Starting phenix.real_space_refine on Wed Mar 20 15:33:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/03_2024/6jpq_9870.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/03_2024/6jpq_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_9870/03_2024/6jpq_9870.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/03_2024/6jpq_9870.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/03_2024/6jpq_9870.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpq_9870/03_2024/6jpq_9870.pdb" } resolution = 4.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.034 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.50, per 1000 atoms: 0.49 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: 11.01 Conformation dependent library (CDL) restraints added in 4.9 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: 2.55 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: 8.62 Time building geometry restraints manager: 11.81 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 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: 0.010 Normalize map: mean=0, sd=1: 0.660 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: 4.960 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 68.210 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 1.131 13.399 38466 Z= 0.633 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 : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.57 % Allowed : 5.17 % Favored : 94.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 455 HIS 0.013 0.004 HIS F 630 PHE 0.023 0.003 PHE C 436 TYR 0.024 0.004 TYR F 601 ARG 0.007 0.001 ARG C 599 *********************** 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 : 3.396 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 REVERT: A 266 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6434 (tm-30) REVERT: A 316 MET cc_start: 0.9590 (mmm) cc_final: 0.9335 (mmm) REVERT: A 410 ILE cc_start: 0.8745 (mt) cc_final: 0.6919 (mt) REVERT: A 640 LEU cc_start: 0.9529 (mm) cc_final: 0.9281 (mm) REVERT: A 674 TRP cc_start: 0.8525 (t60) cc_final: 0.8313 (t-100) REVERT: A 716 LEU cc_start: 0.9775 (mt) cc_final: 0.9380 (pp) REVERT: A 718 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.9199 (pm20) REVERT: A 719 TRP cc_start: 0.9456 (m-10) cc_final: 0.9107 (m-90) REVERT: A 729 LEU cc_start: 0.9411 (mm) cc_final: 0.9194 (mt) REVERT: A 741 PHE cc_start: 0.9592 (m-80) cc_final: 0.8962 (m-80) REVERT: A 1152 HIS cc_start: 0.9633 (m90) cc_final: 0.9361 (m-70) REVERT: B 305 PHE cc_start: 0.9684 (m-10) cc_final: 0.9333 (m-10) REVERT: B 318 ARG cc_start: 0.9418 (tpm170) cc_final: 0.9184 (tpp-160) REVERT: B 320 LEU cc_start: 0.9557 (mt) cc_final: 0.9079 (mt) REVERT: B 351 ARG cc_start: 0.9043 (ptm-80) cc_final: 0.8784 (ttp80) REVERT: B 418 ASP cc_start: 0.8693 (t0) cc_final: 0.8485 (m-30) REVERT: B 442 ASP cc_start: 0.9708 (p0) cc_final: 0.9496 (p0) REVERT: B 519 PHE cc_start: 0.9617 (m-80) cc_final: 0.9210 (m-80) REVERT: B 549 LEU cc_start: 0.9596 (mt) cc_final: 0.9251 (mp) REVERT: B 564 MET cc_start: 0.9405 (ttp) cc_final: 0.8993 (ppp) REVERT: B 584 ASN cc_start: 0.8133 (t0) cc_final: 0.7845 (m-40) REVERT: B 630 HIS cc_start: 0.8006 (t-90) cc_final: 0.7704 (t70) REVERT: B 636 MET cc_start: 0.9473 (pmm) cc_final: 0.8819 (mmt) REVERT: B 727 TYR cc_start: 0.8688 (t80) cc_final: 0.8488 (t80) REVERT: B 1185 MET cc_start: 0.9234 (mtt) cc_final: 0.8993 (mmm) REVERT: C 320 LEU cc_start: 0.8795 (mt) cc_final: 0.7943 (mt) REVERT: C 352 GLN cc_start: 0.9364 (mp10) cc_final: 0.9089 (mt0) REVERT: C 480 ARG cc_start: 0.9504 (mmt90) cc_final: 0.9060 (mmm-85) REVERT: C 671 ILE cc_start: 0.9247 (mt) cc_final: 0.9013 (mt) REVERT: C 690 LEU cc_start: 0.9409 (mt) cc_final: 0.9160 (mt) REVERT: D 281 MET cc_start: 0.7781 (mmt) cc_final: 0.7389 (mmm) REVERT: D 369 PHE cc_start: 0.8614 (m-10) cc_final: 0.8263 (m-80) REVERT: D 430 PHE cc_start: 0.8892 (m-10) cc_final: 0.8687 (m-80) REVERT: D 432 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8320 (mtm-85) REVERT: D 636 MET cc_start: 0.9748 (pmm) cc_final: 0.9534 (pmm) REVERT: E 277 GLN cc_start: 0.9547 (mt0) cc_final: 0.9334 (mt0) REVERT: E 288 TYR cc_start: 0.8931 (m-10) cc_final: 0.8681 (m-10) REVERT: E 371 ASP cc_start: 0.9579 (m-30) cc_final: 0.9324 (p0) REVERT: E 399 MET cc_start: 0.9018 (mmt) cc_final: 0.8692 (mmt) REVERT: E 415 ASN cc_start: 0.8594 (t160) cc_final: 0.7840 (t160) REVERT: E 430 PHE cc_start: 0.7710 (m-10) cc_final: 0.7094 (m-10) REVERT: E 479 LEU cc_start: 0.9557 (mt) cc_final: 0.9314 (mt) REVERT: E 591 ARG cc_start: 0.8611 (mtt90) cc_final: 0.8079 (mmp80) REVERT: E 592 LEU cc_start: 0.9338 (pt) cc_final: 0.8986 (pt) REVERT: E 653 HIS cc_start: 0.9662 (m170) cc_final: 0.9417 (m-70) REVERT: E 697 ASP cc_start: 0.9010 (m-30) cc_final: 0.8809 (t0) REVERT: E 701 PHE cc_start: 0.9281 (t80) cc_final: 0.8678 (t80) REVERT: F 277 GLN cc_start: 0.9837 (mt0) cc_final: 0.9563 (mt0) REVERT: F 298 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8336 (tp40) REVERT: F 356 LEU cc_start: 0.9661 (tt) cc_final: 0.9402 (mt) REVERT: F 432 ARG cc_start: 0.9226 (mmt180) cc_final: 0.8822 (mpp-170) REVERT: F 519 PHE cc_start: 0.9522 (m-80) cc_final: 0.9202 (t80) REVERT: F 523 MET cc_start: 0.8556 (mmm) cc_final: 0.7664 (mmp) REVERT: F 592 LEU cc_start: 0.9703 (pt) cc_final: 0.9464 (pt) REVERT: F 645 GLN cc_start: 0.8727 (pt0) cc_final: 0.8199 (pt0) REVERT: F 652 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8621 (pt) REVERT: F 653 HIS cc_start: 0.9295 (m170) cc_final: 0.8748 (m-70) REVERT: F 678 LEU cc_start: 0.8271 (mm) cc_final: 0.7787 (mm) REVERT: F 686 PHE cc_start: 0.9379 (t80) cc_final: 0.9116 (t80) REVERT: F 689 MET cc_start: 0.9615 (mmm) cc_final: 0.9312 (mmm) REVERT: F 704 LEU cc_start: 0.9359 (tp) cc_final: 0.9151 (tp) REVERT: F 720 PHE cc_start: 0.9216 (m-80) cc_final: 0.9010 (m-80) REVERT: F 738 ILE cc_start: 0.9468 (pt) cc_final: 0.9267 (mm) REVERT: F 741 PHE cc_start: 0.9219 (m-80) cc_final: 0.8637 (m-80) outliers start: 18 outliers final: 2 residues processed: 812 average time/residue: 0.4739 time to fit residues: 562.2141 Evaluate side-chains 525 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 521 time to evaluate : 3.232 ------------------------------------------------------------------------------- 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: 5.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 174 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 268 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 310 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 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 ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN B 384 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 GLN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28404 Z= 0.191 Angle : 0.706 11.896 38466 Z= 0.364 Chirality : 0.045 0.174 4302 Planarity : 0.007 0.090 4950 Dihedral : 6.826 45.284 3762 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.54 % Allowed : 3.96 % Favored : 95.50 % 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: -3.48 (0.13), residues: 3438 helix: -1.74 (0.12), residues: 1536 sheet: -1.16 (0.25), residues: 372 loop : -3.21 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 345 HIS 0.017 0.002 HIS A 653 PHE 0.021 0.002 PHE E 634 TYR 0.031 0.002 TYR A1158 ARG 0.016 0.001 ARG B 480 *********************** 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 667 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 650 time to evaluate : 3.417 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: A 316 MET cc_start: 0.9583 (mmm) cc_final: 0.9352 (mmm) REVERT: A 371 ASP cc_start: 0.9552 (t0) cc_final: 0.9124 (m-30) REVERT: A 402 MET cc_start: 0.7481 (mtp) cc_final: 0.7137 (mtp) REVERT: A 424 LEU cc_start: 0.8990 (mp) cc_final: 0.8408 (mp) REVERT: A 548 LEU cc_start: 0.9093 (mm) cc_final: 0.8798 (mm) REVERT: A 636 MET cc_start: 0.9277 (mpp) cc_final: 0.9041 (mpp) REVERT: A 653 HIS cc_start: 0.9372 (m-70) cc_final: 0.9069 (m-70) REVERT: A 701 PHE cc_start: 0.9234 (t80) cc_final: 0.8968 (t80) REVERT: A 704 LEU cc_start: 0.9522 (tp) cc_final: 0.9264 (mm) REVERT: A 1157 LEU cc_start: 0.9572 (mm) cc_final: 0.9290 (pp) REVERT: B 288 TYR cc_start: 0.9090 (m-80) cc_final: 0.8814 (m-80) REVERT: B 398 LEU cc_start: 0.9490 (mp) cc_final: 0.9131 (mp) REVERT: B 399 MET cc_start: 0.9048 (mmp) cc_final: 0.8761 (mmp) REVERT: B 402 MET cc_start: 0.6430 (mtt) cc_final: 0.6140 (mtm) REVERT: B 519 PHE cc_start: 0.9585 (m-80) cc_final: 0.9207 (m-80) REVERT: B 521 MET cc_start: 0.9630 (mtm) cc_final: 0.9220 (mtp) REVERT: B 545 LEU cc_start: 0.9811 (mp) cc_final: 0.9487 (tp) REVERT: B 564 MET cc_start: 0.9369 (ttp) cc_final: 0.9031 (ppp) REVERT: B 584 ASN cc_start: 0.8182 (t0) cc_final: 0.7932 (m-40) REVERT: B 630 HIS cc_start: 0.8099 (t-90) cc_final: 0.7840 (t70) REVERT: B 636 MET cc_start: 0.9503 (pmm) cc_final: 0.9069 (mpp) REVERT: B 653 HIS cc_start: 0.9398 (m90) cc_final: 0.9130 (m-70) REVERT: B 727 TYR cc_start: 0.8939 (t80) cc_final: 0.8737 (t80) REVERT: C 266 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8367 (tm-30) REVERT: C 399 MET cc_start: 0.9509 (mmp) cc_final: 0.8386 (tmm) REVERT: C 441 ARG cc_start: 0.9068 (tpp80) cc_final: 0.8816 (tpp80) REVERT: C 521 MET cc_start: 0.9777 (mtm) cc_final: 0.9396 (mtm) REVERT: C 523 MET cc_start: 0.9713 (tpp) cc_final: 0.9499 (tpp) REVERT: C 665 ILE cc_start: 0.9653 (mm) cc_final: 0.9441 (mm) REVERT: C 1152 HIS cc_start: 0.9394 (m170) cc_final: 0.9036 (m-70) REVERT: D 281 MET cc_start: 0.7685 (mmt) cc_final: 0.7483 (mmt) REVERT: D 283 MET cc_start: 0.8339 (ptt) cc_final: 0.7903 (ptt) REVERT: D 316 MET cc_start: 0.9213 (mmt) cc_final: 0.8754 (mmm) REVERT: D 320 LEU cc_start: 0.9445 (tp) cc_final: 0.9237 (mt) REVERT: D 416 ARG cc_start: 0.8827 (pmt170) cc_final: 0.8619 (pmt-80) REVERT: D 562 LYS cc_start: 0.9618 (mtmt) cc_final: 0.9299 (ptpp) REVERT: D 591 ARG cc_start: 0.9200 (mtt90) cc_final: 0.8678 (mtm180) REVERT: D 689 MET cc_start: 0.9562 (mmp) cc_final: 0.9338 (mmm) REVERT: E 328 ASN cc_start: 0.8763 (t0) cc_final: 0.8557 (t0) REVERT: E 441 ARG cc_start: 0.9226 (tmt-80) cc_final: 0.8967 (ttp-110) REVERT: E 479 LEU cc_start: 0.9537 (mt) cc_final: 0.9332 (mt) REVERT: E 591 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8080 (mmp80) REVERT: E 592 LEU cc_start: 0.9408 (pt) cc_final: 0.9039 (pt) REVERT: E 636 MET cc_start: 0.9527 (mpp) cc_final: 0.9057 (mmt) REVERT: E 642 ASP cc_start: 0.7928 (t70) cc_final: 0.7718 (t70) REVERT: E 645 GLN cc_start: 0.8152 (pt0) cc_final: 0.7827 (pt0) REVERT: E 653 HIS cc_start: 0.9715 (m-70) cc_final: 0.9374 (m-70) REVERT: E 697 ASP cc_start: 0.9333 (m-30) cc_final: 0.9085 (m-30) REVERT: E 701 PHE cc_start: 0.9178 (t80) cc_final: 0.8530 (t80) REVERT: E 1179 ARG cc_start: 0.9708 (mpp-170) cc_final: 0.9395 (ptt-90) REVERT: F 274 TYR cc_start: 0.9278 (m-10) cc_final: 0.9037 (m-10) REVERT: F 281 MET cc_start: 0.8560 (ptp) cc_final: 0.8352 (ptp) REVERT: F 298 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8507 (pp30) REVERT: F 303 VAL cc_start: 0.9284 (t) cc_final: 0.8951 (t) REVERT: F 351 ARG cc_start: 0.8308 (mmp80) cc_final: 0.7872 (mmp80) REVERT: F 356 LEU cc_start: 0.9671 (tt) cc_final: 0.9459 (mt) REVERT: F 370 PHE cc_start: 0.9016 (m-80) cc_final: 0.8801 (m-80) REVERT: F 432 ARG cc_start: 0.8922 (mmt180) cc_final: 0.8690 (mpp-170) REVERT: F 523 MET cc_start: 0.8451 (mmm) cc_final: 0.8227 (mmm) REVERT: F 527 ILE cc_start: 0.8939 (pt) cc_final: 0.8734 (tt) REVERT: F 584 ASN cc_start: 0.8134 (t0) cc_final: 0.7775 (p0) REVERT: F 622 ILE cc_start: 0.8728 (pt) cc_final: 0.8506 (pt) REVERT: F 636 MET cc_start: 0.9157 (mpp) cc_final: 0.8903 (mmt) REVERT: F 656 LEU cc_start: 0.9804 (tt) cc_final: 0.9504 (tt) REVERT: F 673 ASN cc_start: 0.9239 (t0) cc_final: 0.8920 (m-40) REVERT: F 689 MET cc_start: 0.9693 (mmm) cc_final: 0.9250 (mmm) REVERT: F 697 ASP cc_start: 0.8631 (m-30) cc_final: 0.8271 (m-30) REVERT: F 727 TYR cc_start: 0.8192 (t80) cc_final: 0.7903 (t80) REVERT: F 738 ILE cc_start: 0.9534 (pt) cc_final: 0.9227 (mm) REVERT: F 741 PHE cc_start: 0.9169 (m-80) cc_final: 0.8655 (m-80) outliers start: 17 outliers final: 4 residues processed: 663 average time/residue: 0.4885 time to fit residues: 482.7089 Evaluate side-chains 486 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 482 time to evaluate : 3.376 ------------------------------------------------------------------------------- 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: 2.9990 chunk 96 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 211 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 277 optimal weight: 0.0070 chunk 308 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B1163 ASN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1163 ASN D 352 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 661 HIS E 742 GLN E1163 ASN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN F 653 HIS F 742 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28404 Z= 0.196 Angle : 0.694 10.120 38466 Z= 0.357 Chirality : 0.045 0.187 4302 Planarity : 0.007 0.079 4950 Dihedral : 6.338 44.111 3762 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.26 % Allowed : 4.41 % Favored : 95.34 % 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: -2.98 (0.13), residues: 3438 helix: -1.25 (0.12), residues: 1620 sheet: -0.98 (0.26), residues: 390 loop : -3.13 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 674 HIS 0.014 0.002 HIS A1154 PHE 0.033 0.002 PHE E 741 TYR 0.015 0.001 TYR C 601 ARG 0.011 0.001 ARG B 480 *********************** 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 595 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 587 time to evaluate : 3.531 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: A 320 LEU cc_start: 0.9651 (mt) cc_final: 0.9264 (mt) REVERT: A 371 ASP cc_start: 0.9602 (t0) cc_final: 0.9203 (m-30) REVERT: A 402 MET cc_start: 0.7193 (mtp) cc_final: 0.6976 (mtp) REVERT: A 653 HIS cc_start: 0.9363 (m-70) cc_final: 0.9035 (m-70) REVERT: A 701 PHE cc_start: 0.9394 (t80) cc_final: 0.8858 (t80) REVERT: A 704 LEU cc_start: 0.9508 (tp) cc_final: 0.9232 (mm) REVERT: A 741 PHE cc_start: 0.9169 (m-80) cc_final: 0.8931 (m-80) REVERT: A 1157 LEU cc_start: 0.9530 (mm) cc_final: 0.9286 (pp) REVERT: B 288 TYR cc_start: 0.9027 (m-80) cc_final: 0.8678 (m-80) REVERT: B 399 MET cc_start: 0.9277 (mmp) cc_final: 0.9041 (mmp) REVERT: B 469 GLU cc_start: 0.9636 (pt0) cc_final: 0.9432 (pt0) REVERT: B 519 PHE cc_start: 0.9568 (m-80) cc_final: 0.9199 (m-80) REVERT: B 521 MET cc_start: 0.9663 (mtm) cc_final: 0.9196 (mtm) REVERT: B 564 MET cc_start: 0.9371 (ttp) cc_final: 0.8924 (tmm) REVERT: B 584 ASN cc_start: 0.7983 (t0) cc_final: 0.7726 (m110) REVERT: B 595 PHE cc_start: 0.9362 (m-80) cc_final: 0.9118 (m-10) REVERT: B 630 HIS cc_start: 0.8369 (t-90) cc_final: 0.8082 (t70) REVERT: B 636 MET cc_start: 0.9504 (pmm) cc_final: 0.9274 (mpp) REVERT: B 653 HIS cc_start: 0.9444 (m90) cc_final: 0.9083 (m-70) REVERT: B 691 GLU cc_start: 0.9322 (tm-30) cc_final: 0.9077 (tm-30) REVERT: B 740 PHE cc_start: 0.9111 (t80) cc_final: 0.8881 (t80) REVERT: B 1185 MET cc_start: 0.9172 (mtt) cc_final: 0.8782 (mmm) REVERT: C 266 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8478 (tm-30) REVERT: C 320 LEU cc_start: 0.8630 (mt) cc_final: 0.8017 (mt) REVERT: C 399 MET cc_start: 0.9446 (mmp) cc_final: 0.8265 (tmm) REVERT: C 441 ARG cc_start: 0.9124 (tpp80) cc_final: 0.8896 (tpp80) REVERT: C 442 ASP cc_start: 0.9589 (p0) cc_final: 0.9239 (p0) REVERT: C 480 ARG cc_start: 0.9584 (mmt90) cc_final: 0.9038 (mmm-85) REVERT: C 521 MET cc_start: 0.9770 (mtm) cc_final: 0.9432 (mtp) REVERT: C 523 MET cc_start: 0.9726 (tpp) cc_final: 0.9432 (tpp) REVERT: C 654 LEU cc_start: 0.9480 (tp) cc_final: 0.9236 (tp) REVERT: C 659 ARG cc_start: 0.9272 (ttp80) cc_final: 0.8958 (ttp-110) REVERT: C 1152 HIS cc_start: 0.9218 (m170) cc_final: 0.8722 (m-70) REVERT: D 283 MET cc_start: 0.8388 (ptt) cc_final: 0.7726 (ptt) REVERT: D 316 MET cc_start: 0.9187 (mmt) cc_final: 0.8821 (mmm) REVERT: D 320 LEU cc_start: 0.9442 (tp) cc_final: 0.9234 (mt) REVERT: D 351 ARG cc_start: 0.9374 (mmm160) cc_final: 0.8889 (ttt180) REVERT: D 370 PHE cc_start: 0.9190 (m-80) cc_final: 0.8942 (m-80) REVERT: D 409 ILE cc_start: 0.8754 (mp) cc_final: 0.8331 (mp) REVERT: D 562 LYS cc_start: 0.9660 (mtmt) cc_final: 0.9358 (ptpp) REVERT: D 591 ARG cc_start: 0.9161 (mtt90) cc_final: 0.8824 (mtt-85) REVERT: E 304 LEU cc_start: 0.9482 (mp) cc_final: 0.8998 (pp) REVERT: E 335 MET cc_start: 0.9438 (mmp) cc_final: 0.9102 (mmm) REVERT: E 441 ARG cc_start: 0.9232 (tmt-80) cc_final: 0.8978 (ttp-110) REVERT: E 479 LEU cc_start: 0.9520 (mt) cc_final: 0.9274 (mt) REVERT: E 523 MET cc_start: 0.8951 (mmp) cc_final: 0.8744 (mmm) REVERT: E 592 LEU cc_start: 0.9394 (pt) cc_final: 0.9056 (pt) REVERT: E 642 ASP cc_start: 0.7893 (t70) cc_final: 0.7669 (t70) REVERT: E 645 GLN cc_start: 0.8212 (pt0) cc_final: 0.7932 (pt0) REVERT: E 653 HIS cc_start: 0.9703 (m-70) cc_final: 0.9388 (m-70) REVERT: E 697 ASP cc_start: 0.9268 (m-30) cc_final: 0.8955 (m-30) REVERT: E 701 PHE cc_start: 0.9182 (t80) cc_final: 0.8536 (t80) REVERT: F 297 MET cc_start: 0.9422 (ptt) cc_final: 0.8374 (mmm) REVERT: F 298 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8557 (pp30) REVERT: F 303 VAL cc_start: 0.9367 (t) cc_final: 0.8824 (t) REVERT: F 370 PHE cc_start: 0.9109 (m-80) cc_final: 0.8660 (m-80) REVERT: F 402 MET cc_start: 0.6484 (mtt) cc_final: 0.5943 (mtt) REVERT: F 432 ARG cc_start: 0.8900 (mmt180) cc_final: 0.8635 (mtm-85) REVERT: F 451 HIS cc_start: 0.8531 (m90) cc_final: 0.8218 (m-70) REVERT: F 523 MET cc_start: 0.8458 (mmm) cc_final: 0.8169 (mmm) REVERT: F 527 ILE cc_start: 0.8964 (pt) cc_final: 0.8751 (tt) REVERT: F 539 LYS cc_start: 0.9605 (mmtm) cc_final: 0.9338 (mmtt) REVERT: F 584 ASN cc_start: 0.8026 (t0) cc_final: 0.7682 (p0) REVERT: F 622 ILE cc_start: 0.8791 (pt) cc_final: 0.8558 (pt) REVERT: F 636 MET cc_start: 0.9337 (mpp) cc_final: 0.8981 (mmt) REVERT: F 656 LEU cc_start: 0.9688 (tt) cc_final: 0.9299 (tt) REVERT: F 660 ARG cc_start: 0.9532 (mmp-170) cc_final: 0.9269 (mmm-85) REVERT: F 673 ASN cc_start: 0.9279 (t0) cc_final: 0.8927 (m-40) REVERT: F 689 MET cc_start: 0.9697 (mmm) cc_final: 0.9337 (mmm) REVERT: F 697 ASP cc_start: 0.8773 (m-30) cc_final: 0.8442 (m-30) REVERT: F 727 TYR cc_start: 0.8218 (t80) cc_final: 0.7950 (t80) REVERT: F 741 PHE cc_start: 0.9168 (m-80) cc_final: 0.8677 (m-10) outliers start: 8 outliers final: 2 residues processed: 591 average time/residue: 0.4586 time to fit residues: 402.4318 Evaluate side-chains 447 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 445 time to evaluate : 3.488 ------------------------------------------------------------------------------- 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: 2.9990 chunk 233 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 312 optimal weight: 0.4980 chunk 330 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 295 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 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 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 661 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN F 653 HIS F1163 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28404 Z= 0.192 Angle : 0.674 9.366 38466 Z= 0.346 Chirality : 0.045 0.270 4302 Planarity : 0.006 0.075 4950 Dihedral : 6.070 41.899 3762 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.17 % 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: -2.71 (0.14), residues: 3438 helix: -0.99 (0.12), residues: 1632 sheet: -0.91 (0.26), residues: 390 loop : -3.02 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 674 HIS 0.018 0.001 HIS B1154 PHE 0.018 0.001 PHE F 720 TYR 0.032 0.002 TYR B1158 ARG 0.009 0.001 ARG F 416 *********************** 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 570 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 567 time to evaluate : 3.234 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: A 314 THR cc_start: 0.9240 (p) cc_final: 0.8676 (p) REVERT: A 316 MET cc_start: 0.9615 (tpt) cc_final: 0.9246 (tpp) REVERT: A 318 ARG cc_start: 0.9383 (mtm-85) cc_final: 0.8962 (mmp80) REVERT: A 371 ASP cc_start: 0.9563 (t0) cc_final: 0.9125 (m-30) REVERT: A 402 MET cc_start: 0.7072 (mtp) cc_final: 0.6810 (mtp) REVERT: A 653 HIS cc_start: 0.9385 (m-70) cc_final: 0.9045 (m-70) REVERT: A 701 PHE cc_start: 0.9442 (t80) cc_final: 0.8968 (t80) REVERT: A 704 LEU cc_start: 0.9533 (tp) cc_final: 0.9236 (mm) REVERT: A 741 PHE cc_start: 0.9186 (m-80) cc_final: 0.8942 (m-80) REVERT: A 1157 LEU cc_start: 0.9517 (mm) cc_final: 0.9274 (pp) REVERT: B 288 TYR cc_start: 0.9009 (m-80) cc_final: 0.8724 (m-10) REVERT: B 320 LEU cc_start: 0.9358 (mt) cc_final: 0.9089 (mt) REVERT: B 405 ARG cc_start: 0.8348 (ptt180) cc_final: 0.7577 (mtm110) REVERT: B 469 GLU cc_start: 0.9635 (pt0) cc_final: 0.9397 (pt0) REVERT: B 519 PHE cc_start: 0.9552 (m-80) cc_final: 0.9179 (m-80) REVERT: B 521 MET cc_start: 0.9657 (mtm) cc_final: 0.9250 (mtp) REVERT: B 564 MET cc_start: 0.9355 (ttp) cc_final: 0.8915 (tmm) REVERT: B 595 PHE cc_start: 0.9369 (m-80) cc_final: 0.9131 (m-10) REVERT: B 630 HIS cc_start: 0.8592 (t-90) cc_final: 0.8251 (t70) REVERT: B 636 MET cc_start: 0.9460 (pmm) cc_final: 0.9159 (mpp) REVERT: B 653 HIS cc_start: 0.9474 (m90) cc_final: 0.9122 (m-70) REVERT: B 691 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9059 (tm-30) REVERT: B 740 PHE cc_start: 0.9099 (t80) cc_final: 0.8760 (t80) REVERT: C 266 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8471 (tm-30) REVERT: C 320 LEU cc_start: 0.8632 (mt) cc_final: 0.8037 (mt) REVERT: C 356 LEU cc_start: 0.9508 (mt) cc_final: 0.9199 (mt) REVERT: C 441 ARG cc_start: 0.9135 (tpp80) cc_final: 0.8884 (tpp80) REVERT: C 480 ARG cc_start: 0.9604 (mmt90) cc_final: 0.9065 (mmm-85) REVERT: C 521 MET cc_start: 0.9759 (mtm) cc_final: 0.9385 (mtp) REVERT: C 523 MET cc_start: 0.9714 (tpp) cc_final: 0.9375 (tpp) REVERT: C 689 MET cc_start: 0.9516 (mmp) cc_final: 0.9297 (mmm) REVERT: D 283 MET cc_start: 0.8430 (ptt) cc_final: 0.7979 (ptt) REVERT: D 316 MET cc_start: 0.9514 (mmm) cc_final: 0.9291 (mmm) REVERT: D 320 LEU cc_start: 0.9469 (tp) cc_final: 0.9260 (mt) REVERT: D 350 GLU cc_start: 0.9020 (tp30) cc_final: 0.8698 (tp30) REVERT: D 351 ARG cc_start: 0.9375 (mmm160) cc_final: 0.8938 (ttt180) REVERT: D 370 PHE cc_start: 0.9216 (m-80) cc_final: 0.8958 (m-80) REVERT: D 430 PHE cc_start: 0.9107 (m-10) cc_final: 0.8729 (m-80) REVERT: D 562 LYS cc_start: 0.9670 (mtmt) cc_final: 0.9381 (ptpp) REVERT: D 591 ARG cc_start: 0.9272 (mtt90) cc_final: 0.9058 (mtt-85) REVERT: E 304 LEU cc_start: 0.9466 (mp) cc_final: 0.9029 (pp) REVERT: E 399 MET cc_start: 0.8314 (mmp) cc_final: 0.8083 (mmp) REVERT: E 479 LEU cc_start: 0.9480 (mt) cc_final: 0.9232 (mt) REVERT: E 592 LEU cc_start: 0.9411 (pt) cc_final: 0.9096 (pt) REVERT: E 642 ASP cc_start: 0.7827 (t70) cc_final: 0.7540 (t70) REVERT: E 645 GLN cc_start: 0.8766 (pt0) cc_final: 0.8433 (pt0) REVERT: E 652 ILE cc_start: 0.9587 (mm) cc_final: 0.9283 (pt) REVERT: E 653 HIS cc_start: 0.9713 (m-70) cc_final: 0.9493 (m-70) REVERT: E 697 ASP cc_start: 0.9266 (m-30) cc_final: 0.8462 (t0) REVERT: E 701 PHE cc_start: 0.9259 (t80) cc_final: 0.8519 (t80) REVERT: F 298 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8576 (tp40) REVERT: F 303 VAL cc_start: 0.9254 (t) cc_final: 0.8966 (t) REVERT: F 328 ASN cc_start: 0.8564 (t0) cc_final: 0.8220 (m-40) REVERT: F 354 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8991 (tpp-160) REVERT: F 358 GLU cc_start: 0.9217 (pp20) cc_final: 0.8983 (pp20) REVERT: F 402 MET cc_start: 0.6290 (mtt) cc_final: 0.5823 (mtt) REVERT: F 432 ARG cc_start: 0.8782 (mmt180) cc_final: 0.8561 (mtm-85) REVERT: F 451 HIS cc_start: 0.8425 (m90) cc_final: 0.8196 (m-70) REVERT: F 523 MET cc_start: 0.8396 (mmm) cc_final: 0.8138 (mmm) REVERT: F 525 ARG cc_start: 0.8261 (mtm110) cc_final: 0.8041 (mtm180) REVERT: F 527 ILE cc_start: 0.8902 (pt) cc_final: 0.8688 (tt) REVERT: F 584 ASN cc_start: 0.8239 (t0) cc_final: 0.7846 (p0) REVERT: F 595 PHE cc_start: 0.9302 (m-80) cc_final: 0.8966 (m-10) REVERT: F 622 ILE cc_start: 0.8875 (pt) cc_final: 0.8642 (pt) REVERT: F 636 MET cc_start: 0.9340 (mpp) cc_final: 0.9031 (mmt) REVERT: F 673 ASN cc_start: 0.9296 (t0) cc_final: 0.8944 (m-40) REVERT: F 689 MET cc_start: 0.9728 (mmm) cc_final: 0.9378 (mmm) REVERT: F 727 TYR cc_start: 0.8237 (t80) cc_final: 0.7945 (t80) REVERT: F 741 PHE cc_start: 0.9131 (m-80) cc_final: 0.8596 (m-10) outliers start: 3 outliers final: 2 residues processed: 569 average time/residue: 0.4792 time to fit residues: 408.6898 Evaluate side-chains 432 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 430 time to evaluate : 3.217 ------------------------------------------------------------------------------- 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: 6.9990 chunk 187 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 228 optimal weight: 0.0020 chunk 0 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** 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** A1163 ASN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN ** C 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 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** ** D 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** 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 ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 615 GLN F 645 GLN F 653 HIS F 661 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28404 Z= 0.244 Angle : 0.721 12.725 38466 Z= 0.373 Chirality : 0.046 0.213 4302 Planarity : 0.006 0.071 4950 Dihedral : 6.053 41.673 3762 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.42 % Allowed : 4.18 % Favored : 95.40 % 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: -2.59 (0.14), residues: 3438 helix: -0.93 (0.12), residues: 1626 sheet: -0.96 (0.26), residues: 390 loop : -2.87 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 674 HIS 0.020 0.002 HIS B1154 PHE 0.030 0.002 PHE E 741 TYR 0.044 0.002 TYR B1158 ARG 0.010 0.001 ARG B1179 *********************** 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 547 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 534 time to evaluate : 3.281 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: A 281 MET cc_start: 0.8984 (tpp) cc_final: 0.8725 (tpp) REVERT: A 314 THR cc_start: 0.9335 (p) cc_final: 0.8823 (p) REVERT: A 316 MET cc_start: 0.9666 (tpt) cc_final: 0.9323 (tpp) REVERT: A 318 ARG cc_start: 0.9380 (mtm-85) cc_final: 0.8921 (mmp80) REVERT: A 371 ASP cc_start: 0.9557 (t0) cc_final: 0.9096 (m-30) REVERT: A 653 HIS cc_start: 0.9456 (m-70) cc_final: 0.9181 (m-70) REVERT: A 741 PHE cc_start: 0.9306 (m-80) cc_final: 0.9078 (m-80) REVERT: A 1157 LEU cc_start: 0.9531 (mm) cc_final: 0.9281 (pp) REVERT: B 318 ARG cc_start: 0.9485 (tpm170) cc_final: 0.9232 (tpm170) REVERT: B 320 LEU cc_start: 0.9395 (mt) cc_final: 0.9136 (mt) REVERT: B 405 ARG cc_start: 0.8329 (ptt180) cc_final: 0.7637 (mtm180) REVERT: B 411 ILE cc_start: 0.9670 (mp) cc_final: 0.9455 (mp) REVERT: B 469 GLU cc_start: 0.9664 (pt0) cc_final: 0.9439 (pt0) REVERT: B 519 PHE cc_start: 0.9538 (m-80) cc_final: 0.9183 (m-80) REVERT: B 521 MET cc_start: 0.9658 (mtm) cc_final: 0.9257 (mtp) REVERT: B 564 MET cc_start: 0.9330 (ttp) cc_final: 0.8970 (ppp) REVERT: B 595 PHE cc_start: 0.9359 (m-80) cc_final: 0.9137 (m-10) REVERT: B 630 HIS cc_start: 0.8801 (t-90) cc_final: 0.8409 (t70) REVERT: B 691 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9186 (tm-30) REVERT: B 1185 MET cc_start: 0.9097 (mtt) cc_final: 0.8762 (mmm) REVERT: C 266 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8366 (tm-30) REVERT: C 320 LEU cc_start: 0.8666 (mt) cc_final: 0.8088 (mt) REVERT: C 334 TYR cc_start: 0.8447 (m-80) cc_final: 0.7757 (m-80) REVERT: C 335 MET cc_start: 0.9031 (pmm) cc_final: 0.8448 (tmm) REVERT: C 523 MET cc_start: 0.9699 (tpp) cc_final: 0.9375 (tpp) REVERT: C 656 LEU cc_start: 0.9680 (tp) cc_final: 0.9460 (tp) REVERT: C 1158 TYR cc_start: 0.9615 (m-10) cc_final: 0.9333 (m-80) REVERT: D 283 MET cc_start: 0.8679 (ptt) cc_final: 0.8368 (ptt) REVERT: D 316 MET cc_start: 0.9544 (mmm) cc_final: 0.9343 (mmm) REVERT: D 320 LEU cc_start: 0.9481 (tp) cc_final: 0.9216 (mt) REVERT: D 430 PHE cc_start: 0.9076 (m-10) cc_final: 0.8718 (m-80) REVERT: D 562 LYS cc_start: 0.9698 (mtmt) cc_final: 0.9437 (ptpp) REVERT: E 304 LEU cc_start: 0.9471 (mp) cc_final: 0.9243 (pp) REVERT: E 591 ARG cc_start: 0.8756 (mtt90) cc_final: 0.8434 (mtt-85) REVERT: E 592 LEU cc_start: 0.9471 (pt) cc_final: 0.9146 (pt) REVERT: E 645 GLN cc_start: 0.8518 (pt0) cc_final: 0.8265 (pt0) REVERT: E 657 GLU cc_start: 0.9681 (mp0) cc_final: 0.9467 (mp0) REVERT: E 674 TRP cc_start: 0.8835 (t60) cc_final: 0.8628 (t60) REVERT: E 697 ASP cc_start: 0.9249 (m-30) cc_final: 0.9004 (m-30) REVERT: E 701 PHE cc_start: 0.9367 (t80) cc_final: 0.8590 (t80) REVERT: F 297 MET cc_start: 0.9389 (ptt) cc_final: 0.8575 (mmm) REVERT: F 298 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8564 (tp40) REVERT: F 303 VAL cc_start: 0.9360 (t) cc_final: 0.9011 (t) REVERT: F 354 ARG cc_start: 0.9257 (tpp80) cc_final: 0.8994 (tpp-160) REVERT: F 357 PHE cc_start: 0.9215 (m-10) cc_final: 0.9001 (m-10) REVERT: F 358 GLU cc_start: 0.9175 (pp20) cc_final: 0.8908 (pp20) REVERT: F 370 PHE cc_start: 0.9154 (m-80) cc_final: 0.8782 (m-80) REVERT: F 402 MET cc_start: 0.6123 (mtt) cc_final: 0.5737 (mtt) REVERT: F 432 ARG cc_start: 0.8873 (mmt180) cc_final: 0.8616 (mtm-85) REVERT: F 451 HIS cc_start: 0.8612 (m90) cc_final: 0.8383 (m-70) REVERT: F 507 ILE cc_start: 0.2874 (pt) cc_final: 0.0944 (pt) REVERT: F 523 MET cc_start: 0.8409 (mmm) cc_final: 0.8191 (mmm) REVERT: F 526 MET cc_start: 0.6512 (ptp) cc_final: 0.6306 (ptt) REVERT: F 595 PHE cc_start: 0.9344 (m-80) cc_final: 0.9035 (m-10) REVERT: F 598 LEU cc_start: 0.9386 (tt) cc_final: 0.9164 (mp) REVERT: F 622 ILE cc_start: 0.9065 (pt) cc_final: 0.8849 (pt) REVERT: F 636 MET cc_start: 0.9326 (mpp) cc_final: 0.9062 (mmt) REVERT: F 653 HIS cc_start: 0.9364 (m90) cc_final: 0.8967 (m90) REVERT: F 654 LEU cc_start: 0.9688 (tp) cc_final: 0.9478 (tp) REVERT: F 657 GLU cc_start: 0.9589 (mp0) cc_final: 0.9189 (mp0) REVERT: F 660 ARG cc_start: 0.9354 (mmp80) cc_final: 0.8890 (mmm-85) REVERT: F 673 ASN cc_start: 0.9334 (t0) cc_final: 0.9061 (m-40) REVERT: F 689 MET cc_start: 0.9745 (mmm) cc_final: 0.9376 (mmm) REVERT: F 741 PHE cc_start: 0.9136 (m-80) cc_final: 0.8623 (m-10) outliers start: 13 outliers final: 4 residues processed: 546 average time/residue: 0.4361 time to fit residues: 357.7870 Evaluate side-chains 418 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 414 time to evaluate : 3.221 ------------------------------------------------------------------------------- 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: 6.9990 chunk 297 optimal weight: 0.8980 chunk 65 optimal weight: 0.0170 chunk 194 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 274 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 109 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A1149 GLN ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN C 364 GLN C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS D 364 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 645 GLN D 653 HIS D 724 GLN ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 GLN ** 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 645 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 28404 Z= 0.160 Angle : 0.679 9.631 38466 Z= 0.339 Chirality : 0.046 0.226 4302 Planarity : 0.006 0.069 4950 Dihedral : 5.741 41.585 3762 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % 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: -2.39 (0.14), residues: 3438 helix: -0.70 (0.13), residues: 1680 sheet: -0.84 (0.27), residues: 390 loop : -2.93 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 345 HIS 0.011 0.002 HIS C1154 PHE 0.019 0.001 PHE E 686 TYR 0.024 0.001 TYR F 601 ARG 0.014 0.000 ARG D 354 *********************** 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 577 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 574 time to evaluate : 3.305 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: A 281 MET cc_start: 0.8855 (tpp) cc_final: 0.8548 (tpp) REVERT: A 314 THR cc_start: 0.9126 (p) cc_final: 0.8538 (p) REVERT: A 316 MET cc_start: 0.9670 (tpt) cc_final: 0.9282 (tpp) REVERT: A 318 ARG cc_start: 0.9342 (mtm-85) cc_final: 0.9034 (mmp80) REVERT: A 320 LEU cc_start: 0.9672 (mt) cc_final: 0.9402 (mt) REVERT: A 371 ASP cc_start: 0.9577 (t0) cc_final: 0.9143 (m-30) REVERT: A 402 MET cc_start: 0.6437 (mtm) cc_final: 0.6180 (mtm) REVERT: A 410 ILE cc_start: 0.8913 (mp) cc_final: 0.8644 (mp) REVERT: A 653 HIS cc_start: 0.9536 (m-70) cc_final: 0.9281 (m-70) REVERT: A 689 MET cc_start: 0.9634 (mmm) cc_final: 0.9355 (mmm) REVERT: A 729 LEU cc_start: 0.9411 (mt) cc_final: 0.9210 (mt) REVERT: A 741 PHE cc_start: 0.9251 (m-80) cc_final: 0.8970 (m-80) REVERT: A 1154 HIS cc_start: 0.9611 (t70) cc_final: 0.9383 (t70) REVERT: A 1157 LEU cc_start: 0.9479 (mm) cc_final: 0.9212 (pp) REVERT: B 318 ARG cc_start: 0.9425 (tpm170) cc_final: 0.9167 (tpm170) REVERT: B 320 LEU cc_start: 0.9429 (mt) cc_final: 0.9181 (mt) REVERT: B 405 ARG cc_start: 0.8140 (ptt180) cc_final: 0.7536 (mtm110) REVERT: B 411 ILE cc_start: 0.9631 (mp) cc_final: 0.9430 (mp) REVERT: B 469 GLU cc_start: 0.9665 (pt0) cc_final: 0.9428 (pt0) REVERT: B 519 PHE cc_start: 0.9552 (m-80) cc_final: 0.9202 (m-80) REVERT: B 521 MET cc_start: 0.9652 (mtm) cc_final: 0.9222 (mtp) REVERT: B 564 MET cc_start: 0.9335 (ttp) cc_final: 0.8931 (tmm) REVERT: B 595 PHE cc_start: 0.9307 (m-80) cc_final: 0.9034 (m-10) REVERT: B 630 HIS cc_start: 0.8741 (t-90) cc_final: 0.8329 (t70) REVERT: B 636 MET cc_start: 0.9277 (mpp) cc_final: 0.9049 (mpp) REVERT: B 653 HIS cc_start: 0.9497 (m90) cc_final: 0.9096 (m-70) REVERT: B 691 GLU cc_start: 0.9447 (tm-30) cc_final: 0.9226 (tm-30) REVERT: B 1154 HIS cc_start: 0.9146 (t70) cc_final: 0.8850 (t70) REVERT: B 1185 MET cc_start: 0.9054 (mtt) cc_final: 0.8820 (mmm) REVERT: C 266 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8420 (tm-30) REVERT: C 320 LEU cc_start: 0.8629 (mt) cc_final: 0.8051 (mt) REVERT: C 334 TYR cc_start: 0.8407 (m-80) cc_final: 0.7826 (m-80) REVERT: C 335 MET cc_start: 0.9160 (pmm) cc_final: 0.8905 (pmm) REVERT: C 441 ARG cc_start: 0.9003 (tpp80) cc_final: 0.8797 (tpp80) REVERT: C 480 ARG cc_start: 0.9647 (mmt90) cc_final: 0.9147 (mmm-85) REVERT: C 523 MET cc_start: 0.9705 (tpp) cc_final: 0.9360 (tpp) REVERT: C 560 LEU cc_start: 0.9660 (tt) cc_final: 0.9347 (mt) REVERT: C 592 LEU cc_start: 0.9498 (pt) cc_final: 0.9132 (pt) REVERT: C 636 MET cc_start: 0.9105 (pmm) cc_final: 0.8682 (pmm) REVERT: C 656 LEU cc_start: 0.9764 (tp) cc_final: 0.9460 (tp) REVERT: C 661 HIS cc_start: 0.7692 (m90) cc_final: 0.7460 (m90) REVERT: C 689 MET cc_start: 0.9561 (mmp) cc_final: 0.9349 (mpp) REVERT: D 281 MET cc_start: 0.7688 (tpp) cc_final: 0.7317 (tpp) REVERT: D 283 MET cc_start: 0.8716 (ptt) cc_final: 0.8255 (ptt) REVERT: D 320 LEU cc_start: 0.9496 (tp) cc_final: 0.9269 (mt) REVERT: D 371 ASP cc_start: 0.9311 (m-30) cc_final: 0.8438 (p0) REVERT: D 372 GLU cc_start: 0.8471 (mp0) cc_final: 0.8036 (mp0) REVERT: D 430 PHE cc_start: 0.9212 (m-10) cc_final: 0.8996 (m-80) REVERT: D 562 LYS cc_start: 0.9656 (mtmt) cc_final: 0.9360 (ptpp) REVERT: D 592 LEU cc_start: 0.9025 (mm) cc_final: 0.8721 (mm) REVERT: D 656 LEU cc_start: 0.9767 (tp) cc_final: 0.9484 (tp) REVERT: D 742 GLN cc_start: 0.9766 (pp30) cc_final: 0.9555 (pp30) REVERT: E 304 LEU cc_start: 0.9471 (mp) cc_final: 0.9134 (pp) REVERT: E 328 ASN cc_start: 0.8831 (t0) cc_final: 0.8261 (p0) REVERT: E 523 MET cc_start: 0.9101 (mmp) cc_final: 0.8878 (mmp) REVERT: E 591 ARG cc_start: 0.8662 (mtt90) cc_final: 0.8149 (mmp80) REVERT: E 592 LEU cc_start: 0.9386 (pt) cc_final: 0.9017 (pt) REVERT: E 641 GLN cc_start: 0.9518 (pp30) cc_final: 0.9220 (pt0) REVERT: E 652 ILE cc_start: 0.9643 (mm) cc_final: 0.9144 (pt) REVERT: E 653 HIS cc_start: 0.9730 (m90) cc_final: 0.9290 (m-70) REVERT: E 674 TRP cc_start: 0.8753 (t60) cc_final: 0.8545 (t60) REVERT: E 685 THR cc_start: 0.8988 (m) cc_final: 0.8782 (p) REVERT: E 697 ASP cc_start: 0.9269 (m-30) cc_final: 0.8458 (t70) REVERT: E 701 PHE cc_start: 0.9305 (t80) cc_final: 0.8684 (t80) REVERT: E 741 PHE cc_start: 0.9358 (m-80) cc_final: 0.9119 (m-80) REVERT: F 370 PHE cc_start: 0.9025 (m-80) cc_final: 0.8769 (m-80) REVERT: F 402 MET cc_start: 0.6153 (mtt) cc_final: 0.5836 (mtt) REVERT: F 451 HIS cc_start: 0.8397 (m90) cc_final: 0.8128 (m-70) REVERT: F 507 ILE cc_start: 0.2901 (pt) cc_final: 0.2333 (pt) REVERT: F 523 MET cc_start: 0.8210 (mmm) cc_final: 0.7937 (mmm) REVERT: F 595 PHE cc_start: 0.9338 (m-80) cc_final: 0.8933 (m-10) REVERT: F 636 MET cc_start: 0.9416 (mpp) cc_final: 0.9150 (mmt) REVERT: F 640 LEU cc_start: 0.9146 (mm) cc_final: 0.8848 (mm) REVERT: F 689 MET cc_start: 0.9705 (mmm) cc_final: 0.8535 (mtt) REVERT: F 741 PHE cc_start: 0.9066 (m-80) cc_final: 0.8471 (m-10) outliers start: 3 outliers final: 1 residues processed: 576 average time/residue: 0.4415 time to fit residues: 382.5113 Evaluate side-chains 442 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 441 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 8.9990 chunk 188 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 187 optimal weight: 0.0870 chunk 278 optimal weight: 30.0000 chunk 184 optimal weight: 30.0000 chunk 329 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 489 ASN C 506 GLN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1152 HIS ** 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 277 GLN ** E 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN F 298 GLN ** 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: 0.8015 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28404 Z= 0.220 Angle : 0.715 11.370 38466 Z= 0.367 Chirality : 0.047 0.257 4302 Planarity : 0.006 0.137 4950 Dihedral : 5.732 40.619 3762 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -2.35 (0.14), residues: 3438 helix: -0.73 (0.13), residues: 1656 sheet: -0.93 (0.26), residues: 390 loop : -2.76 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 462 HIS 0.012 0.002 HIS D1154 PHE 0.031 0.002 PHE C 357 TYR 0.046 0.002 TYR B 601 ARG 0.027 0.001 ARG F 692 *********************** 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 517 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 3.375 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: A 314 THR cc_start: 0.9192 (p) cc_final: 0.8643 (p) REVERT: A 316 MET cc_start: 0.9673 (tpt) cc_final: 0.9295 (tpp) REVERT: A 318 ARG cc_start: 0.9352 (mtm-85) cc_final: 0.9050 (mmp80) REVERT: A 320 LEU cc_start: 0.9693 (mt) cc_final: 0.9416 (mt) REVERT: A 371 ASP cc_start: 0.9576 (t0) cc_final: 0.9149 (m-30) REVERT: A 640 LEU cc_start: 0.9569 (mm) cc_final: 0.9175 (tp) REVERT: A 653 HIS cc_start: 0.9517 (m-70) cc_final: 0.9213 (m-70) REVERT: A 673 ASN cc_start: 0.9545 (t0) cc_final: 0.9322 (t0) REVERT: A 689 MET cc_start: 0.9657 (mmm) cc_final: 0.9382 (mmm) REVERT: A 697 ASP cc_start: 0.8807 (m-30) cc_final: 0.8563 (m-30) REVERT: A 741 PHE cc_start: 0.9207 (m-80) cc_final: 0.8981 (m-80) REVERT: A 1157 LEU cc_start: 0.9554 (mm) cc_final: 0.9228 (pp) REVERT: B 318 ARG cc_start: 0.9504 (tpm170) cc_final: 0.9249 (tpm170) REVERT: B 320 LEU cc_start: 0.9415 (mt) cc_final: 0.9183 (mt) REVERT: B 405 ARG cc_start: 0.8188 (ptt180) cc_final: 0.7697 (mtm180) REVERT: B 411 ILE cc_start: 0.9663 (mp) cc_final: 0.9421 (mp) REVERT: B 469 GLU cc_start: 0.9675 (pt0) cc_final: 0.9438 (pt0) REVERT: B 519 PHE cc_start: 0.9538 (m-80) cc_final: 0.9198 (m-80) REVERT: B 521 MET cc_start: 0.9633 (mtm) cc_final: 0.9204 (mtp) REVERT: B 564 MET cc_start: 0.9297 (ttp) cc_final: 0.8928 (ppp) REVERT: B 595 PHE cc_start: 0.9366 (m-80) cc_final: 0.9108 (m-10) REVERT: B 636 MET cc_start: 0.9674 (mpp) cc_final: 0.9265 (mpp) REVERT: B 691 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9204 (tm-30) REVERT: C 266 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8445 (tm-30) REVERT: C 320 LEU cc_start: 0.8642 (mt) cc_final: 0.8072 (mt) REVERT: C 334 TYR cc_start: 0.8449 (m-80) cc_final: 0.7881 (m-80) REVERT: C 335 MET cc_start: 0.9192 (pmm) cc_final: 0.8917 (pmm) REVERT: C 480 ARG cc_start: 0.9680 (mmt90) cc_final: 0.9143 (mmm-85) REVERT: C 523 MET cc_start: 0.9708 (tpp) cc_final: 0.9375 (tpp) REVERT: C 592 LEU cc_start: 0.9390 (pt) cc_final: 0.9097 (pt) REVERT: C 636 MET cc_start: 0.9117 (pmm) cc_final: 0.8729 (pmm) REVERT: C 661 HIS cc_start: 0.7890 (m90) cc_final: 0.7460 (m90) REVERT: C 689 MET cc_start: 0.9609 (mmp) cc_final: 0.9380 (mmm) REVERT: C 1152 HIS cc_start: 0.9272 (m170) cc_final: 0.8871 (m-70) REVERT: D 281 MET cc_start: 0.7843 (tpp) cc_final: 0.7608 (tpp) REVERT: D 283 MET cc_start: 0.8770 (ptt) cc_final: 0.8343 (ptt) REVERT: D 351 ARG cc_start: 0.9472 (mmm160) cc_final: 0.9241 (ttt180) REVERT: D 371 ASP cc_start: 0.9390 (m-30) cc_final: 0.9190 (m-30) REVERT: D 416 ARG cc_start: 0.8079 (pmt-80) cc_final: 0.7736 (ppt170) REVERT: D 430 PHE cc_start: 0.9128 (m-10) cc_final: 0.8668 (m-80) REVERT: D 562 LYS cc_start: 0.9706 (mtmt) cc_final: 0.9429 (ptpp) REVERT: D 592 LEU cc_start: 0.9049 (mm) cc_final: 0.8718 (mm) REVERT: E 304 LEU cc_start: 0.9473 (mp) cc_final: 0.9147 (pp) REVERT: E 328 ASN cc_start: 0.8893 (t0) cc_final: 0.8260 (p0) REVERT: E 430 PHE cc_start: 0.8474 (m-10) cc_final: 0.8263 (m-80) REVERT: E 592 LEU cc_start: 0.9488 (pt) cc_final: 0.9185 (pt) REVERT: E 641 GLN cc_start: 0.9550 (pp30) cc_final: 0.9267 (pt0) REVERT: E 652 ILE cc_start: 0.9504 (mm) cc_final: 0.9100 (pt) REVERT: E 653 HIS cc_start: 0.9724 (m90) cc_final: 0.9413 (m-70) REVERT: E 657 GLU cc_start: 0.9668 (mp0) cc_final: 0.9397 (mp0) REVERT: E 670 ASP cc_start: 0.8469 (t0) cc_final: 0.8243 (t0) REVERT: E 685 THR cc_start: 0.9141 (m) cc_final: 0.8811 (m) REVERT: E 697 ASP cc_start: 0.9221 (m-30) cc_final: 0.8949 (m-30) REVERT: E 701 PHE cc_start: 0.9349 (t80) cc_final: 0.8754 (t80) REVERT: F 283 MET cc_start: 0.8447 (ptm) cc_final: 0.8192 (ptm) REVERT: F 370 PHE cc_start: 0.9091 (m-80) cc_final: 0.8682 (m-80) REVERT: F 402 MET cc_start: 0.6016 (mtt) cc_final: 0.5803 (mtt) REVERT: F 451 HIS cc_start: 0.8524 (m90) cc_final: 0.8259 (m-70) REVERT: F 466 MET cc_start: 0.9280 (ptt) cc_final: 0.8937 (ptt) REVERT: F 595 PHE cc_start: 0.9410 (m-80) cc_final: 0.9031 (m-10) REVERT: F 636 MET cc_start: 0.9475 (mpp) cc_final: 0.9223 (mmt) REVERT: F 741 PHE cc_start: 0.9040 (m-80) cc_final: 0.8523 (m-10) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.4456 time to fit residues: 348.7239 Evaluate side-chains 403 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.303 ------------------------------------------------------------------------------- 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: 4.9990 chunk 131 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 224 optimal weight: 0.4980 chunk 162 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 259 optimal weight: 7.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 489 ASN C 506 GLN C 615 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 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28404 Z= 0.200 Angle : 0.709 9.641 38466 Z= 0.361 Chirality : 0.047 0.226 4302 Planarity : 0.006 0.139 4950 Dihedral : 5.723 40.515 3762 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 24.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: -2.27 (0.14), residues: 3438 helix: -0.69 (0.13), residues: 1644 sheet: -0.95 (0.27), residues: 390 loop : -2.64 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 674 HIS 0.020 0.002 HIS B1154 PHE 0.031 0.002 PHE C 519 TYR 0.043 0.002 TYR B1158 ARG 0.014 0.001 ARG F 692 *********************** 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 518 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 3.293 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: A 281 MET cc_start: 0.8829 (tpp) cc_final: 0.8605 (tpp) REVERT: A 314 THR cc_start: 0.9153 (p) cc_final: 0.8614 (p) REVERT: A 316 MET cc_start: 0.9693 (tpt) cc_final: 0.9293 (tpp) REVERT: A 318 ARG cc_start: 0.9340 (mtm-85) cc_final: 0.9060 (mmp80) REVERT: A 320 LEU cc_start: 0.9702 (mt) cc_final: 0.9432 (mt) REVERT: A 334 TYR cc_start: 0.8579 (t80) cc_final: 0.8362 (t80) REVERT: A 371 ASP cc_start: 0.9539 (t0) cc_final: 0.9095 (m-30) REVERT: A 402 MET cc_start: 0.7025 (mtm) cc_final: 0.6776 (mtt) REVERT: A 410 ILE cc_start: 0.8760 (mp) cc_final: 0.8528 (mp) REVERT: A 653 HIS cc_start: 0.9550 (m-70) cc_final: 0.9272 (m-70) REVERT: A 673 ASN cc_start: 0.9566 (t0) cc_final: 0.9364 (t0) REVERT: A 697 ASP cc_start: 0.8835 (m-30) cc_final: 0.8590 (m-30) REVERT: A 704 LEU cc_start: 0.9644 (tp) cc_final: 0.9282 (mm) REVERT: A 741 PHE cc_start: 0.9156 (m-80) cc_final: 0.8941 (m-80) REVERT: A 1157 LEU cc_start: 0.9549 (mm) cc_final: 0.9212 (pp) REVERT: B 303 VAL cc_start: 0.9314 (t) cc_final: 0.9098 (t) REVERT: B 318 ARG cc_start: 0.9506 (tpm170) cc_final: 0.9251 (tpm170) REVERT: B 320 LEU cc_start: 0.9434 (mt) cc_final: 0.9224 (mt) REVERT: B 405 ARG cc_start: 0.8082 (ptt180) cc_final: 0.7574 (mtm180) REVERT: B 411 ILE cc_start: 0.9648 (mp) cc_final: 0.9390 (mp) REVERT: B 469 GLU cc_start: 0.9659 (pt0) cc_final: 0.9409 (pt0) REVERT: B 519 PHE cc_start: 0.9551 (m-80) cc_final: 0.9237 (m-80) REVERT: B 521 MET cc_start: 0.9629 (mtm) cc_final: 0.9180 (mtp) REVERT: B 564 MET cc_start: 0.9296 (ttp) cc_final: 0.8925 (ppp) REVERT: B 595 PHE cc_start: 0.9356 (m-80) cc_final: 0.9089 (m-10) REVERT: B 636 MET cc_start: 0.9722 (mpp) cc_final: 0.9459 (mpp) REVERT: B 653 HIS cc_start: 0.9515 (m90) cc_final: 0.9214 (m170) REVERT: C 266 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8442 (tm-30) REVERT: C 320 LEU cc_start: 0.8642 (mt) cc_final: 0.8076 (mt) REVERT: C 334 TYR cc_start: 0.8469 (m-80) cc_final: 0.7887 (m-80) REVERT: C 335 MET cc_start: 0.9274 (pmm) cc_final: 0.8992 (pmm) REVERT: C 399 MET cc_start: 0.9303 (mmp) cc_final: 0.9014 (mmt) REVERT: C 480 ARG cc_start: 0.9691 (mmt90) cc_final: 0.9172 (mmm-85) REVERT: C 523 MET cc_start: 0.9645 (tpp) cc_final: 0.9367 (tpp) REVERT: C 592 LEU cc_start: 0.9466 (pt) cc_final: 0.9167 (pt) REVERT: C 636 MET cc_start: 0.9120 (pmm) cc_final: 0.8725 (pmm) REVERT: C 661 HIS cc_start: 0.7789 (m90) cc_final: 0.7342 (m90) REVERT: C 1152 HIS cc_start: 0.9332 (m170) cc_final: 0.8974 (m-70) REVERT: D 281 MET cc_start: 0.8125 (tpp) cc_final: 0.7906 (tpp) REVERT: D 283 MET cc_start: 0.8818 (ptt) cc_final: 0.8373 (ptt) REVERT: D 351 ARG cc_start: 0.9480 (mmm160) cc_final: 0.9242 (ttt180) REVERT: D 370 PHE cc_start: 0.9285 (m-80) cc_final: 0.9034 (m-80) REVERT: D 430 PHE cc_start: 0.9113 (m-10) cc_final: 0.8639 (m-80) REVERT: D 562 LYS cc_start: 0.9710 (mtmt) cc_final: 0.9432 (ptpp) REVERT: D 591 ARG cc_start: 0.9381 (mtt90) cc_final: 0.8836 (mtp85) REVERT: D 592 LEU cc_start: 0.9032 (mm) cc_final: 0.8634 (mm) REVERT: D 595 PHE cc_start: 0.9498 (m-80) cc_final: 0.9237 (m-10) REVERT: D 656 LEU cc_start: 0.9718 (tp) cc_final: 0.9068 (tp) REVERT: D 660 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8473 (ptt180) REVERT: E 304 LEU cc_start: 0.9452 (mp) cc_final: 0.9112 (pp) REVERT: E 328 ASN cc_start: 0.8773 (t0) cc_final: 0.8214 (p0) REVERT: E 415 ASN cc_start: 0.8681 (p0) cc_final: 0.8166 (t0) REVERT: E 430 PHE cc_start: 0.8509 (m-10) cc_final: 0.8201 (m-80) REVERT: E 523 MET cc_start: 0.9205 (mmp) cc_final: 0.8995 (mmm) REVERT: E 592 LEU cc_start: 0.9488 (pt) cc_final: 0.9188 (pt) REVERT: E 636 MET cc_start: 0.9656 (mpp) cc_final: 0.9188 (mmt) REVERT: E 641 GLN cc_start: 0.9537 (pp30) cc_final: 0.9315 (pp30) REVERT: E 652 ILE cc_start: 0.9705 (mm) cc_final: 0.9242 (pt) REVERT: E 657 GLU cc_start: 0.9646 (mp0) cc_final: 0.9374 (mp0) REVERT: E 697 ASP cc_start: 0.9206 (m-30) cc_final: 0.8937 (m-30) REVERT: E 701 PHE cc_start: 0.9411 (t80) cc_final: 0.8744 (t80) REVERT: F 328 ASN cc_start: 0.8626 (t0) cc_final: 0.8125 (p0) REVERT: F 370 PHE cc_start: 0.9092 (m-80) cc_final: 0.8663 (m-80) REVERT: F 402 MET cc_start: 0.6046 (mtt) cc_final: 0.5683 (mtt) REVERT: F 451 HIS cc_start: 0.8450 (m90) cc_final: 0.8152 (m-70) REVERT: F 466 MET cc_start: 0.9160 (ptt) cc_final: 0.8853 (ptt) REVERT: F 595 PHE cc_start: 0.9425 (m-80) cc_final: 0.9040 (m-10) REVERT: F 636 MET cc_start: 0.9468 (mpp) cc_final: 0.9197 (mmt) REVERT: F 741 PHE cc_start: 0.9039 (m-80) cc_final: 0.8514 (m-10) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.4367 time to fit residues: 344.2723 Evaluate side-chains 400 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 3.265 ------------------------------------------------------------------------------- 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: 20.0000 chunk 315 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 307 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 277 optimal weight: 0.8980 chunk 290 optimal weight: 20.0000 chunk 306 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN B 506 GLN C 352 GLN C 489 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 GLN D 645 GLN ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28404 Z= 0.189 Angle : 0.698 10.605 38466 Z= 0.354 Chirality : 0.047 0.243 4302 Planarity : 0.006 0.067 4950 Dihedral : 5.612 40.999 3762 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -2.17 (0.14), residues: 3438 helix: -0.66 (0.13), residues: 1650 sheet: -0.87 (0.27), residues: 390 loop : -2.54 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 345 HIS 0.018 0.002 HIS B1154 PHE 0.029 0.002 PHE C 357 TYR 0.045 0.002 TYR B1158 ARG 0.009 0.001 ARG F 692 *********************** 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 517 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 3.151 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: A 281 MET cc_start: 0.8765 (tpp) cc_final: 0.8544 (tpp) REVERT: A 314 THR cc_start: 0.9319 (p) cc_final: 0.8804 (p) REVERT: A 316 MET cc_start: 0.9693 (tpt) cc_final: 0.9316 (tpp) REVERT: A 318 ARG cc_start: 0.9376 (mtm-85) cc_final: 0.9107 (mmp80) REVERT: A 320 LEU cc_start: 0.9703 (mt) cc_final: 0.9458 (mt) REVERT: A 371 ASP cc_start: 0.9560 (t0) cc_final: 0.9110 (m-30) REVERT: A 402 MET cc_start: 0.7007 (mtm) cc_final: 0.6758 (mtt) REVERT: A 410 ILE cc_start: 0.9017 (mp) cc_final: 0.8590 (mm) REVERT: A 653 HIS cc_start: 0.9504 (m-70) cc_final: 0.9240 (m-70) REVERT: A 673 ASN cc_start: 0.9587 (t0) cc_final: 0.9375 (t0) REVERT: A 689 MET cc_start: 0.9744 (tpp) cc_final: 0.9525 (tpp) REVERT: A 697 ASP cc_start: 0.8890 (m-30) cc_final: 0.8651 (m-30) REVERT: A 704 LEU cc_start: 0.9669 (tp) cc_final: 0.9307 (mm) REVERT: A 741 PHE cc_start: 0.9117 (m-80) cc_final: 0.8913 (m-80) REVERT: A 1152 HIS cc_start: 0.9573 (m90) cc_final: 0.9199 (m90) REVERT: A 1157 LEU cc_start: 0.9532 (mm) cc_final: 0.9210 (pp) REVERT: B 399 MET cc_start: 0.9223 (mmp) cc_final: 0.8978 (mmp) REVERT: B 400 ASP cc_start: 0.9612 (m-30) cc_final: 0.9196 (p0) REVERT: B 405 ARG cc_start: 0.8030 (ptt180) cc_final: 0.7765 (mtm110) REVERT: B 411 ILE cc_start: 0.9667 (mp) cc_final: 0.9452 (mp) REVERT: B 469 GLU cc_start: 0.9662 (pt0) cc_final: 0.9407 (pt0) REVERT: B 519 PHE cc_start: 0.9538 (m-80) cc_final: 0.9228 (m-80) REVERT: B 521 MET cc_start: 0.9651 (mtm) cc_final: 0.9226 (mtp) REVERT: B 564 MET cc_start: 0.9237 (ttp) cc_final: 0.8952 (ppp) REVERT: B 595 PHE cc_start: 0.9352 (m-80) cc_final: 0.9089 (m-10) REVERT: B 653 HIS cc_start: 0.9509 (m90) cc_final: 0.9224 (m170) REVERT: C 266 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8438 (tm-30) REVERT: C 320 LEU cc_start: 0.8636 (mt) cc_final: 0.8075 (mt) REVERT: C 334 TYR cc_start: 0.8457 (m-80) cc_final: 0.7838 (m-80) REVERT: C 335 MET cc_start: 0.9270 (pmm) cc_final: 0.8989 (pmm) REVERT: C 480 ARG cc_start: 0.9713 (mmt90) cc_final: 0.9195 (mmm-85) REVERT: C 519 PHE cc_start: 0.9476 (m-10) cc_final: 0.9203 (m-10) REVERT: C 523 MET cc_start: 0.9675 (tpp) cc_final: 0.9324 (tpp) REVERT: C 592 LEU cc_start: 0.9549 (pt) cc_final: 0.9321 (pt) REVERT: C 595 PHE cc_start: 0.9531 (m-80) cc_final: 0.9327 (m-80) REVERT: C 636 MET cc_start: 0.9143 (pmm) cc_final: 0.8666 (pmm) REVERT: C 1152 HIS cc_start: 0.9350 (m170) cc_final: 0.9100 (m-70) REVERT: D 281 MET cc_start: 0.8156 (tpp) cc_final: 0.7944 (tpp) REVERT: D 283 MET cc_start: 0.8809 (ptt) cc_final: 0.8350 (ptt) REVERT: D 351 ARG cc_start: 0.9491 (mmm160) cc_final: 0.9268 (ttt180) REVERT: D 370 PHE cc_start: 0.9291 (m-80) cc_final: 0.9022 (m-80) REVERT: D 371 ASP cc_start: 0.9270 (m-30) cc_final: 0.9025 (m-30) REVERT: D 430 PHE cc_start: 0.9104 (m-10) cc_final: 0.8600 (m-80) REVERT: D 527 ILE cc_start: 0.9587 (pt) cc_final: 0.9305 (pt) REVERT: D 562 LYS cc_start: 0.9712 (mtmt) cc_final: 0.9441 (ptpp) REVERT: D 591 ARG cc_start: 0.9332 (mtt90) cc_final: 0.8713 (mtp85) REVERT: D 592 LEU cc_start: 0.9028 (mm) cc_final: 0.8608 (mm) REVERT: D 595 PHE cc_start: 0.9505 (m-80) cc_final: 0.9232 (m-10) REVERT: E 304 LEU cc_start: 0.9424 (mp) cc_final: 0.9065 (pp) REVERT: E 316 MET cc_start: 0.9191 (mtt) cc_final: 0.8961 (mtt) REVERT: E 324 CYS cc_start: 0.9502 (t) cc_final: 0.9284 (t) REVERT: E 328 ASN cc_start: 0.8733 (t0) cc_final: 0.8196 (p0) REVERT: E 415 ASN cc_start: 0.8501 (p0) cc_final: 0.7916 (t0) REVERT: E 430 PHE cc_start: 0.8589 (m-10) cc_final: 0.8168 (m-80) REVERT: E 523 MET cc_start: 0.9190 (mmp) cc_final: 0.8948 (mmm) REVERT: E 641 GLN cc_start: 0.9544 (pp30) cc_final: 0.9340 (pp30) REVERT: E 653 HIS cc_start: 0.9840 (m-70) cc_final: 0.9554 (m90) REVERT: E 666 ILE cc_start: 0.8702 (mm) cc_final: 0.8255 (mp) REVERT: E 674 TRP cc_start: 0.8838 (t-100) cc_final: 0.8358 (m100) REVERT: E 686 PHE cc_start: 0.9600 (t80) cc_final: 0.9366 (t80) REVERT: E 697 ASP cc_start: 0.9205 (m-30) cc_final: 0.8915 (m-30) REVERT: E 699 ILE cc_start: 0.8952 (mm) cc_final: 0.8532 (mm) REVERT: E 701 PHE cc_start: 0.9410 (t80) cc_final: 0.8774 (t80) REVERT: F 328 ASN cc_start: 0.8607 (t0) cc_final: 0.8157 (p0) REVERT: F 370 PHE cc_start: 0.9074 (m-80) cc_final: 0.8639 (m-80) REVERT: F 402 MET cc_start: 0.6115 (mtt) cc_final: 0.5672 (mtt) REVERT: F 451 HIS cc_start: 0.8458 (m90) cc_final: 0.8153 (m-70) REVERT: F 466 MET cc_start: 0.9176 (ptt) cc_final: 0.8846 (ptt) REVERT: F 595 PHE cc_start: 0.9404 (m-80) cc_final: 0.8992 (m-10) REVERT: F 601 TYR cc_start: 0.8067 (t80) cc_final: 0.7842 (t80) REVERT: F 636 MET cc_start: 0.9544 (mpp) cc_final: 0.9325 (mmt) REVERT: F 656 LEU cc_start: 0.9695 (tt) cc_final: 0.9453 (tt) REVERT: F 660 ARG cc_start: 0.9473 (mmp80) cc_final: 0.9248 (mmm-85) REVERT: F 741 PHE cc_start: 0.9007 (m-80) cc_final: 0.8460 (m-10) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.4374 time to fit residues: 342.8526 Evaluate side-chains 408 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.283 ------------------------------------------------------------------------------- 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: 10.0000 chunk 324 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 340 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 209 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 352 GLN C 489 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 277 GLN ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN F 645 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28404 Z= 0.229 Angle : 0.734 9.086 38466 Z= 0.375 Chirality : 0.047 0.237 4302 Planarity : 0.006 0.067 4950 Dihedral : 5.721 40.423 3762 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -2.22 (0.14), residues: 3438 helix: -0.66 (0.13), residues: 1620 sheet: -1.12 (0.26), residues: 402 loop : -2.52 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 719 HIS 0.016 0.002 HIS B1154 PHE 0.026 0.002 PHE E 741 TYR 0.048 0.002 TYR B1158 ARG 0.012 0.001 ARG F 692 ********************** 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 510 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 3.221 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: A 281 MET cc_start: 0.8826 (tpp) cc_final: 0.8599 (tpp) REVERT: A 314 THR cc_start: 0.9263 (p) cc_final: 0.8784 (p) REVERT: A 316 MET cc_start: 0.9700 (tpt) cc_final: 0.9399 (tpp) REVERT: A 318 ARG cc_start: 0.9318 (mtm-85) cc_final: 0.9101 (mmp80) REVERT: A 320 LEU cc_start: 0.9715 (mt) cc_final: 0.9468 (mt) REVERT: A 334 TYR cc_start: 0.8690 (t80) cc_final: 0.8304 (t80) REVERT: A 371 ASP cc_start: 0.9493 (t0) cc_final: 0.9032 (m-30) REVERT: A 402 MET cc_start: 0.7038 (mtm) cc_final: 0.6796 (mtt) REVERT: A 539 LYS cc_start: 0.9372 (mmtm) cc_final: 0.9110 (pttp) REVERT: A 653 HIS cc_start: 0.9482 (m-70) cc_final: 0.9220 (m-70) REVERT: A 673 ASN cc_start: 0.9606 (t0) cc_final: 0.9399 (t0) REVERT: A 1152 HIS cc_start: 0.9562 (m90) cc_final: 0.9154 (m90) REVERT: A 1157 LEU cc_start: 0.9566 (mm) cc_final: 0.9265 (pp) REVERT: B 316 MET cc_start: 0.9168 (tpp) cc_final: 0.8871 (tpp) REVERT: B 318 ARG cc_start: 0.9517 (tpm170) cc_final: 0.9268 (tpm170) REVERT: B 320 LEU cc_start: 0.9460 (mt) cc_final: 0.9234 (mt) REVERT: B 399 MET cc_start: 0.9207 (mmp) cc_final: 0.8966 (mmp) REVERT: B 400 ASP cc_start: 0.9577 (m-30) cc_final: 0.9232 (p0) REVERT: B 405 ARG cc_start: 0.7967 (ptt180) cc_final: 0.7676 (mtm110) REVERT: B 411 ILE cc_start: 0.9694 (mp) cc_final: 0.9445 (mp) REVERT: B 469 GLU cc_start: 0.9656 (pt0) cc_final: 0.9426 (pt0) REVERT: B 521 MET cc_start: 0.9673 (mtm) cc_final: 0.9275 (mtp) REVERT: B 564 MET cc_start: 0.9180 (ttp) cc_final: 0.8888 (ppp) REVERT: B 595 PHE cc_start: 0.9377 (m-80) cc_final: 0.9129 (m-10) REVERT: B 716 LEU cc_start: 0.9610 (mt) cc_final: 0.9388 (pp) REVERT: B 1154 HIS cc_start: 0.9105 (t70) cc_final: 0.8852 (t-90) REVERT: C 266 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8388 (tm-30) REVERT: C 320 LEU cc_start: 0.8677 (mt) cc_final: 0.8118 (mt) REVERT: C 334 TYR cc_start: 0.8512 (m-80) cc_final: 0.7893 (m-80) REVERT: C 335 MET cc_start: 0.9353 (pmm) cc_final: 0.9038 (pmm) REVERT: C 350 GLU cc_start: 0.9399 (tp30) cc_final: 0.7910 (mp0) REVERT: C 398 LEU cc_start: 0.9288 (mt) cc_final: 0.8837 (mt) REVERT: C 399 MET cc_start: 0.9466 (mpp) cc_final: 0.8807 (ttt) REVERT: C 480 ARG cc_start: 0.9717 (mmt90) cc_final: 0.9209 (mmm-85) REVERT: C 519 PHE cc_start: 0.9519 (m-10) cc_final: 0.9270 (m-10) REVERT: C 523 MET cc_start: 0.9702 (tpp) cc_final: 0.9332 (tpp) REVERT: C 592 LEU cc_start: 0.9562 (pt) cc_final: 0.9293 (pt) REVERT: C 595 PHE cc_start: 0.9455 (m-80) cc_final: 0.9228 (m-80) REVERT: C 636 MET cc_start: 0.9173 (pmm) cc_final: 0.8726 (pmm) REVERT: C 689 MET cc_start: 0.9614 (mmp) cc_final: 0.9330 (mmm) REVERT: C 1152 HIS cc_start: 0.9397 (m170) cc_final: 0.9179 (m-70) REVERT: D 281 MET cc_start: 0.8212 (tpp) cc_final: 0.7815 (tpp) REVERT: D 283 MET cc_start: 0.8852 (ptt) cc_final: 0.8411 (ptt) REVERT: D 351 ARG cc_start: 0.9513 (mmm160) cc_final: 0.9269 (ttt180) REVERT: D 369 PHE cc_start: 0.9061 (m-80) cc_final: 0.8611 (m-80) REVERT: D 370 PHE cc_start: 0.9269 (m-80) cc_final: 0.9055 (m-80) REVERT: D 371 ASP cc_start: 0.9329 (m-30) cc_final: 0.9100 (m-30) REVERT: D 430 PHE cc_start: 0.8989 (m-10) cc_final: 0.8488 (m-80) REVERT: D 479 LEU cc_start: 0.9322 (mt) cc_final: 0.9086 (mt) REVERT: D 523 MET cc_start: 0.9673 (ptp) cc_final: 0.9463 (ptp) REVERT: D 562 LYS cc_start: 0.9769 (mtmt) cc_final: 0.9527 (ptpp) REVERT: D 592 LEU cc_start: 0.9044 (mm) cc_final: 0.8727 (mm) REVERT: E 288 TYR cc_start: 0.9180 (m-80) cc_final: 0.8926 (m-80) REVERT: E 304 LEU cc_start: 0.9429 (mp) cc_final: 0.9111 (pp) REVERT: E 316 MET cc_start: 0.9199 (mtt) cc_final: 0.8975 (mtt) REVERT: E 324 CYS cc_start: 0.9497 (t) cc_final: 0.9274 (t) REVERT: E 328 ASN cc_start: 0.8842 (t0) cc_final: 0.8339 (p0) REVERT: E 430 PHE cc_start: 0.8775 (m-10) cc_final: 0.8417 (m-80) REVERT: E 653 HIS cc_start: 0.9829 (m-70) cc_final: 0.9568 (m-70) REVERT: E 666 ILE cc_start: 0.9083 (mm) cc_final: 0.8820 (mm) REVERT: E 697 ASP cc_start: 0.9212 (m-30) cc_final: 0.8965 (m-30) REVERT: E 701 PHE cc_start: 0.9600 (t80) cc_final: 0.9097 (t80) REVERT: F 328 ASN cc_start: 0.8663 (t0) cc_final: 0.8225 (p0) REVERT: F 370 PHE cc_start: 0.9145 (m-80) cc_final: 0.8740 (m-80) REVERT: F 402 MET cc_start: 0.6092 (mtt) cc_final: 0.5649 (mtt) REVERT: F 451 HIS cc_start: 0.8470 (m90) cc_final: 0.8156 (m-70) REVERT: F 466 MET cc_start: 0.9115 (ptt) cc_final: 0.8775 (ptt) REVERT: F 595 PHE cc_start: 0.9448 (m-80) cc_final: 0.9063 (m-10) REVERT: F 601 TYR cc_start: 0.8170 (t80) cc_final: 0.7903 (t80) REVERT: F 636 MET cc_start: 0.9558 (mpp) cc_final: 0.9343 (mmt) REVERT: F 673 ASN cc_start: 0.9147 (p0) cc_final: 0.8939 (p0) REVERT: F 741 PHE cc_start: 0.8968 (m-80) cc_final: 0.8441 (m-10) REVERT: F 1154 HIS cc_start: 0.8909 (t70) cc_final: 0.8399 (t70) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.4346 time to fit residues: 336.6285 Evaluate side-chains 402 residues out of total 3132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 3.192 ------------------------------------------------------------------------------- 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: 7.9990 chunk 289 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 271 optimal weight: 0.1980 chunk 113 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN C 352 GLN C 489 ASN ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN ** D1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.080250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055724 restraints weight = 176125.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.057001 restraints weight = 135872.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.057843 restraints weight = 110969.329| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28404 Z= 0.178 Angle : 0.704 10.242 38466 Z= 0.356 Chirality : 0.047 0.274 4302 Planarity : 0.006 0.074 4950 Dihedral : 5.530 40.677 3762 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -2.07 (0.14), residues: 3438 helix: -0.51 (0.13), residues: 1614 sheet: -0.89 (0.26), residues: 390 loop : -2.51 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F1162 HIS 0.011 0.001 HIS B1154 PHE 0.028 0.001 PHE C 357 TYR 0.029 0.001 TYR F 601 ARG 0.010 0.001 ARG C 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6872.49 seconds wall clock time: 125 minutes 4.64 seconds (7504.64 seconds total)