Starting phenix.real_space_refine (version: dev) on Fri Feb 17 22:35:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj1_25152/02_2023/7sj1_25152_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj1_25152/02_2023/7sj1_25152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj1_25152/02_2023/7sj1_25152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj1_25152/02_2023/7sj1_25152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj1_25152/02_2023/7sj1_25152_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sj1_25152/02_2023/7sj1_25152_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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 Process input model Symmetric amino acids flipped Residue "A GLU 247": "OE1" <-> "OE2" Residue "B GLU 247": "OE1" <-> "OE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "D GLU 247": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6463 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1527 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 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: 248 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: 248 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: 248 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: 248 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.39, per 1000 atoms: 0.68 Number of scatterers: 6463 At special positions: 0 Unit cell: (95.46, 95.46, 64.5, 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 1021 8.00 N 956 7.00 C 4456 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: 2.63 Conformation dependent library (CDL) restraints added in 1.0 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 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 227 through 248 removed outlier: 4.304A pdb=" N THR A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 297 Processing helix chain 'A' and resid 311 through 325 removed outlier: 3.653A 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 377 removed outlier: 4.178A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE A 372 " --> pdb=" O ARG A 368 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 417 removed outlier: 3.999A pdb=" N MET A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 4.658A pdb=" N PHE A 434 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.732A 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: 5.653A pdb=" N VAL A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 248 removed outlier: 4.304A pdb=" N THR B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 297 Processing helix chain 'B' and resid 311 through 325 removed outlier: 3.653A 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 377 removed outlier: 4.178A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE B 372 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ARG B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 417 removed outlier: 3.999A pdb=" N MET B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 removed outlier: 4.658A pdb=" N PHE B 434 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.732A 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: 5.653A pdb=" N VAL B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 248 removed outlier: 4.305A pdb=" N THR C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 297 Processing helix chain 'C' and resid 311 through 325 removed outlier: 3.653A 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 377 removed outlier: 4.177A pdb=" N VAL C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHE C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER C 376 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 417 removed outlier: 4.000A pdb=" N MET C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 441 removed outlier: 4.657A pdb=" N PHE C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.733A 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: 5.654A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 248 removed outlier: 4.304A pdb=" N THR D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 297 Processing helix chain 'D' and resid 311 through 325 removed outlier: 3.653A 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 377 removed outlier: 4.178A pdb=" N VAL D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG D 371 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE D 372 " --> pdb=" O ARG D 368 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE D 373 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS D 374 " --> pdb=" O PHE D 370 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG D 377 " --> pdb=" O PHE D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 417 removed outlier: 4.000A pdb=" N MET D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 441 removed outlier: 4.658A pdb=" N PHE D 434 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.732A 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: 5.653A pdb=" N VAL D 476 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1236 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: 1.65 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 888 1.31 - 1.44: 1768 1.44 - 1.56: 3799 1.56 - 1.68: 69 1.68 - 1.81: 44 Bond restraints: 6568 Sorted by residual: bond pdb=" C21 POV C 706 " pdb=" O22 POV C 706 " ideal model delta sigma weight residual 1.205 1.415 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV B 707 " pdb=" O22 POV B 707 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV A 705 " pdb=" O22 POV A 705 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV D 708 " pdb=" O22 POV D 708 " ideal model delta sigma weight residual 1.205 1.414 -0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C21 POV A 705 " pdb=" O21 POV A 705 " ideal model delta sigma weight residual 1.330 1.199 0.131 2.00e-02 2.50e+03 4.31e+01 ... (remaining 6563 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.94: 140 106.94 - 113.71: 3899 113.71 - 120.48: 2526 120.48 - 127.25: 2187 127.25 - 134.02: 52 Bond angle restraints: 8804 Sorted by residual: angle pdb=" C THR B 449 " pdb=" N PRO B 450 " pdb=" CA PRO B 450 " ideal model delta sigma weight residual 119.56 115.15 4.41 1.02e+00 9.61e-01 1.87e+01 angle pdb=" C THR D 449 " pdb=" N PRO D 450 " pdb=" CA PRO D 450 " ideal model delta sigma weight residual 119.56 115.16 4.40 1.02e+00 9.61e-01 1.86e+01 angle pdb=" C THR A 449 " pdb=" N PRO A 450 " pdb=" CA PRO A 450 " ideal model delta sigma weight residual 119.56 115.18 4.38 1.02e+00 9.61e-01 1.84e+01 angle pdb=" C THR C 449 " pdb=" N PRO C 450 " pdb=" CA PRO C 450 " ideal model delta sigma weight residual 119.56 115.20 4.36 1.02e+00 9.61e-01 1.82e+01 angle pdb=" C32 POV B 708 " pdb=" C31 POV B 708 " pdb=" O31 POV B 708 " ideal model delta sigma weight residual 110.66 120.51 -9.85 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.19: 3532 24.19 - 48.38: 232 48.38 - 72.57: 52 72.57 - 96.76: 0 96.76 - 120.95: 4 Dihedral angle restraints: 3820 sinusoidal: 1552 harmonic: 2268 Sorted by residual: 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 51.66 120.95 1 3.00e+01 1.11e-03 1.62e+01 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 51.68 120.93 1 3.00e+01 1.11e-03 1.61e+01 dihedral pdb=" C3 POV A 701 " pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " pdb=" C32 POV A 701 " ideal model delta sinusoidal sigma weight residual 172.61 51.69 120.92 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 3817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 645 0.029 - 0.057: 252 0.057 - 0.086: 125 0.086 - 0.114: 29 0.114 - 0.143: 21 Chirality restraints: 1072 Sorted by residual: chirality pdb=" CA THR C 449 " pdb=" N THR C 449 " pdb=" C THR C 449 " pdb=" CB THR C 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA THR D 449 " pdb=" N THR D 449 " pdb=" C THR D 449 " pdb=" CB THR D 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA THR B 449 " pdb=" N THR B 449 " pdb=" C THR B 449 " pdb=" CB THR B 449 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 1069 not shown) Planarity restraints: 1016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 433 " -0.013 2.00e-02 2.50e+03 1.27e-02 2.80e+00 pdb=" CG PHE A 433 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 433 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 433 " -0.013 2.00e-02 2.50e+03 1.26e-02 2.78e+00 pdb=" CG PHE B 433 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 433 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 433 " -0.013 2.00e-02 2.50e+03 1.25e-02 2.72e+00 pdb=" CG PHE C 433 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 433 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 433 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 433 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 433 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 433 " 0.000 2.00e-02 2.50e+03 ... (remaining 1013 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 2446 2.91 - 3.47: 7656 3.47 - 4.02: 10870 4.02 - 4.58: 16437 4.58 - 5.14: 22726 Nonbonded interactions: 60135 Sorted by model distance: nonbonded pdb=" O VAL B 407 " pdb=" OG SER B 411 " model vdw 2.351 2.440 nonbonded pdb=" O VAL A 407 " pdb=" OG SER A 411 " model vdw 2.351 2.440 nonbonded pdb=" O VAL D 407 " pdb=" OG SER D 411 " model vdw 2.351 2.440 nonbonded pdb=" O VAL C 407 " pdb=" OG SER C 411 " model vdw 2.351 2.440 nonbonded pdb=" O THR C 441 " pdb=" OG1 THR C 442 " model vdw 2.365 2.440 ... (remaining 60130 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 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 4456 2.51 5 N 956 2.21 5 O 1021 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.600 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: 6.560 Check model and map are aligned: 0.100 Process input model: 20.950 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.070 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:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.011 0.210 6568 Z= 0.722 Angle : 1.007 9.847 8804 Z= 0.418 Chirality : 0.041 0.143 1072 Planarity : 0.004 0.037 1016 Dihedral : 16.654 120.953 2340 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.61 % 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: 2.80 (0.31), residues: 752 helix: 2.17 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.63 (0.58), residues: 148 *********************** 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 171 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 0.703 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 171 average time/residue: 1.0817 time to fit residues: 194.9760 Evaluate side-chains 129 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.817 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7802 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 6568 Z= 0.266 Angle : 0.597 8.484 8804 Z= 0.313 Chirality : 0.041 0.131 1072 Planarity : 0.005 0.039 1016 Dihedral : 13.545 86.308 1044 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 2.42 % 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: 2.71 (0.30), residues: 752 helix: 2.12 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.54 (0.59), residues: 148 *********************** 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 143 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.759 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 131 average time/residue: 1.3399 time to fit residues: 183.4557 Evaluate side-chains 126 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 3 residues processed: 8 average time/residue: 0.5557 time to fit residues: 5.7811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 0.0050 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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: 0.7766 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6568 Z= 0.187 Angle : 0.518 5.775 8804 Z= 0.272 Chirality : 0.038 0.125 1072 Planarity : 0.004 0.038 1016 Dihedral : 11.614 73.784 1044 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.31), residues: 752 helix: 2.13 (0.20), residues: 604 sheet: None (None), residues: 0 loop : 0.35 (0.58), residues: 148 *********************** 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 130 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.710 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 121 average time/residue: 1.3511 time to fit residues: 171.2320 Evaluate side-chains 107 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0737 time to fit residues: 1.6698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 6568 Z= 0.209 Angle : 0.545 5.839 8804 Z= 0.285 Chirality : 0.039 0.149 1072 Planarity : 0.005 0.043 1016 Dihedral : 10.551 60.990 1044 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 3.18 % 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: 2.59 (0.31), residues: 752 helix: 2.12 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.09 (0.59), residues: 148 *********************** 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 131 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.767 Fit side-chains outliers start: 21 outliers final: 4 residues processed: 126 average time/residue: 1.3973 time to fit residues: 184.6575 Evaluate side-chains 111 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.646 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0607 time to fit residues: 1.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 0.0060 chunk 18 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 6568 Z= 0.194 Angle : 0.535 5.204 8804 Z= 0.282 Chirality : 0.041 0.209 1072 Planarity : 0.005 0.037 1016 Dihedral : 9.817 57.827 1044 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 2.12 % 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: 2.68 (0.31), residues: 752 helix: 2.20 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.06 (0.58), residues: 148 *********************** 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 124 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.731 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 116 average time/residue: 1.4614 time to fit residues: 176.7548 Evaluate side-chains 106 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5645 time to fit residues: 5.8873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 14 optimal weight: 0.0270 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 70 optimal weight: 0.0980 overall best weight: 0.2230 ------------------------------------------------------------------------------- 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: 0.7724 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 6568 Z= 0.152 Angle : 0.511 8.991 8804 Z= 0.266 Chirality : 0.040 0.150 1072 Planarity : 0.004 0.033 1016 Dihedral : 8.930 52.166 1044 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.31), residues: 752 helix: 2.27 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.06 (0.58), residues: 148 *********************** 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 113 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.731 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 1.4368 time to fit residues: 163.4898 Evaluate side-chains 93 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0599 time to fit residues: 1.3845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 22 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6568 Z= 0.182 Angle : 0.540 8.657 8804 Z= 0.280 Chirality : 0.041 0.147 1072 Planarity : 0.005 0.041 1016 Dihedral : 8.487 47.655 1044 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 1.97 % 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: 2.81 (0.32), residues: 752 helix: 2.25 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.27 (0.59), residues: 148 *********************** 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 105 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.737 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 1.6573 time to fit residues: 164.4263 Evaluate side-chains 91 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.0549 time to fit residues: 1.3966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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: 0.7751 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6568 Z= 0.170 Angle : 0.556 8.307 8804 Z= 0.284 Chirality : 0.040 0.133 1072 Planarity : 0.005 0.033 1016 Dihedral : 8.130 46.581 1044 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.31), residues: 752 helix: 2.26 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.24 (0.58), residues: 148 *********************** 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 102 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.816 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 99 average time/residue: 1.5150 time to fit residues: 156.3566 Evaluate side-chains 92 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0595 time to fit residues: 1.0861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7740 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6568 Z= 0.169 Angle : 0.589 13.485 8804 Z= 0.291 Chirality : 0.040 0.146 1072 Planarity : 0.004 0.032 1016 Dihedral : 7.698 46.250 1044 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 0.76 % 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: 2.87 (0.31), residues: 752 helix: 2.30 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.28 (0.58), residues: 148 *********************** 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 98 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.679 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 96 average time/residue: 1.5296 time to fit residues: 152.9513 Evaluate side-chains 92 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6568 Z= 0.171 Angle : 0.615 14.961 8804 Z= 0.297 Chirality : 0.041 0.151 1072 Planarity : 0.004 0.032 1016 Dihedral : 7.422 45.941 1044 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 0.45 % 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: 2.92 (0.31), residues: 752 helix: 2.33 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.29 (0.57), residues: 148 ********************** 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 99 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.700 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 1.4764 time to fit residues: 147.8423 Evaluate side-chains 96 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0591 time to fit residues: 1.3116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 62 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.184114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140583 restraints weight = 6718.101| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.08 r_work: 0.3681 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6568 Z= 0.190 Angle : 0.625 14.543 8804 Z= 0.304 Chirality : 0.042 0.161 1072 Planarity : 0.005 0.037 1016 Dihedral : 7.406 46.516 1044 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 0.45 % 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: 2.89 (0.31), residues: 752 helix: 2.34 (0.21), residues: 604 sheet: None (None), residues: 0 loop : 0.16 (0.57), residues: 148 =============================================================================== Job complete usr+sys time: 2972.88 seconds wall clock time: 53 minutes 49.07 seconds (3229.07 seconds total)