Starting phenix.real_space_refine on Tue Apr 9 19:01:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9e_20695/04_2024/6u9e_20695.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9e_20695/04_2024/6u9e_20695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9e_20695/04_2024/6u9e_20695.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9e_20695/04_2024/6u9e_20695.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9e_20695/04_2024/6u9e_20695.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u9e_20695/04_2024/6u9e_20695.pdb" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 10881 2.51 5 N 2871 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4731 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 559} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4731 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 559} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4731 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 6, 'PTRANS': 17, 'TRANS': 559} Chain breaks: 4 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 994 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'TRANS': 131} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 8.95, per 1000 atoms: 0.52 Number of scatterers: 17175 At special positions: 0 Unit cell: (103.79, 103.79, 206.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3387 8.00 N 2871 7.00 C 10881 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: 5.46 Conformation dependent library (CDL) restraints added in 2.7 seconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 40 sheets defined 8.8% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.909A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.671A pdb=" N LYS A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.625A pdb=" N GLN A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 removed outlier: 3.575A pdb=" N GLN A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.869A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 578 " --> pdb=" O CYS A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 697 through 701 removed outlier: 3.643A pdb=" N MET A 700 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 701 " --> pdb=" O LYS A 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 701' Processing helix chain 'A' and resid 772 through 776 removed outlier: 4.110A pdb=" N ASN A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.908A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 328 through 335 Processing helix chain 'C' and resid 347 through 353 removed outlier: 3.670A pdb=" N LYS C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 398 removed outlier: 3.624A pdb=" N GLN C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 428 removed outlier: 3.574A pdb=" N GLN C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 removed outlier: 3.870A pdb=" N LYS C 576 " --> pdb=" O LYS C 572 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 578 " --> pdb=" O CYS C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 623 No H-bonds generated for 'chain 'C' and resid 621 through 623' Processing helix chain 'C' and resid 697 through 701 removed outlier: 3.643A pdb=" N MET C 700 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 701 " --> pdb=" O LYS C 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 697 through 701' Processing helix chain 'C' and resid 772 through 776 removed outlier: 4.110A pdb=" N ASN C 776 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 removed outlier: 3.908A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 254' Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 347 through 353 removed outlier: 3.671A pdb=" N LYS E 353 " --> pdb=" O ASP E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 398 removed outlier: 3.624A pdb=" N GLN E 395 " --> pdb=" O PHE E 391 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 396 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.575A pdb=" N GLN E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 581 removed outlier: 3.869A pdb=" N LYS E 576 " --> pdb=" O LYS E 572 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN E 577 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 578 " --> pdb=" O CYS E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 623 No H-bonds generated for 'chain 'E' and resid 621 through 623' Processing helix chain 'E' and resid 697 through 701 removed outlier: 3.643A pdb=" N MET E 700 " --> pdb=" O ALA E 697 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 701 " --> pdb=" O LYS E 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 697 through 701' Processing helix chain 'E' and resid 772 through 776 removed outlier: 4.110A pdb=" N ASN E 776 " --> pdb=" O SER E 773 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 188 removed outlier: 3.555A pdb=" N SER A 269 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 187 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.638A pdb=" N CYS A 227 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 223 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 239 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 301 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.638A pdb=" N CYS A 227 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 564 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS A 616 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ARG A 564 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR A 614 " --> pdb=" O ARG A 564 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 451 " --> pdb=" O THR A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA5, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.568A pdb=" N TYR A 416 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AA7, first strand: chain 'A' and resid 480 through 481 removed outlier: 7.034A pdb=" N LYS A 466 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 637 through 640 removed outlier: 6.857A pdb=" N LEU A 736 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 692 through 695 removed outlier: 3.603A pdb=" N LEU A 713 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB2, first strand: chain 'A' and resid 800 through 802 removed outlier: 3.540A pdb=" N SER A 802 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 814 " --> pdb=" O SER A 802 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 179 through 188 removed outlier: 3.555A pdb=" N SER C 269 " --> pdb=" O LYS C 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 187 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 300 through 301 removed outlier: 3.520A pdb=" N HIS C 301 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 239 " --> pdb=" O PHE C 322 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 227 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS C 223 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 564 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS C 616 " --> pdb=" O SER C 562 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG C 564 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 614 " --> pdb=" O ARG C 564 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS C 451 " --> pdb=" O THR C 526 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 344 Processing sheet with id=AB6, first strand: chain 'C' and resid 363 through 365 removed outlier: 3.568A pdb=" N TYR C 416 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 461 through 462 Processing sheet with id=AB8, first strand: chain 'C' and resid 480 through 481 removed outlier: 7.034A pdb=" N LYS C 466 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 637 through 640 removed outlier: 6.856A pdb=" N LEU C 736 " --> pdb=" O ILE C 748 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 692 through 695 removed outlier: 3.603A pdb=" N LEU C 713 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 781 through 783 Processing sheet with id=AC3, first strand: chain 'C' and resid 800 through 802 removed outlier: 3.540A pdb=" N SER C 802 " --> pdb=" O ARG C 814 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 814 " --> pdb=" O SER C 802 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 179 through 188 removed outlier: 3.555A pdb=" N SER E 269 " --> pdb=" O LYS E 179 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS E 187 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 301 removed outlier: 3.520A pdb=" N HIS E 301 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE E 239 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS E 227 " --> pdb=" O ASN E 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E 223 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 564 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LYS E 616 " --> pdb=" O SER E 562 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG E 564 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR E 614 " --> pdb=" O ARG E 564 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 451 " --> pdb=" O THR E 526 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 342 through 344 Processing sheet with id=AC7, first strand: chain 'E' and resid 363 through 365 removed outlier: 3.568A pdb=" N TYR E 416 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 461 through 462 Processing sheet with id=AC9, first strand: chain 'E' and resid 480 through 481 removed outlier: 7.034A pdb=" N LYS E 466 " --> pdb=" O ASN E 499 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 637 through 640 removed outlier: 6.857A pdb=" N LEU E 736 " --> pdb=" O ILE E 748 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS E 744 " --> pdb=" O GLN E 740 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 692 through 695 removed outlier: 3.602A pdb=" N LEU E 713 " --> pdb=" O TYR E 692 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 781 through 783 Processing sheet with id=AD4, first strand: chain 'E' and resid 800 through 802 removed outlier: 3.539A pdb=" N SER E 802 " --> pdb=" O ARG E 814 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG E 814 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.589A pdb=" N LEU B 15 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.536A pdb=" N ILE B 44 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASN F 55 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER B 46 " --> pdb=" O ASN F 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 68 through 71 removed outlier: 3.537A pdb=" N ASN B 55 " --> pdb=" O SER D 46 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.514A pdb=" N SER B 76 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 100 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN D 116 " --> pdb=" O ILE F 109 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP B 124 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 123 " --> pdb=" O ILE F 132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 131 through 132 removed outlier: 3.657A pdb=" N ILE D 125 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP D 124 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B 107 " --> pdb=" O ASN F 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.509A pdb=" N ILE D 132 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE F 125 " --> pdb=" O ILE D 132 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 117 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN B 116 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 76 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.588A pdb=" N LEU D 15 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 68 through 71 removed outlier: 6.176A pdb=" N GLN D 51 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N SER F 46 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE D 53 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.588A pdb=" N LEU F 15 " --> pdb=" O LEU F 30 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 891 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: 5.67 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5385 1.33 - 1.45: 2417 1.45 - 1.57: 9583 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 17430 Sorted by residual: bond pdb=" CA ASN C 723 " pdb=" C ASN C 723 " ideal model delta sigma weight residual 1.523 1.483 0.041 1.80e-02 3.09e+03 5.07e+00 bond pdb=" CA ASN E 723 " pdb=" C ASN E 723 " ideal model delta sigma weight residual 1.523 1.483 0.041 1.80e-02 3.09e+03 5.07e+00 bond pdb=" CA ASN A 723 " pdb=" C ASN A 723 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.80e-02 3.09e+03 5.04e+00 bond pdb=" CB ASN A 387 " pdb=" CG ASN A 387 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.35e+00 bond pdb=" CB ASN E 387 " pdb=" CG ASN E 387 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.32e+00 ... (remaining 17425 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.68: 241 105.68 - 112.75: 9492 112.75 - 119.82: 5558 119.82 - 126.89: 8079 126.89 - 133.96: 105 Bond angle restraints: 23475 Sorted by residual: angle pdb=" N SER D 127 " pdb=" CA SER D 127 " pdb=" C SER D 127 " ideal model delta sigma weight residual 107.73 114.15 -6.42 1.34e+00 5.57e-01 2.30e+01 angle pdb=" N SER B 127 " pdb=" CA SER B 127 " pdb=" C SER B 127 " ideal model delta sigma weight residual 107.73 114.15 -6.42 1.34e+00 5.57e-01 2.29e+01 angle pdb=" N SER F 127 " pdb=" CA SER F 127 " pdb=" C SER F 127 " ideal model delta sigma weight residual 107.73 114.12 -6.39 1.34e+00 5.57e-01 2.27e+01 angle pdb=" N SER E 558 " pdb=" CA SER E 558 " pdb=" C SER E 558 " ideal model delta sigma weight residual 110.24 116.06 -5.82 1.30e+00 5.92e-01 2.00e+01 angle pdb=" N SER A 558 " pdb=" CA SER A 558 " pdb=" C SER A 558 " ideal model delta sigma weight residual 110.24 116.05 -5.81 1.30e+00 5.92e-01 2.00e+01 ... (remaining 23470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 10194 14.80 - 29.61: 533 29.61 - 44.41: 54 44.41 - 59.22: 1 59.22 - 74.02: 3 Dihedral angle restraints: 10785 sinusoidal: 4404 harmonic: 6381 Sorted by residual: dihedral pdb=" CA ASN C 218 " pdb=" C ASN C 218 " pdb=" N PRO C 219 " pdb=" CA PRO C 219 " ideal model delta harmonic sigma weight residual -180.00 -141.75 -38.25 0 5.00e+00 4.00e-02 5.85e+01 dihedral pdb=" CA ASN E 218 " pdb=" C ASN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA ASN A 218 " pdb=" C ASN A 218 " pdb=" N PRO A 219 " pdb=" CA PRO A 219 " ideal model delta harmonic sigma weight residual -180.00 -141.81 -38.19 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 10782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1618 0.051 - 0.101: 738 0.101 - 0.152: 288 0.152 - 0.203: 42 0.203 - 0.254: 11 Chirality restraints: 2697 Sorted by residual: chirality pdb=" CB ILE A 455 " pdb=" CA ILE A 455 " pdb=" CG1 ILE A 455 " pdb=" CG2 ILE A 455 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 455 " pdb=" CA ILE C 455 " pdb=" CG1 ILE C 455 " pdb=" CG2 ILE C 455 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE E 455 " pdb=" CA ILE E 455 " pdb=" CG1 ILE E 455 " pdb=" CG2 ILE E 455 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2694 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 673 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C GLN A 673 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 673 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 674 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 673 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C GLN E 673 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN E 673 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU E 674 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 673 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C GLN C 673 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN C 673 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU C 674 " 0.016 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3013 2.76 - 3.30: 14065 3.30 - 3.83: 25765 3.83 - 4.37: 29322 4.37 - 4.90: 52128 Nonbonded interactions: 124293 Sorted by model distance: nonbonded pdb=" O TYR C 505 " pdb=" OG SER C 686 " model vdw 2.228 2.440 nonbonded pdb=" O TYR A 505 " pdb=" OG SER A 686 " model vdw 2.229 2.440 nonbonded pdb=" O TYR E 505 " pdb=" OG SER E 686 " model vdw 2.229 2.440 nonbonded pdb=" OG SER C 773 " pdb=" OE1 GLN E 783 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR B 72 " pdb=" OG SER B 75 " model vdw 2.283 2.440 ... (remaining 124288 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.150 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: 0.020 Extract box with map and model: 9.440 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 41.960 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.008 0.076 17430 Z= 0.555 Angle : 1.081 10.046 23475 Z= 0.597 Chirality : 0.064 0.254 2697 Planarity : 0.005 0.048 3012 Dihedral : 9.089 74.022 6603 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 5.88 % Twisted General : 0.72 % 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: -4.33 (0.15), residues: 2112 helix: -4.47 (0.17), residues: 150 sheet: -1.84 (0.19), residues: 705 loop : -3.45 (0.14), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 334 HIS 0.013 0.003 HIS F 6 PHE 0.024 0.004 PHE E 293 TYR 0.029 0.003 TYR A 712 ARG 0.008 0.001 ARG E 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.8844 (m-30) cc_final: 0.8485 (m-30) REVERT: A 488 LEU cc_start: 0.7856 (mt) cc_final: 0.7588 (pp) REVERT: A 506 ILE cc_start: 0.8994 (mt) cc_final: 0.8682 (tt) REVERT: A 639 ASN cc_start: 0.8231 (t0) cc_final: 0.7775 (p0) REVERT: A 689 ASP cc_start: 0.7944 (m-30) cc_final: 0.7717 (t0) REVERT: A 733 ASP cc_start: 0.8323 (m-30) cc_final: 0.7996 (m-30) REVERT: C 225 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7449 (mt-10) REVERT: C 326 PHE cc_start: 0.8423 (m-80) cc_final: 0.7581 (m-10) REVERT: C 390 ASP cc_start: 0.8998 (m-30) cc_final: 0.8666 (m-30) REVERT: C 488 LEU cc_start: 0.8496 (mt) cc_final: 0.8219 (pp) REVERT: C 506 ILE cc_start: 0.9016 (mt) cc_final: 0.8715 (tt) REVERT: C 689 ASP cc_start: 0.7913 (m-30) cc_final: 0.7599 (t0) REVERT: C 792 LEU cc_start: 0.9124 (mt) cc_final: 0.8740 (tt) REVERT: E 390 ASP cc_start: 0.8786 (m-30) cc_final: 0.8324 (m-30) REVERT: E 488 LEU cc_start: 0.8892 (mt) cc_final: 0.8587 (pp) REVERT: E 506 ILE cc_start: 0.8963 (mt) cc_final: 0.8571 (tt) REVERT: E 527 SER cc_start: 0.9140 (m) cc_final: 0.8666 (p) REVERT: E 536 THR cc_start: 0.8085 (p) cc_final: 0.7847 (p) REVERT: E 544 ASP cc_start: 0.7608 (m-30) cc_final: 0.7408 (t70) REVERT: E 545 ASN cc_start: 0.7035 (m-40) cc_final: 0.6405 (t0) REVERT: E 751 ILE cc_start: 0.8664 (mt) cc_final: 0.8247 (mm) REVERT: E 792 LEU cc_start: 0.9147 (mt) cc_final: 0.8732 (tt) REVERT: B 52 ILE cc_start: 0.9485 (mt) cc_final: 0.9034 (mm) REVERT: F 26 CYS cc_start: 0.8428 (m) cc_final: 0.8042 (p) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.3010 time to fit residues: 205.7297 Evaluate side-chains 226 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 452 GLN A 499 ASN A 753 ASN C 192 ASN C 753 ASN C 796 ASN ** E 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 HIS E 265 GLN E 545 ASN E 548 ASN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 753 ASN E 796 ASN B 99 ASN B 118 GLN D 118 GLN F 90 ASN F 118 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17430 Z= 0.221 Angle : 0.668 7.707 23475 Z= 0.358 Chirality : 0.051 0.166 2697 Planarity : 0.003 0.045 3012 Dihedral : 7.312 30.851 2241 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 0.15 % Allowed : 2.03 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.16), residues: 2112 helix: -3.38 (0.27), residues: 162 sheet: -1.65 (0.20), residues: 672 loop : -3.26 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 236 HIS 0.004 0.001 HIS E 211 PHE 0.014 0.001 PHE A 362 TYR 0.013 0.001 TYR C 620 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 315 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 VAL cc_start: 0.9369 (t) cc_final: 0.9041 (p) REVERT: A 228 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6052 (mt-10) REVERT: A 390 ASP cc_start: 0.9113 (m-30) cc_final: 0.8865 (m-30) REVERT: A 506 ILE cc_start: 0.9084 (mt) cc_final: 0.8787 (tt) REVERT: A 567 LEU cc_start: 0.9064 (mt) cc_final: 0.8681 (mt) REVERT: A 778 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7864 (mp0) REVERT: C 326 PHE cc_start: 0.8158 (m-80) cc_final: 0.7537 (m-10) REVERT: C 431 VAL cc_start: 0.7625 (t) cc_final: 0.7379 (p) REVERT: C 506 ILE cc_start: 0.9064 (mt) cc_final: 0.8785 (tt) REVERT: C 656 TYR cc_start: 0.8992 (p90) cc_final: 0.8783 (p90) REVERT: C 689 ASP cc_start: 0.7950 (m-30) cc_final: 0.7678 (t0) REVERT: C 778 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8211 (mp0) REVERT: C 792 LEU cc_start: 0.9059 (mt) cc_final: 0.8683 (tt) REVERT: E 330 LEU cc_start: 0.9282 (tp) cc_final: 0.9064 (tp) REVERT: E 454 LEU cc_start: 0.9152 (tp) cc_final: 0.8883 (tp) REVERT: E 506 ILE cc_start: 0.8929 (mt) cc_final: 0.8603 (tt) REVERT: E 527 SER cc_start: 0.8922 (m) cc_final: 0.8451 (t) REVERT: E 544 ASP cc_start: 0.7628 (m-30) cc_final: 0.7343 (t70) REVERT: E 545 ASN cc_start: 0.6950 (m110) cc_final: 0.6694 (t0) REVERT: E 751 ILE cc_start: 0.8728 (mt) cc_final: 0.8308 (mm) REVERT: B 83 LYS cc_start: 0.7938 (mttt) cc_final: 0.7701 (tttt) REVERT: D 52 ILE cc_start: 0.9388 (mt) cc_final: 0.9117 (mm) REVERT: F 121 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7205 (mm-40) outliers start: 3 outliers final: 1 residues processed: 317 average time/residue: 0.2715 time to fit residues: 134.1024 Evaluate side-chains 189 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 0.0670 chunk 131 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 507 GLN C 265 GLN E 192 ASN E 548 ASN E 685 ASN D 55 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17430 Z= 0.188 Angle : 0.620 7.519 23475 Z= 0.329 Chirality : 0.050 0.197 2697 Planarity : 0.003 0.057 3012 Dihedral : 6.550 28.078 2241 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 0.15 % Allowed : 2.03 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.16), residues: 2112 helix: -2.79 (0.31), residues: 162 sheet: -1.37 (0.20), residues: 678 loop : -3.02 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 236 HIS 0.003 0.001 HIS F 6 PHE 0.010 0.001 PHE A 362 TYR 0.010 0.001 TYR E 712 ARG 0.004 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.9090 (m-30) cc_final: 0.8877 (m-30) REVERT: A 700 MET cc_start: 0.8129 (mtm) cc_final: 0.7850 (mtp) REVERT: A 779 MET cc_start: 0.8811 (tpp) cc_final: 0.8429 (ttt) REVERT: C 436 ASP cc_start: 0.6926 (t0) cc_final: 0.6718 (t0) REVERT: C 506 ILE cc_start: 0.9076 (mt) cc_final: 0.8794 (tt) REVERT: C 778 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8097 (mp0) REVERT: C 792 LEU cc_start: 0.9085 (mt) cc_final: 0.8720 (tt) REVERT: E 226 VAL cc_start: 0.9398 (t) cc_final: 0.9002 (p) REVERT: E 252 PHE cc_start: 0.7913 (m-80) cc_final: 0.7589 (m-10) REVERT: E 454 LEU cc_start: 0.9221 (tp) cc_final: 0.8962 (tp) REVERT: E 506 ILE cc_start: 0.8832 (mt) cc_final: 0.8514 (tt) REVERT: E 527 SER cc_start: 0.8911 (m) cc_final: 0.8461 (t) REVERT: E 544 ASP cc_start: 0.7759 (m-30) cc_final: 0.7375 (t70) REVERT: E 779 MET cc_start: 0.8791 (mtp) cc_final: 0.8409 (ttt) REVERT: B 83 LYS cc_start: 0.7879 (mttt) cc_final: 0.7639 (tttt) REVERT: D 29 LYS cc_start: 0.8882 (mttt) cc_final: 0.8369 (mptt) REVERT: D 52 ILE cc_start: 0.9411 (mt) cc_final: 0.9110 (mm) REVERT: D 70 LEU cc_start: 0.9438 (mp) cc_final: 0.9223 (mp) REVERT: F 26 CYS cc_start: 0.7979 (m) cc_final: 0.7744 (p) outliers start: 3 outliers final: 1 residues processed: 278 average time/residue: 0.2567 time to fit residues: 114.5132 Evaluate side-chains 173 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 194 optimal weight: 3.9990 chunk 205 optimal weight: 0.0470 chunk 101 optimal weight: 0.0070 chunk 184 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN C 563 GLN E 211 HIS E 452 GLN E 685 ASN D 51 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17430 Z= 0.146 Angle : 0.578 7.006 23475 Z= 0.307 Chirality : 0.049 0.185 2697 Planarity : 0.003 0.045 3012 Dihedral : 6.031 27.014 2241 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 0.05 % Allowed : 1.37 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.17), residues: 2112 helix: -2.52 (0.34), residues: 144 sheet: -1.17 (0.20), residues: 702 loop : -2.86 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 236 HIS 0.004 0.001 HIS E 211 PHE 0.009 0.001 PHE E 270 TYR 0.010 0.001 TYR A 692 ARG 0.006 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 390 ASP cc_start: 0.9063 (m-30) cc_final: 0.8846 (m-30) REVERT: A 440 LYS cc_start: 0.7268 (mptt) cc_final: 0.6859 (tttp) REVERT: A 529 ASN cc_start: 0.8860 (t0) cc_final: 0.8335 (m-40) REVERT: A 700 MET cc_start: 0.8225 (mtm) cc_final: 0.7933 (mtp) REVERT: E 252 PHE cc_start: 0.7807 (m-80) cc_final: 0.7591 (m-80) REVERT: E 330 LEU cc_start: 0.9255 (tp) cc_final: 0.9028 (tp) REVERT: E 454 LEU cc_start: 0.9229 (tp) cc_final: 0.8953 (tp) REVERT: E 473 THR cc_start: 0.7584 (p) cc_final: 0.7016 (p) REVERT: E 506 ILE cc_start: 0.8715 (mt) cc_final: 0.8468 (tt) REVERT: E 778 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8030 (mp0) REVERT: E 779 MET cc_start: 0.8513 (mtp) cc_final: 0.8283 (ttt) REVERT: B 29 LYS cc_start: 0.8846 (mttt) cc_final: 0.8430 (mptt) REVERT: D 29 LYS cc_start: 0.8781 (mttt) cc_final: 0.8281 (mptt) REVERT: D 69 LEU cc_start: 0.9024 (mt) cc_final: 0.8620 (mt) REVERT: F 54 GLU cc_start: 0.7725 (mp0) cc_final: 0.7506 (mp0) outliers start: 1 outliers final: 1 residues processed: 264 average time/residue: 0.2548 time to fit residues: 107.1581 Evaluate side-chains 174 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 84 optimal weight: 0.0870 chunk 175 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 796 ASN C 563 GLN E 370 ASN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 90 ASN F 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17430 Z= 0.335 Angle : 0.679 7.612 23475 Z= 0.359 Chirality : 0.051 0.223 2697 Planarity : 0.003 0.055 3012 Dihedral : 6.513 28.012 2241 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.17), residues: 2112 helix: -2.25 (0.35), residues: 156 sheet: -1.22 (0.20), residues: 744 loop : -2.93 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 236 HIS 0.004 0.001 HIS F 6 PHE 0.018 0.002 PHE A 362 TYR 0.020 0.001 TYR A 656 ARG 0.005 0.001 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 ASP cc_start: 0.7947 (t0) cc_final: 0.7512 (t0) REVERT: A 527 SER cc_start: 0.9180 (m) cc_final: 0.8731 (t) REVERT: C 792 LEU cc_start: 0.8874 (mt) cc_final: 0.8470 (tt) REVERT: E 330 LEU cc_start: 0.9402 (tp) cc_final: 0.9130 (tp) REVERT: E 390 ASP cc_start: 0.9090 (m-30) cc_final: 0.8883 (m-30) REVERT: E 454 LEU cc_start: 0.9271 (tp) cc_final: 0.8992 (tp) REVERT: E 506 ILE cc_start: 0.8931 (mt) cc_final: 0.8580 (tt) REVERT: E 527 SER cc_start: 0.9209 (m) cc_final: 0.8670 (t) REVERT: B 90 ASN cc_start: 0.8466 (m110) cc_final: 0.8262 (m110) REVERT: D 29 LYS cc_start: 0.8827 (mttt) cc_final: 0.8247 (mptt) REVERT: D 67 GLU cc_start: 0.7719 (tt0) cc_final: 0.7450 (tt0) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2592 time to fit residues: 93.8870 Evaluate side-chains 148 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN C 563 GLN E 211 HIS E 452 GLN E 796 ASN D 51 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17430 Z= 0.184 Angle : 0.587 7.333 23475 Z= 0.312 Chirality : 0.049 0.204 2697 Planarity : 0.003 0.046 3012 Dihedral : 6.017 27.195 2241 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 0.05 % Allowed : 1.58 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.17), residues: 2112 helix: -1.92 (0.36), residues: 156 sheet: -1.12 (0.21), residues: 681 loop : -2.76 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 236 HIS 0.005 0.001 HIS E 211 PHE 0.016 0.001 PHE A 362 TYR 0.014 0.001 TYR A 656 ARG 0.004 0.000 ARG C 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7804 (t70) cc_final: 0.7471 (t70) REVERT: A 349 ASP cc_start: 0.8416 (p0) cc_final: 0.7849 (p0) REVERT: A 350 ASP cc_start: 0.8275 (m-30) cc_final: 0.8045 (m-30) REVERT: A 438 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6953 (ptmt) REVERT: A 440 LYS cc_start: 0.7549 (mptt) cc_final: 0.6896 (tttp) REVERT: A 527 SER cc_start: 0.9105 (m) cc_final: 0.8622 (t) REVERT: A 563 GLN cc_start: 0.8519 (mt0) cc_final: 0.7750 (mm-40) REVERT: C 567 LEU cc_start: 0.9279 (mt) cc_final: 0.8494 (mt) REVERT: C 792 LEU cc_start: 0.8894 (mt) cc_final: 0.8543 (tt) REVERT: E 225 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7626 (mt-10) REVERT: E 226 VAL cc_start: 0.9467 (t) cc_final: 0.9256 (p) REVERT: E 330 LEU cc_start: 0.9353 (tp) cc_final: 0.9099 (tp) REVERT: E 454 LEU cc_start: 0.9286 (tp) cc_final: 0.9001 (tp) REVERT: E 506 ILE cc_start: 0.8741 (mt) cc_final: 0.8297 (tt) REVERT: E 527 SER cc_start: 0.9156 (m) cc_final: 0.8664 (t) REVERT: E 779 MET cc_start: 0.8451 (mtp) cc_final: 0.8096 (ttt) REVERT: B 9 ASN cc_start: 0.9157 (m-40) cc_final: 0.8908 (t0) REVERT: B 29 LYS cc_start: 0.8929 (mttt) cc_final: 0.8453 (mptt) REVERT: D 29 LYS cc_start: 0.8741 (mttt) cc_final: 0.8229 (mptt) REVERT: F 41 THR cc_start: 0.9132 (t) cc_final: 0.8897 (m) outliers start: 1 outliers final: 1 residues processed: 217 average time/residue: 0.2801 time to fit residues: 98.4807 Evaluate side-chains 157 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 611 ASN C 303 ASN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 545 ASN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 17430 Z= 0.383 Angle : 0.725 7.766 23475 Z= 0.382 Chirality : 0.052 0.201 2697 Planarity : 0.004 0.057 3012 Dihedral : 6.750 28.494 2241 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.17), residues: 2112 helix: -1.95 (0.37), residues: 156 sheet: -1.33 (0.21), residues: 615 loop : -2.85 (0.15), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 236 HIS 0.004 0.001 HIS E 301 PHE 0.021 0.002 PHE A 449 TYR 0.017 0.002 TYR A 656 ARG 0.004 0.001 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8583 (p0) cc_final: 0.8022 (p0) REVERT: A 527 SER cc_start: 0.9327 (m) cc_final: 0.8709 (p) REVERT: C 792 LEU cc_start: 0.8811 (mt) cc_final: 0.8571 (tt) REVERT: E 225 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 330 LEU cc_start: 0.9440 (tp) cc_final: 0.9229 (tp) REVERT: E 506 ILE cc_start: 0.8843 (mt) cc_final: 0.8427 (tt) REVERT: E 683 ILE cc_start: 0.9399 (mm) cc_final: 0.9157 (mm) REVERT: B 67 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8432 (tm-30) REVERT: D 29 LYS cc_start: 0.8856 (mttt) cc_final: 0.8249 (mptt) REVERT: F 67 GLU cc_start: 0.7853 (tt0) cc_final: 0.7643 (tt0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2543 time to fit residues: 77.5696 Evaluate side-chains 124 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 325 GLN A 452 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN C 563 GLN E 211 HIS E 452 GLN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17430 Z= 0.194 Angle : 0.607 6.588 23475 Z= 0.321 Chirality : 0.049 0.194 2697 Planarity : 0.003 0.050 3012 Dihedral : 6.105 27.642 2241 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.10 % Allowed : 0.51 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.17), residues: 2112 helix: -1.69 (0.38), residues: 156 sheet: -1.28 (0.21), residues: 636 loop : -2.72 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 236 HIS 0.008 0.001 HIS A 211 PHE 0.015 0.001 PHE A 449 TYR 0.016 0.001 TYR A 656 ARG 0.002 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8598 (p0) cc_final: 0.8008 (p0) REVERT: A 350 ASP cc_start: 0.8235 (m-30) cc_final: 0.8008 (m-30) REVERT: A 779 MET cc_start: 0.8510 (ttt) cc_final: 0.8230 (ttt) REVERT: C 749 GLU cc_start: 0.8661 (tp30) cc_final: 0.8430 (tt0) REVERT: E 506 ILE cc_start: 0.8720 (mt) cc_final: 0.8279 (tt) REVERT: E 683 ILE cc_start: 0.9342 (mm) cc_final: 0.9098 (mm) REVERT: B 9 ASN cc_start: 0.9133 (m-40) cc_final: 0.8767 (t0) REVERT: B 29 LYS cc_start: 0.8886 (mttt) cc_final: 0.8451 (mptt) REVERT: D 29 LYS cc_start: 0.8782 (mttt) cc_final: 0.8271 (mptt) REVERT: F 41 THR cc_start: 0.9203 (t) cc_final: 0.8994 (m) REVERT: F 67 GLU cc_start: 0.7825 (tt0) cc_final: 0.7609 (tt0) outliers start: 2 outliers final: 2 residues processed: 196 average time/residue: 0.2509 time to fit residues: 80.0073 Evaluate side-chains 139 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 179 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 452 GLN C 211 HIS ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN E 563 GLN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17430 Z= 0.240 Angle : 0.622 7.063 23475 Z= 0.329 Chirality : 0.049 0.194 2697 Planarity : 0.003 0.056 3012 Dihedral : 6.081 27.438 2241 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.17), residues: 2112 helix: -1.68 (0.38), residues: 156 sheet: -1.14 (0.20), residues: 678 loop : -2.76 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 236 HIS 0.007 0.001 HIS C 211 PHE 0.014 0.001 PHE A 362 TYR 0.017 0.001 TYR A 656 ARG 0.003 0.000 ARG E 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 567 LEU cc_start: 0.9270 (tp) cc_final: 0.9022 (tt) REVERT: C 749 GLU cc_start: 0.8672 (tp30) cc_final: 0.8446 (tt0) REVERT: E 330 LEU cc_start: 0.9400 (tp) cc_final: 0.9154 (tp) REVERT: E 506 ILE cc_start: 0.8739 (mt) cc_final: 0.8276 (tt) REVERT: E 683 ILE cc_start: 0.9367 (mm) cc_final: 0.9131 (mm) REVERT: B 9 ASN cc_start: 0.9046 (m-40) cc_final: 0.8587 (t0) REVERT: B 29 LYS cc_start: 0.8889 (mttt) cc_final: 0.8427 (mptt) REVERT: B 90 ASN cc_start: 0.8518 (m110) cc_final: 0.8304 (m110) REVERT: D 29 LYS cc_start: 0.8779 (mttt) cc_final: 0.8236 (mptt) REVERT: F 29 LYS cc_start: 0.8837 (mttt) cc_final: 0.8455 (mptt) REVERT: F 41 THR cc_start: 0.9217 (t) cc_final: 0.9004 (m) outliers start: 1 outliers final: 1 residues processed: 191 average time/residue: 0.2521 time to fit residues: 78.1433 Evaluate side-chains 133 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN E 211 HIS E 432 ASN E 452 GLN ** E 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17430 Z= 0.274 Angle : 0.645 6.907 23475 Z= 0.341 Chirality : 0.050 0.184 2697 Planarity : 0.003 0.054 3012 Dihedral : 6.236 27.719 2241 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.17), residues: 2112 helix: -1.68 (0.38), residues: 156 sheet: -1.13 (0.20), residues: 678 loop : -2.77 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 236 HIS 0.008 0.001 HIS E 211 PHE 0.017 0.001 PHE E 326 TYR 0.018 0.001 TYR A 656 ARG 0.003 0.001 ARG A 478 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 749 GLU cc_start: 0.8681 (tp30) cc_final: 0.8446 (tt0) REVERT: E 330 LEU cc_start: 0.9449 (tp) cc_final: 0.9182 (tp) REVERT: E 506 ILE cc_start: 0.8754 (mt) cc_final: 0.8291 (tt) REVERT: E 683 ILE cc_start: 0.9403 (mm) cc_final: 0.9167 (mm) REVERT: B 9 ASN cc_start: 0.9046 (m-40) cc_final: 0.8546 (t0) REVERT: B 29 LYS cc_start: 0.8926 (mttt) cc_final: 0.8470 (mptt) REVERT: D 29 LYS cc_start: 0.8774 (mttt) cc_final: 0.8258 (mptt) REVERT: F 29 LYS cc_start: 0.8843 (mttt) cc_final: 0.8470 (mptt) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.2615 time to fit residues: 75.3021 Evaluate side-chains 129 residues out of total 2019 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 452 GLN C 211 HIS ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080243 restraints weight = 31585.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081112 restraints weight = 23960.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081473 restraints weight = 18389.381| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17430 Z= 0.219 Angle : 0.614 6.848 23475 Z= 0.325 Chirality : 0.049 0.275 2697 Planarity : 0.003 0.052 3012 Dihedral : 5.971 27.605 2241 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.01 % 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: -2.96 (0.18), residues: 2112 helix: -1.57 (0.39), residues: 156 sheet: -1.07 (0.20), residues: 708 loop : -2.69 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 236 HIS 0.010 0.001 HIS A 211 PHE 0.015 0.001 PHE E 326 TYR 0.018 0.001 TYR A 656 ARG 0.003 0.000 ARG E 564 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3319.75 seconds wall clock time: 62 minutes 15.74 seconds (3735.74 seconds total)