Starting phenix.real_space_refine (version: dev) on Thu Dec 15 22:23:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/12_2022/6jpq_9870.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/12_2022/6jpq_9870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/12_2022/6jpq_9870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/12_2022/6jpq_9870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/12_2022/6jpq_9870.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/12_2022/6jpq_9870.pdb" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.034 sd= 0.576 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 764": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 351": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 761": "NH1" <-> "NH2" Residue "C ARG 764": "NH1" <-> "NH2" Residue "D ARG 294": "NH1" <-> "NH2" Residue "D ARG 351": "NH1" <-> "NH2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D ARG 425": "NH1" <-> "NH2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 761": "NH1" <-> "NH2" Residue "D ARG 764": "NH1" <-> "NH2" Residue "E ARG 294": "NH1" <-> "NH2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E ARG 354": "NH1" <-> "NH2" Residue "E ARG 425": "NH1" <-> "NH2" Residue "E ARG 426": "NH1" <-> "NH2" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E ARG 504": "NH1" <-> "NH2" Residue "E ARG 591": "NH1" <-> "NH2" Residue "E ARG 761": "NH1" <-> "NH2" Residue "E ARG 764": "NH1" <-> "NH2" Residue "F ARG 294": "NH1" <-> "NH2" Residue "F ARG 351": "NH1" <-> "NH2" Residue "F ARG 354": "NH1" <-> "NH2" Residue "F ARG 425": "NH1" <-> "NH2" Residue "F ARG 426": "NH1" <-> "NH2" Residue "F TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 761": "NH1" <-> "NH2" Residue "F ARG 764": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 27768 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "B" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "C" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "D" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "E" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Chain: "F" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4628 Classifications: {'peptide': 577} Link IDs: {'CIS': 2, 'PTRANS': 42, 'TRANS': 532} Chain breaks: 1 Time building chain proxies: 15.30, per 1000 atoms: 0.55 Number of scatterers: 27768 At special positions: 0 Unit cell: (116.58, 162.14, 152.76, 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 132 16.00 O 5124 8.00 N 4734 7.00 C 17778 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: 12.07 Conformation dependent library (CDL) restraints added in 4.7 seconds 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6624 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 18 sheets defined 48.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 313 through 328 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.128A pdb=" N VAL A 392 " --> pdb=" O HIS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 465 through 471 Processing helix chain 'A' and resid 475 through 495 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.775A pdb=" N PHE A 519 " --> pdb=" O LYS A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.996A pdb=" N SER A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU A 551 " --> pdb=" O PRO A 547 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 577 Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.655A pdb=" N LEU A 592 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 635 through 640 Processing helix chain 'A' and resid 646 through 660 Processing helix chain 'A' and resid 679 through 692 removed outlier: 3.674A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 743 through 748 Processing helix chain 'A' and resid 1130 through 1139 Processing helix chain 'A' and resid 1146 through 1164 Processing helix chain 'A' and resid 1174 through 1185 Processing helix chain 'B' and resid 271 through 283 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 386 through 400 removed outlier: 4.128A pdb=" N VAL B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 475 through 495 Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.775A pdb=" N PHE B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.997A pdb=" N SER B 533 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU B 551 " --> pdb=" O PRO B 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 Processing helix chain 'B' and resid 585 through 595 removed outlier: 3.654A pdb=" N LEU B 592 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 635 through 640 Processing helix chain 'B' and resid 646 through 660 Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 1130 through 1139 Processing helix chain 'B' and resid 1146 through 1164 Processing helix chain 'B' and resid 1174 through 1185 Processing helix chain 'C' and resid 271 through 283 Processing helix chain 'C' and resid 283 through 288 Processing helix chain 'C' and resid 290 through 295 Processing helix chain 'C' and resid 313 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 372 through 377 Processing helix chain 'C' and resid 386 through 400 removed outlier: 4.129A pdb=" N VAL C 392 " --> pdb=" O HIS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 475 through 495 Processing helix chain 'C' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.996A pdb=" N SER C 533 " --> pdb=" O SER C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU C 551 " --> pdb=" O PRO C 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP C 555 " --> pdb=" O GLU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 577 Processing helix chain 'C' and resid 585 through 595 removed outlier: 3.655A pdb=" N LEU C 592 " --> pdb=" O TYR C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 625 Processing helix chain 'C' and resid 635 through 640 Processing helix chain 'C' and resid 646 through 660 Processing helix chain 'C' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 720 Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 743 through 748 Processing helix chain 'C' and resid 1130 through 1139 Processing helix chain 'C' and resid 1146 through 1164 Processing helix chain 'C' and resid 1174 through 1185 Processing helix chain 'D' and resid 271 through 283 Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 290 through 295 Processing helix chain 'D' and resid 313 through 328 Processing helix chain 'D' and resid 348 through 363 Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 386 through 400 removed outlier: 4.129A pdb=" N VAL D 392 " --> pdb=" O HIS D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 453 Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 475 through 495 Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.996A pdb=" N SER D 533 " --> pdb=" O SER D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU D 551 " --> pdb=" O PRO D 547 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP D 555 " --> pdb=" O GLU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 577 Processing helix chain 'D' and resid 585 through 595 removed outlier: 3.654A pdb=" N LEU D 592 " --> pdb=" O TYR D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 625 Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 646 through 660 Processing helix chain 'D' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 720 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 1130 through 1139 Processing helix chain 'D' and resid 1146 through 1164 Processing helix chain 'D' and resid 1174 through 1185 Processing helix chain 'E' and resid 271 through 283 Processing helix chain 'E' and resid 283 through 288 Processing helix chain 'E' and resid 290 through 295 Processing helix chain 'E' and resid 313 through 328 Processing helix chain 'E' and resid 348 through 363 Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 386 through 400 removed outlier: 4.129A pdb=" N VAL E 392 " --> pdb=" O HIS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 465 through 471 Processing helix chain 'E' and resid 475 through 495 Processing helix chain 'E' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE E 519 " --> pdb=" O LYS E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.995A pdb=" N SER E 533 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 564 removed outlier: 5.831A pdb=" N GLU E 551 " --> pdb=" O PRO E 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP E 555 " --> pdb=" O GLU E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 Processing helix chain 'E' and resid 585 through 595 removed outlier: 3.653A pdb=" N LEU E 592 " --> pdb=" O TYR E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 625 Processing helix chain 'E' and resid 635 through 640 Processing helix chain 'E' and resid 646 through 660 Processing helix chain 'E' and resid 679 through 692 removed outlier: 3.673A pdb=" N GLU E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 720 Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 743 through 748 Processing helix chain 'E' and resid 1130 through 1139 Processing helix chain 'E' and resid 1146 through 1164 Processing helix chain 'E' and resid 1174 through 1185 Processing helix chain 'F' and resid 271 through 283 Processing helix chain 'F' and resid 283 through 288 Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 313 through 328 Processing helix chain 'F' and resid 348 through 363 Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'F' and resid 386 through 400 removed outlier: 4.128A pdb=" N VAL F 392 " --> pdb=" O HIS F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 453 Processing helix chain 'F' and resid 465 through 471 Processing helix chain 'F' and resid 475 through 495 Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.774A pdb=" N PHE F 519 " --> pdb=" O LYS F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 533 removed outlier: 3.995A pdb=" N SER F 533 " --> pdb=" O SER F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 564 removed outlier: 5.832A pdb=" N GLU F 551 " --> pdb=" O PRO F 547 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP F 555 " --> pdb=" O GLU F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 577 Processing helix chain 'F' and resid 585 through 595 removed outlier: 3.654A pdb=" N LEU F 592 " --> pdb=" O TYR F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'F' and resid 635 through 640 Processing helix chain 'F' and resid 646 through 660 Processing helix chain 'F' and resid 679 through 692 removed outlier: 3.674A pdb=" N GLU F 691 " --> pdb=" O SER F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 720 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 743 through 748 Processing helix chain 'F' and resid 1130 through 1139 Processing helix chain 'F' and resid 1146 through 1164 Processing helix chain 'F' and resid 1174 through 1185 Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER A 332 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE A 369 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 334 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP A 371 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG A 336 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER A 366 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE A 411 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 368 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA A 413 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE A 370 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A 303 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.542A pdb=" N LYS B 762 " --> pdb=" O ASP A 579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER A 664 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 702 " --> pdb=" O SER A 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 666 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 704 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 668 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 762 through 763 removed outlier: 3.663A pdb=" N LYS A 762 " --> pdb=" O ASP F 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 332 through 337 removed outlier: 6.797A pdb=" N SER B 332 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE B 369 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR B 334 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ASP B 371 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG B 336 " --> pdb=" O ASP B 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER B 366 " --> pdb=" O ILE B 409 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ILE B 411 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 368 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA B 413 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE B 370 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL B 303 " --> pdb=" O GLY B 412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 579 removed outlier: 3.604A pdb=" N LYS C 762 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER B 664 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU B 702 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 666 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU B 704 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 668 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER C 332 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE C 369 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 334 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP C 371 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG C 336 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER C 366 " --> pdb=" O ILE C 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE C 411 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 368 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA C 413 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE C 370 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL C 303 " --> pdb=" O GLY C 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 578 through 579 Processing sheet with id=AB1, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER C 664 " --> pdb=" O LEU C 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU C 702 " --> pdb=" O SER C 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 666 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU C 704 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 668 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER D 332 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE D 369 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR D 334 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP D 371 " --> pdb=" O TYR D 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG D 336 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER D 366 " --> pdb=" O ILE D 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE D 411 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 368 " --> pdb=" O ILE D 411 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA D 413 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE D 370 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL D 303 " --> pdb=" O GLY D 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 578 through 579 removed outlier: 3.511A pdb=" N LYS E 762 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 630 through 633 removed outlier: 6.983A pdb=" N SER D 664 " --> pdb=" O LEU D 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU D 702 " --> pdb=" O SER D 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 666 " --> pdb=" O LEU D 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU D 704 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE D 668 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 332 through 337 removed outlier: 6.796A pdb=" N SER E 332 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE E 369 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR E 334 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP E 371 " --> pdb=" O TYR E 334 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG E 336 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N SER E 366 " --> pdb=" O ILE E 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE E 411 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE E 368 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA E 413 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE E 370 " --> pdb=" O ALA E 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL E 303 " --> pdb=" O GLY E 412 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 578 through 579 removed outlier: 3.659A pdb=" N LYS F 762 " --> pdb=" O ASP E 579 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.984A pdb=" N SER E 664 " --> pdb=" O LEU E 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU E 702 " --> pdb=" O SER E 664 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 666 " --> pdb=" O LEU E 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU E 704 " --> pdb=" O ILE E 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE E 668 " --> pdb=" O LEU E 704 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 332 through 337 removed outlier: 6.795A pdb=" N SER F 332 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE F 369 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR F 334 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASP F 371 " --> pdb=" O TYR F 334 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG F 336 " --> pdb=" O ASP F 371 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N SER F 366 " --> pdb=" O ILE F 409 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE F 411 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE F 368 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA F 413 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE F 370 " --> pdb=" O ALA F 413 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL F 303 " --> pdb=" O GLY F 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 630 through 633 removed outlier: 6.983A pdb=" N SER F 664 " --> pdb=" O LEU F 700 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU F 702 " --> pdb=" O SER F 664 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 666 " --> pdb=" O LEU F 702 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU F 704 " --> pdb=" O ILE F 666 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE F 668 " --> pdb=" O LEU F 704 " (cutoff:3.500A) 1115 hydrogen bonds defined for protein. 3306 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: 9.40 Time building geometry restraints manager: 13.00 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: 8895 1.34 - 1.46: 5310 1.46 - 1.57: 13971 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 28404 Sorted by residual: bond pdb=" C LEU A 284 " pdb=" N PRO A 285 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.19e-02 7.06e+03 6.68e+00 bond pdb=" C LEU E 284 " pdb=" N PRO E 285 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.19e-02 7.06e+03 6.65e+00 bond pdb=" C LEU C 284 " pdb=" N PRO C 285 " ideal model delta sigma weight residual 1.335 1.365 -0.031 1.19e-02 7.06e+03 6.61e+00 bond pdb=" C LEU F 284 " pdb=" N PRO F 285 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.19e-02 7.06e+03 6.56e+00 bond pdb=" C LEU D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.19e-02 7.06e+03 6.46e+00 ... (remaining 28399 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.16: 1025 106.16 - 113.13: 15314 113.13 - 120.11: 10529 120.11 - 127.08: 11243 127.08 - 134.06: 355 Bond angle restraints: 38466 Sorted by residual: angle pdb=" C GLN F 615 " pdb=" N THR F 616 " pdb=" CA THR F 616 " ideal model delta sigma weight residual 122.61 129.85 -7.24 1.56e+00 4.11e-01 2.15e+01 angle pdb=" C GLN A 615 " pdb=" N THR A 616 " pdb=" CA THR A 616 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.14e+01 angle pdb=" C GLN B 615 " pdb=" N THR B 616 " pdb=" CA THR B 616 " ideal model delta sigma weight residual 122.61 129.82 -7.21 1.56e+00 4.11e-01 2.13e+01 angle pdb=" C GLN C 615 " pdb=" N THR C 616 " pdb=" CA THR C 616 " ideal model delta sigma weight residual 122.61 129.81 -7.20 1.56e+00 4.11e-01 2.13e+01 angle pdb=" C GLN D 615 " pdb=" N THR D 616 " pdb=" CA THR D 616 " ideal model delta sigma weight residual 122.61 129.79 -7.18 1.56e+00 4.11e-01 2.12e+01 ... (remaining 38461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 16102 15.08 - 30.16: 1136 30.16 - 45.25: 264 45.25 - 60.33: 30 60.33 - 75.41: 54 Dihedral angle restraints: 17586 sinusoidal: 7422 harmonic: 10164 Sorted by residual: dihedral pdb=" CA GLN C 298 " pdb=" C GLN C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta harmonic sigma weight residual -180.00 -121.96 -58.04 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA GLN E 298 " pdb=" C GLN E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta harmonic sigma weight residual -180.00 -122.01 -57.99 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA GLN F 298 " pdb=" C GLN F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta harmonic sigma weight residual -180.00 -122.02 -57.98 0 5.00e+00 4.00e-02 1.34e+02 ... (remaining 17583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2563 0.047 - 0.094: 1236 0.094 - 0.141: 394 0.141 - 0.189: 77 0.189 - 0.236: 32 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CA THR C1132 " pdb=" N THR C1132 " pdb=" C THR C1132 " pdb=" CB THR C1132 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA THR F1132 " pdb=" N THR F1132 " pdb=" C THR F1132 " pdb=" CB THR F1132 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA THR B1132 " pdb=" N THR B1132 " pdb=" C THR B1132 " pdb=" CB THR B1132 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 4299 not shown) Planarity restraints: 4950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 298 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO B 299 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 299 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 299 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 298 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO D 299 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 298 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO F 299 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO F 299 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO F 299 " -0.046 5.00e-02 4.00e+02 ... (remaining 4947 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2938 2.74 - 3.28: 28400 3.28 - 3.82: 48358 3.82 - 4.36: 56889 4.36 - 4.90: 89636 Nonbonded interactions: 226221 Sorted by model distance: nonbonded pdb=" OG SER A 393 " pdb=" O LYS B 337 " model vdw 2.195 2.440 nonbonded pdb=" O LYS A 337 " pdb=" OG SER F 393 " model vdw 2.195 2.440 nonbonded pdb=" O LEU C1137 " pdb=" OG SER C1141 " model vdw 2.241 2.440 nonbonded pdb=" O LEU D1137 " pdb=" OG SER D1141 " model vdw 2.241 2.440 nonbonded pdb=" O LEU E1137 " pdb=" OG SER E1141 " model vdw 2.241 2.440 ... (remaining 226216 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 17778 2.51 5 N 4734 2.21 5 O 5124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.540 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: 6.380 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.240 Process input model: 72.520 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.006 0.060 28404 Z= 0.416 Angle : 1.130 13.399 38466 Z= 0.632 Chirality : 0.061 0.236 4302 Planarity : 0.009 0.086 4950 Dihedral : 12.175 75.410 10962 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 4.76 % 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: -5.01 (0.11), residues: 3438 helix: -3.34 (0.08), residues: 1548 sheet: -1.76 (0.23), residues: 384 loop : -3.68 (0.13), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 798 time to evaluate : 3.446 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 812 average time/residue: 0.4862 time to fit residues: 585.5895 Evaluate side-chains 499 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 3.374 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2592 time to fit residues: 5.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 0.1980 chunk 268 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 310 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS A 384 GLN A 386 GLN A 454 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 506 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A1152 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 384 GLN B 454 ASN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN B 506 GLN B 624 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 384 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN C 506 GLN C 645 GLN C1152 HIS D 306 HIS D 384 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN D 506 GLN D 589 GLN D 645 GLN D 653 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN E 506 GLN E 589 GLN ** E 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 ASN F 384 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN F 506 GLN F 589 GLN F 645 GLN F 653 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 28404 Z= 0.184 Angle : 0.711 11.114 38466 Z= 0.364 Chirality : 0.045 0.252 4302 Planarity : 0.007 0.095 4950 Dihedral : 6.793 45.330 3762 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -3.40 (0.13), residues: 3438 helix: -1.67 (0.12), residues: 1518 sheet: -1.15 (0.25), residues: 372 loop : -3.16 (0.15), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 655 time to evaluate : 3.509 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 669 average time/residue: 0.4525 time to fit residues: 447.8854 Evaluate side-chains 474 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 470 time to evaluate : 3.328 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2669 time to fit residues: 6.5569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 211 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 615 GLN A 645 GLN A 661 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 454 ASN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN D 645 GLN D 653 HIS D 661 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 HIS E 742 GLN F 298 GLN ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN F1154 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 28404 Z= 0.165 Angle : 0.688 9.335 38466 Z= 0.348 Chirality : 0.046 0.252 4302 Planarity : 0.006 0.076 4950 Dihedral : 6.227 45.521 3762 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.88 (0.13), residues: 3438 helix: -1.10 (0.12), residues: 1590 sheet: -0.76 (0.27), residues: 372 loop : -3.16 (0.14), residues: 1476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 606 time to evaluate : 3.599 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: 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: 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: 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: 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: 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: 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: symmetry clash outliers start: 12 outliers final: 6 residues processed: 613 average time/residue: 0.4650 time to fit residues: 429.3584 Evaluate side-chains 453 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 447 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2794 time to fit residues: 7.8231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 34 optimal weight: 0.0170 chunk 148 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 312 optimal weight: 0.1980 chunk 330 optimal weight: 30.0000 chunk 163 optimal weight: 0.8980 chunk 295 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 overall best weight: 3.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1163 ASN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 HIS C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 ASN D 277 GLN ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 506 GLN D 645 GLN D 653 HIS D 661 HIS ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1163 ASN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 661 HIS E1163 ASN ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN F 661 HIS F1154 HIS F1163 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 28404 Z= 0.199 Angle : 0.690 9.472 38466 Z= 0.353 Chirality : 0.046 0.232 4302 Planarity : 0.006 0.076 4950 Dihedral : 5.967 41.878 3762 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.52 (0.14), residues: 3438 helix: -0.75 (0.13), residues: 1584 sheet: -0.83 (0.26), residues: 390 loop : -2.98 (0.15), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 553 time to evaluate : 3.482 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 562 average time/residue: 0.4584 time to fit residues: 388.8879 Evaluate side-chains 401 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 398 time to evaluate : 3.364 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2884 time to fit residues: 6.7236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 9.9990 chunk 187 optimal weight: 0.0470 chunk 4 optimal weight: 7.9990 chunk 246 optimal weight: 0.2980 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 168 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 overall best weight: 3.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 645 GLN A1163 ASN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 653 HIS D 724 GLN ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 GLN F 742 GLN ** F1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 28404 Z= 0.200 Angle : 0.700 9.221 38466 Z= 0.355 Chirality : 0.046 0.258 4302 Planarity : 0.006 0.073 4950 Dihedral : 5.837 41.726 3762 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.45 (0.14), residues: 3438 helix: -0.81 (0.12), residues: 1644 sheet: -0.85 (0.26), residues: 390 loop : -2.84 (0.16), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 535 time to evaluate : 3.679 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: 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: 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: 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: 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: 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: symmetry clash outliers start: 8 outliers final: 4 residues processed: 543 average time/residue: 0.4379 time to fit residues: 359.6343 Evaluate side-chains 391 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 387 time to evaluate : 3.456 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2725 time to fit residues: 6.7259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 3.9990 chunk 297 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 330 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 589 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN C 615 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 645 GLN D 653 HIS ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 590 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 615 GLN F 645 GLN F1154 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 28404 Z= 0.288 Angle : 0.779 10.316 38466 Z= 0.402 Chirality : 0.048 0.269 4302 Planarity : 0.006 0.077 4950 Dihedral : 6.110 40.952 3762 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 32.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.50 (0.14), residues: 3438 helix: -0.88 (0.12), residues: 1608 sheet: -1.17 (0.26), residues: 402 loop : -2.68 (0.16), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 505 time to evaluate : 3.658 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 512 average time/residue: 0.4295 time to fit residues: 337.0671 Evaluate side-chains 374 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 369 time to evaluate : 3.591 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3033 time to fit residues: 7.5589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 0.4980 chunk 37 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 187 optimal weight: 0.0370 chunk 278 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 645 GLN A1154 HIS ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 364 GLN C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 653 HIS ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN F 415 ASN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 28404 Z= 0.177 Angle : 0.721 11.165 38466 Z= 0.361 Chirality : 0.047 0.259 4302 Planarity : 0.006 0.073 4950 Dihedral : 5.799 41.194 3762 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.19 (0.14), residues: 3438 helix: -0.61 (0.13), residues: 1602 sheet: -0.88 (0.27), residues: 390 loop : -2.59 (0.16), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 527 time to evaluate : 3.585 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: 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: 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: 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: 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: 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 outliers start: 3 outliers final: 1 residues processed: 530 average time/residue: 0.4314 time to fit residues: 349.8215 Evaluate side-chains 398 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 397 time to evaluate : 3.613 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3013 time to fit residues: 5.5231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 645 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 653 HIS ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** E 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 645 GLN ** F1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 28404 Z= 0.189 Angle : 0.723 9.693 38466 Z= 0.365 Chirality : 0.047 0.267 4302 Planarity : 0.006 0.075 4950 Dihedral : 5.677 40.125 3762 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3438 helix: -0.67 (0.13), residues: 1626 sheet: -0.86 (0.27), residues: 390 loop : -2.56 (0.16), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 3.589 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.4427 time to fit residues: 346.3488 Evaluate side-chains 372 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 306 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 645 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN D 653 HIS ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 590 GLN ** E 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN ** F1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 28404 Z= 0.202 Angle : 0.731 10.023 38466 Z= 0.370 Chirality : 0.048 0.251 4302 Planarity : 0.006 0.074 4950 Dihedral : 5.680 40.151 3762 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.16 (0.14), residues: 3438 helix: -0.62 (0.13), residues: 1602 sheet: -0.85 (0.27), residues: 390 loop : -2.53 (0.16), residues: 1446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 3.703 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.4272 time to fit residues: 326.4788 Evaluate side-chains 369 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.641 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 198 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 340 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 GLN ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 590 GLN E 653 HIS ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN F1154 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 28404 Z= 0.226 Angle : 0.753 9.714 38466 Z= 0.381 Chirality : 0.048 0.252 4302 Planarity : 0.006 0.075 4950 Dihedral : 5.725 39.996 3762 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 27.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.24 (0.14), residues: 3438 helix: -0.68 (0.13), residues: 1596 sheet: -1.12 (0.27), residues: 402 loop : -2.50 (0.16), residues: 1440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 3.605 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 497 average time/residue: 0.4146 time to fit residues: 318.0507 Evaluate side-chains 379 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 4.722 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 6.9990 chunk 289 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 40 optimal weight: 0.0470 chunk 75 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 279 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 645 GLN A1149 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS D 364 GLN D 489 ASN D 645 GLN ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN E 653 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN ** F 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.080696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.055900 restraints weight = 180809.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.057248 restraints weight = 138854.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058076 restraints weight = 113924.213| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 28404 Z= 0.173 Angle : 0.752 19.009 38466 Z= 0.373 Chirality : 0.049 0.276 4302 Planarity : 0.006 0.073 4950 Dihedral : 5.530 40.110 3762 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 2.38 % 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: -2.05 (0.14), residues: 3438 helix: -0.52 (0.13), residues: 1590 sheet: -0.85 (0.27), residues: 390 loop : -2.44 (0.16), residues: 1458 =============================================================================== Job complete usr+sys time: 6572.65 seconds wall clock time: 120 minutes 14.54 seconds (7214.54 seconds total)