56.749 1068 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.90 % Allowed : 14.46 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.32), residues: 752 helix: 2.52 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.38 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 289 HIS 0.001 0.000 HIS B 378 PHE 0.007 0.001 PHE D 433 TYR 0.006 0.001 TYR B 485 ARG 0.005 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.748 Fit side-chains REVERT: A 380 LYS cc_start: 0.8342 (tppp) cc_final: 0.8084 (mmtp) REVERT: A 487 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6945 (ttp-170) REVERT: B 316 ASP cc_start: 0.7462 (m-30) cc_final: 0.7190 (m-30) REVERT: B 487 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6944 (ttp-170) REVERT: C 380 LYS cc_start: 0.8342 (tppp) cc_final: 0.8062 (mmtp) REVERT: C 487 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6935 (ttp-170) REVERT: D 316 ASP cc_start: 0.7473 (m-30) cc_final: 0.7201 (m-30) REVERT: D 380 LYS cc_start: 0.8353 (tppp) cc_final: 0.8073 (mmtp) REVERT: D 487 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6951 (ttp-170) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 1.3835 time to fit residues: 161.8313 Evaluate side-chains 115 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6612 Z= 0.284 Angle : 0.500 5.120 8868 Z= 0.262 Chirality : 0.040 0.149 1072 Planarity : 0.004 0.026 1020 Dihedral : 8.964 57.297 1064 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 13.55 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.32), residues: 752 helix: 2.45 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.44 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 454 HIS 0.003 0.002 HIS A 378 PHE 0.010 0.001 PHE D 416 TYR 0.007 0.001 TYR D 485 ARG 0.003 0.001 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.751 Fit side-chains REVERT: A 380 LYS cc_start: 0.8364 (tppp) cc_final: 0.8103 (mmtp) REVERT: A 487 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6972 (ttp-170) REVERT: B 380 LYS cc_start: 0.8345 (tppp) cc_final: 0.7882 (tptp) REVERT: B 487 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6974 (ttp-170) REVERT: C 380 LYS cc_start: 0.8354 (tppp) cc_final: 0.7890 (tptp) REVERT: C 487 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6967 (ttp-170) REVERT: D 380 LYS cc_start: 0.8357 (tppp) cc_final: 0.7886 (tptp) REVERT: D 487 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6971 (ttp-170) outliers start: 10 outliers final: 1 residues processed: 116 average time/residue: 1.3339 time to fit residues: 161.7418 Evaluate side-chains 109 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6612 Z= 0.184 Angle : 0.453 5.040 8868 Z= 0.237 Chirality : 0.038 0.141 1072 Planarity : 0.004 0.027 1020 Dihedral : 8.374 58.312 1060 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.75 % Allowed : 15.21 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.32), residues: 752 helix: 2.45 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.57 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.002 0.001 HIS C 378 PHE 0.007 0.001 PHE B 410 TYR 0.007 0.001 TYR D 485 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.922 Fit side-chains REVERT: A 380 LYS cc_start: 0.8344 (tppp) cc_final: 0.8092 (mmtp) REVERT: A 487 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6944 (ttp-170) REVERT: B 380 LYS cc_start: 0.8353 (tppp) cc_final: 0.7893 (tptp) REVERT: B 487 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6955 (ttp-170) REVERT: C 316 ASP cc_start: 0.7501 (m-30) cc_final: 0.7296 (m-30) REVERT: C 380 LYS cc_start: 0.8353 (tppp) cc_final: 0.7889 (tptp) REVERT: C 487 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6960 (ttp-170) REVERT: D 380 LYS cc_start: 0.8360 (tppp) cc_final: 0.7890 (tptp) REVERT: D 487 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6956 (ttp-170) outliers start: 5 outliers final: 4 residues processed: 110 average time/residue: 1.4786 time to fit residues: 170.2842 Evaluate side-chains 115 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6612 Z= 0.166 Angle : 0.441 5.096 8868 Z= 0.230 Chirality : 0.037 0.137 1072 Planarity : 0.003 0.024 1020 Dihedral : 7.942 59.318 1060 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.51 % Allowed : 14.46 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.32), residues: 752 helix: 2.47 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.61 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 454 HIS 0.002 0.001 HIS B 378 PHE 0.007 0.001 PHE B 410 TYR 0.008 0.001 TYR B 485 ARG 0.004 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.733 Fit side-chains REVERT: A 380 LYS cc_start: 0.8343 (tppp) cc_final: 0.8064 (mmtp) REVERT: A 487 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6971 (ttp-170) REVERT: B 380 LYS cc_start: 0.8343 (tppp) cc_final: 0.7853 (tptp) REVERT: B 487 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6948 (ttp-170) REVERT: C 316 ASP cc_start: 0.7464 (m-30) cc_final: 0.7240 (m-30) REVERT: C 380 LYS cc_start: 0.8329 (tppp) cc_final: 0.7850 (tptp) REVERT: C 487 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6962 (ttp-170) REVERT: D 380 LYS cc_start: 0.8346 (tppp) cc_final: 0.7858 (tptp) REVERT: D 487 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6944 (ttp-170) outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 1.3882 time to fit residues: 170.1828 Evaluate side-chains 122 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6612 Z= 0.161 Angle : 0.439 5.049 8868 Z= 0.229 Chirality : 0.037 0.137 1072 Planarity : 0.003 0.026 1020 Dihedral : 7.824 59.525 1060 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.66 % Allowed : 14.16 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.32), residues: 752 helix: 2.51 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.61 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.002 0.001 HIS A 378 PHE 0.007 0.001 PHE B 410 TYR 0.007 0.001 TYR D 485 ARG 0.004 0.000 ARG D 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.742 Fit side-chains REVERT: A 380 LYS cc_start: 0.8343 (tppp) cc_final: 0.8075 (mmtp) REVERT: A 487 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6965 (ttp-170) REVERT: B 380 LYS cc_start: 0.8342 (tppp) cc_final: 0.7858 (tptp) REVERT: B 487 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6945 (ttp-170) REVERT: C 316 ASP cc_start: 0.7462 (m-30) cc_final: 0.7238 (m-30) REVERT: C 380 LYS cc_start: 0.8317 (tppp) cc_final: 0.7845 (tptp) REVERT: C 487 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6945 (ttp-170) REVERT: D 380 LYS cc_start: 0.8346 (tppp) cc_final: 0.7863 (tptp) REVERT: D 487 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6946 (ttp-170) outliers start: 11 outliers final: 9 residues processed: 119 average time/residue: 1.4627 time to fit residues: 182.4775 Evaluate side-chains 124 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 487 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.089627 restraints weight = 7199.330| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.70 r_work: 0.2807 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6612 Z= 0.242 Angle : 0.477 5.145 8868 Z= 0.250 Chirality : 0.039 0.146 1072 Planarity : 0.004 0.025 1020 Dihedral : 8.287 57.916 1060 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.66 % Allowed : 14.16 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.32), residues: 752 helix: 2.43 (0.21), residues: 624 sheet: None (None), residues: 0 loop : 0.64 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 454 HIS 0.003 0.001 HIS A 378 PHE 0.009 0.001 PHE D 416 TYR 0.008 0.001 TYR D 485 ARG 0.003 0.000 ARG D 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.74 seconds wall clock time: 58 minutes 27.49 seconds (3507.49 seconds total)