Starting phenix.real_space_refine on Mon Mar 11 15:26:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t54_25694/03_2024/7t54_25694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t54_25694/03_2024/7t54_25694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t54_25694/03_2024/7t54_25694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t54_25694/03_2024/7t54_25694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t54_25694/03_2024/7t54_25694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t54_25694/03_2024/7t54_25694_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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 P 6 5.49 5 S 20 5.16 5 C 5310 2.51 5 N 1570 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B GLU 700": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 4245 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1336 Unresolved non-hydrogen angles: 1697 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 629 Chain: "B" Number of atoms: 4245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 4245 Classifications: {'peptide': 708} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1336 Unresolved non-hydrogen angles: 1697 Unresolved non-hydrogen dihedrals: 1098 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 629 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.65, per 1000 atoms: 0.66 Number of scatterers: 8552 At special positions: 0 Unit cell: (128.75, 87.55, 135.96, 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) S 20 16.00 P 6 15.00 O 1646 8.00 N 1570 7.00 C 5310 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: 3.79 Conformation dependent library (CDL) restraints added in 2.2 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 8 sheets defined 57.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.784A pdb=" N CYS A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 196 Proline residue: A 164 - end of helix removed outlier: 6.131A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 250 removed outlier: 3.509A pdb=" N SER A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 264 through 304 removed outlier: 4.337A pdb=" N ARG A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 327 through 353 removed outlier: 4.514A pdb=" N GLN A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 364 through 417 removed outlier: 3.845A pdb=" N THR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 462 Proline residue: A 438 - end of helix Proline residue: A 447 - end of helix removed outlier: 5.199A pdb=" N GLN A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 454 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.811A pdb=" N LEU A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 589 through 598 Processing helix chain 'A' and resid 603 through 607 removed outlier: 4.251A pdb=" N LYS A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 603 through 607' Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 656 through 668 removed outlier: 3.664A pdb=" N ILE A 661 " --> pdb=" O GLU A 658 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 663 " --> pdb=" O HIS A 660 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 666 " --> pdb=" O ASP A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 710 Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 125 through 131 Processing helix chain 'B' and resid 159 through 196 Proline residue: B 164 - end of helix removed outlier: 6.054A pdb=" N LYS B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR B 168 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 251 removed outlier: 3.638A pdb=" N TYR B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 264 through 304 removed outlier: 4.271A pdb=" N ARG B 269 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS B 275 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 353 removed outlier: 4.679A pdb=" N LYS B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 3.728A pdb=" N ASN B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 364 through 417 removed outlier: 3.508A pdb=" N SER B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 462 Proline residue: B 438 - end of helix Proline residue: B 447 - end of helix removed outlier: 5.186A pdb=" N GLN B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 454 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.825A pdb=" N LEU B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 589 through 598 Processing helix chain 'B' and resid 603 through 607 removed outlier: 4.320A pdb=" N LYS B 607 " --> pdb=" O ASP B 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 607' Processing helix chain 'B' and resid 625 through 639 removed outlier: 3.592A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.512A pdb=" N HIS B 660 " --> pdb=" O THR B 657 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 661 " --> pdb=" O GLU B 658 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP B 663 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR B 666 " --> pdb=" O ASP B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 710 Processing helix chain 'B' and resid 713 through 721 Processing sheet with id= A, first strand: chain 'A' and resid 87 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 111 through 115 Processing sheet with id= C, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= D, first strand: chain 'A' and resid 697 through 702 removed outlier: 7.204A pdb=" N LEU A 692 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 701 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 690 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 689 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 693 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL A 674 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 517 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 676 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 87 through 92 Processing sheet with id= F, first strand: chain 'B' and resid 111 through 113 removed outlier: 4.072A pdb=" N ILE B 111 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 123 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL B 113 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 486 through 489 Processing sheet with id= H, first strand: chain 'B' and resid 697 through 702 removed outlier: 7.184A pdb=" N LEU B 692 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 701 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 690 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS B 689 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 693 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 674 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE B 517 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 676 " --> pdb=" O ILE B 517 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1692 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: 2.94 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3042 1.34 - 1.46: 748 1.46 - 1.58: 4780 1.58 - 1.69: 12 1.69 - 1.81: 36 Bond restraints: 8618 Sorted by residual: bond pdb=" N ILE B 656 " pdb=" CA ILE B 656 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.85e+00 bond pdb=" N ILE A 656 " pdb=" CA ILE A 656 " ideal model delta sigma weight residual 1.461 1.495 -0.035 1.19e-02 7.06e+03 8.48e+00 bond pdb=" N VAL A 250 " pdb=" CA VAL A 250 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" N LEU A 653 " pdb=" CA LEU A 653 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.22e-02 6.72e+03 6.53e+00 bond pdb=" N SER A 655 " pdb=" CA SER A 655 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.41e+00 ... (remaining 8613 not shown) Histogram of bond angle deviations from ideal: 98.04 - 106.37: 94 106.37 - 114.69: 5143 114.69 - 123.02: 6151 123.02 - 131.35: 423 131.35 - 139.68: 9 Bond angle restraints: 11820 Sorted by residual: angle pdb=" N PHE B 478 " pdb=" CA PHE B 478 " pdb=" C PHE B 478 " ideal model delta sigma weight residual 111.36 121.43 -10.07 1.09e+00 8.42e-01 8.53e+01 angle pdb=" N ASP B 477 " pdb=" CA ASP B 477 " pdb=" C ASP B 477 " ideal model delta sigma weight residual 109.07 118.60 -9.53 1.61e+00 3.86e-01 3.51e+01 angle pdb=" C ASP B 654 " pdb=" CA ASP B 654 " pdb=" CB ASP B 654 " ideal model delta sigma weight residual 117.23 111.55 5.68 1.36e+00 5.41e-01 1.74e+01 angle pdb=" C GLU B 648 " pdb=" CA GLU B 648 " pdb=" CB GLU B 648 " ideal model delta sigma weight residual 116.54 112.00 4.54 1.15e+00 7.56e-01 1.56e+01 angle pdb=" C GLU A 44 " pdb=" N MET A 45 " pdb=" CA MET A 45 " ideal model delta sigma weight residual 122.38 115.67 6.71 1.81e+00 3.05e-01 1.37e+01 ... (remaining 11815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 4793 16.13 - 32.26: 231 32.26 - 48.40: 58 48.40 - 64.53: 24 64.53 - 80.66: 2 Dihedral angle restraints: 5108 sinusoidal: 1048 harmonic: 4060 Sorted by residual: dihedral pdb=" N SER B 481 " pdb=" C SER B 481 " pdb=" CA SER B 481 " pdb=" CB SER B 481 " ideal model delta harmonic sigma weight residual 122.80 133.61 -10.81 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C SER B 481 " pdb=" N SER B 481 " pdb=" CA SER B 481 " pdb=" CB SER B 481 " ideal model delta harmonic sigma weight residual -122.60 -132.85 10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" CA GLU B 339 " pdb=" C GLU B 339 " pdb=" N ASP B 340 " pdb=" CA ASP B 340 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 5105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1381 0.081 - 0.162: 123 0.162 - 0.242: 4 0.242 - 0.323: 1 0.323 - 0.404: 1 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA SER B 481 " pdb=" N SER B 481 " pdb=" C SER B 481 " pdb=" CB SER B 481 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA PHE B 478 " pdb=" N PHE B 478 " pdb=" C PHE B 478 " pdb=" CB PHE B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ASP B 477 " pdb=" N ASP B 477 " pdb=" C ASP B 477 " pdb=" CB ASP B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1507 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 475 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C SER B 475 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 475 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP B 476 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 247 " 0.009 2.00e-02 2.50e+03 9.27e-03 1.72e+00 pdb=" CG TYR B 247 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 247 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 247 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 247 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 247 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 247 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 480 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C ILE B 480 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE B 480 " -0.008 2.00e-02 2.50e+03 pdb=" N SER B 481 " -0.007 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 58 2.64 - 3.21: 8212 3.21 - 3.77: 12818 3.77 - 4.34: 14806 4.34 - 4.90: 24456 Nonbonded interactions: 60350 Sorted by model distance: nonbonded pdb=" O ASN A 622 " pdb=" ND2 ASN A 622 " model vdw 2.078 2.520 nonbonded pdb=" OH TYR B 246 " pdb=" OE2 GLU B 461 " model vdw 2.215 2.440 nonbonded pdb=" N SER B 68 " pdb=" O GLU B 140 " model vdw 2.360 2.520 nonbonded pdb=" NH1 ARG B 269 " pdb=" OD1 ASN B 457 " model vdw 2.418 2.520 nonbonded pdb=" OE2 GLU B 339 " pdb=" ND2 ASN B 457 " model vdw 2.426 2.520 ... (remaining 60345 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.000 Extract box with map and model: 5.990 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 29.240 Find NCS groups from input model: 0.540 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.004 0.041 8618 Z= 0.252 Angle : 0.696 10.069 11820 Z= 0.464 Chirality : 0.045 0.404 1510 Planarity : 0.003 0.038 1578 Dihedral : 12.143 80.661 2480 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 0.68 % Allowed : 0.68 % Favored : 98.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1408 helix: 2.25 (0.19), residues: 786 sheet: -1.46 (0.43), residues: 146 loop : -2.09 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.003 0.001 HIS B 249 PHE 0.009 0.001 PHE B 270 TYR 0.022 0.001 TYR B 247 ARG 0.008 0.001 ARG A 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 0.2080 time to fit residues: 14.6694 Evaluate side-chains 29 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0980 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 50.0000 chunk 56 optimal weight: 0.0010 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 ASN B 679 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8618 Z= 0.177 Angle : 0.559 7.087 11820 Z= 0.329 Chirality : 0.041 0.149 1510 Planarity : 0.004 0.067 1578 Dihedral : 7.072 56.234 1518 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.98 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1408 helix: 2.49 (0.18), residues: 826 sheet: -1.15 (0.40), residues: 166 loop : -2.34 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 718 HIS 0.005 0.001 HIS A 249 PHE 0.007 0.001 PHE A 257 TYR 0.010 0.001 TYR A 536 ARG 0.007 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1801 time to fit residues: 7.0054 Evaluate side-chains 25 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 50.0000 chunk 39 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8618 Z= 0.241 Angle : 0.570 6.589 11820 Z= 0.332 Chirality : 0.039 0.126 1510 Planarity : 0.003 0.035 1578 Dihedral : 7.432 57.714 1518 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.11 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1408 helix: 1.91 (0.18), residues: 834 sheet: -1.54 (0.42), residues: 132 loop : -2.47 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 718 HIS 0.003 0.002 HIS B 548 PHE 0.017 0.002 PHE A 257 TYR 0.011 0.001 TYR A 612 ARG 0.005 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1729 time to fit residues: 5.5508 Evaluate side-chains 22 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 14 optimal weight: 40.0000 chunk 60 optimal weight: 0.2980 chunk 85 optimal weight: 30.0000 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 0.0170 chunk 121 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8618 Z= 0.115 Angle : 0.468 7.528 11820 Z= 0.268 Chirality : 0.040 0.130 1510 Planarity : 0.002 0.019 1578 Dihedral : 6.277 51.885 1518 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1408 helix: 2.04 (0.18), residues: 820 sheet: -1.30 (0.41), residues: 146 loop : -2.28 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 718 HIS 0.002 0.001 HIS A 249 PHE 0.011 0.001 PHE A 257 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2322 time to fit residues: 8.1458 Evaluate side-chains 22 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 100 optimal weight: 0.0870 chunk 55 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 0.0970 chunk 0 optimal weight: 50.0000 chunk 69 optimal weight: 30.0000 chunk 121 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 overall best weight: 3.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8618 Z= 0.201 Angle : 0.511 5.776 11820 Z= 0.302 Chirality : 0.039 0.129 1510 Planarity : 0.002 0.019 1578 Dihedral : 7.079 58.120 1518 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.53 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1408 helix: 2.13 (0.18), residues: 808 sheet: -1.31 (0.43), residues: 114 loop : -2.26 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 718 HIS 0.003 0.001 HIS B 548 PHE 0.015 0.002 PHE A 493 TYR 0.010 0.001 TYR B 612 ARG 0.008 0.001 ARG A 489 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1675 time to fit residues: 5.6232 Evaluate side-chains 22 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 33 optimal weight: 8.9990 chunk 135 optimal weight: 0.0170 chunk 112 optimal weight: 8.9990 chunk 62 optimal weight: 0.0170 chunk 11 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 20.0000 chunk 130 optimal weight: 0.3980 overall best weight: 1.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8618 Z= 0.118 Angle : 0.459 6.052 11820 Z= 0.266 Chirality : 0.039 0.121 1510 Planarity : 0.002 0.018 1578 Dihedral : 6.291 50.221 1518 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1408 helix: 2.21 (0.18), residues: 812 sheet: -0.83 (0.46), residues: 114 loop : -2.21 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.002 0.001 HIS B 249 PHE 0.011 0.001 PHE B 257 TYR 0.006 0.001 TYR A 612 ARG 0.001 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1626 time to fit residues: 5.2614 Evaluate side-chains 21 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 30.0000 chunk 77 optimal weight: 0.2980 chunk 98 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 84 optimal weight: 30.0000 chunk 82 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.0870 overall best weight: 3.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8618 Z= 0.179 Angle : 0.484 7.107 11820 Z= 0.286 Chirality : 0.039 0.122 1510 Planarity : 0.002 0.020 1578 Dihedral : 6.829 58.210 1518 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.53 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1408 helix: 2.09 (0.18), residues: 822 sheet: -1.15 (0.49), residues: 106 loop : -2.23 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 718 HIS 0.003 0.001 HIS A 548 PHE 0.012 0.001 PHE B 493 TYR 0.010 0.001 TYR A 612 ARG 0.003 0.000 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1659 time to fit residues: 5.5938 Evaluate side-chains 21 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 91 optimal weight: 10.0000 chunk 66 optimal weight: 0.0670 chunk 12 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 679 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8618 Z= 0.221 Angle : 0.528 7.294 11820 Z= 0.317 Chirality : 0.040 0.186 1510 Planarity : 0.003 0.028 1578 Dihedral : 6.982 57.259 1518 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1408 helix: 2.01 (0.18), residues: 816 sheet: -1.44 (0.49), residues: 106 loop : -2.38 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 718 HIS 0.004 0.002 HIS A 548 PHE 0.017 0.002 PHE A 493 TYR 0.011 0.001 TYR A 612 ARG 0.005 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1606 time to fit residues: 5.2191 Evaluate side-chains 22 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0020 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 0.0470 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 overall best weight: 2.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.7771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8618 Z= 0.140 Angle : 0.492 6.651 11820 Z= 0.289 Chirality : 0.040 0.175 1510 Planarity : 0.002 0.024 1578 Dihedral : 6.571 57.071 1518 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1408 helix: 2.08 (0.18), residues: 822 sheet: -1.34 (0.50), residues: 106 loop : -2.35 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 718 HIS 0.002 0.001 HIS A 548 PHE 0.011 0.001 PHE A 257 TYR 0.008 0.001 TYR B 389 ARG 0.004 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1716 time to fit residues: 5.5410 Evaluate side-chains 22 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 128 optimal weight: 0.0060 chunk 111 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 85 optimal weight: 30.0000 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 40.0000 chunk 118 optimal weight: 8.9990 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.8146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8618 Z= 0.149 Angle : 0.490 7.075 11820 Z= 0.288 Chirality : 0.040 0.180 1510 Planarity : 0.002 0.023 1578 Dihedral : 6.702 70.481 1518 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 0.46 % Allowed : 0.46 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1408 helix: 2.17 (0.18), residues: 822 sheet: -1.45 (0.50), residues: 106 loop : -2.36 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 718 HIS 0.002 0.001 HIS A 548 PHE 0.010 0.001 PHE A 257 TYR 0.007 0.001 TYR A 389 ARG 0.002 0.000 ARG A 630 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1646 time to fit residues: 5.5709 Evaluate side-chains 22 residues out of total 605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 overall best weight: 7.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 602 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.032763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.027248 restraints weight = 72975.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.027411 restraints weight = 64987.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.027635 restraints weight = 57821.047| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.9079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8618 Z= 0.343 Angle : 0.663 7.830 11820 Z= 0.392 Chirality : 0.042 0.187 1510 Planarity : 0.004 0.037 1578 Dihedral : 8.026 85.839 1518 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.66 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1408 helix: 1.42 (0.17), residues: 796 sheet: -2.69 (0.38), residues: 126 loop : -2.97 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 718 HIS 0.005 0.002 HIS A 548 PHE 0.028 0.003 PHE A 493 TYR 0.016 0.002 TYR B 612 ARG 0.005 0.001 ARG B 489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1435.61 seconds wall clock time: 26 minutes 39.67 seconds (1599.67 seconds total)